manual-references.json

[
  {
    "id": "biorxiv:10.1101/2021.07.06.451385",
    "type": "article-journal",
    "container-title": "bioRxiv",
    "page": "2021.07.06.451385",
    "DOI": "10.1101/2021.07.06.451385",
    "abstract": "Pediatric brain tumors are the leading cause of cancer death in children with an urgent need for innovative therapies. Here we show that the cell surface oncoprotein glypican 2 (GPC2) is highly expressed on multiple lethal pediatric brain tumors, including medulloblastomas, embryonal tumors with multi-layered rosettes, other CNS embryonal tumors, as well as definable subsets of highly malignant gliomas. To target GPC2 on these pediatric brain tumors with adoptive cellular therapies and mitigate potential inflammatory neurotoxicity, we developed four mRNA chimeric antigen receptor (CAR) T cell constructs using the highly GPC2-specific fully human D3 single chain variable fragment. First, we validated and prioritized these CARs using in vitro cytotoxicity and T cell degranulation assays with GPC2-expressing neuroblastoma cells. Next, we expanded the testing of the two most potent GPC2-directed CAR constructs prioritized from these studies to GPC2-expressing medulloblastoma and high-grade glioma cell lines, showing significant GPC2-specific cell death in multiple models. Finally, locoregional delivery bi-weekly of two to four million GPC2-directed mRNA CAR T cells induced significant and sustained tumor regression in two orthotopic medulloblastoma models, and significantly prolonged survival in an aggressive orthotopic thalamic diffuse midline glioma model. No GPC2-directed CAR T cell related neurologic or systemic toxicity was observed. Taken together, these data show that GPC2 is a highly differentially expressed cell surface protein on multiple malignant pediatric brain tumors that can be targeted safely with local delivery of mRNA CAR T cells.One Sentence Summary Glypican 2 is expressed on the surface of multiple pediatric brain tumors and can be successfully targeted with mRNA chimeric antigen receptor T cells.Competing Interest StatementT.S. is currently employed by Spark Therapeutics. K.K. is currently employed by BioNTech and is an inventor on a patent related to use of nucleoside-modified mRNA. D.M.B. is currently employed by Tmunity Therapeutics. J.B.F., D.M.B, J.M.M., and K.R.B. hold patents for the discovery and development of immunotherapies for cancer, including patents related to GPC2-directed immunotherapies. K.R.B. and J.M.M. receive research funding from Tmunity for research on GPC2-directed immunotherapies and J.B.F., D.M.B, J.M.M., and K.R.B. receive royalties from Tmunity for licensing of GPC2-related intellectual property. J.M.M. is a founder of both Tantigen Bio and Hula Therapeutics, focused on cellular therapies for childhood cancers, but neither are working on GPC2-directed therapeutics. All other authors have nothing to disclose.",
    "genre": "preprint",
    "language": "en",
    "source": "DOI.org (Crossref)",
    "title": "Development of GPC2-directed chimeric antigen receptors using mRNA for pediatric brain tumors",
    "URL": "https://www.biorxiv.org/content/10.1101/2021.07.06.451385v2",
    "author": [
      {
        "family": "Foster",
        "given": "Jessica B."
      },
      {
        "family": "Griffin",
        "given": "Crystal"
      },
      {
        "family": "Rokita",
        "given": "Jo Lynne"
      },
      {
        "family": "Stern",
        "given": "Allison"
      },
      {
        "family": "Brimley",
        "given": "Cameron"
      },
      {
        "family": "Rathi",
        "given": "Komal"
      },
      {
        "family": "Lane",
        "given": "Maria V."
      },
      {
        "family": "Buongervino",
        "given": "Samantha N."
      },
      {
        "family": "Smith",
        "given": "Tiffany"
      },
      {
        "family": "Madsen",
        "given": "Peter J."
      },
      {
        "family": "Martinez",
        "given": "Daniel"
      },
      {
        "family": "Wechsler-Reya",
        "given": "Robert J."
      },
      {
        "family": "Karikó",
        "given": "Katalin"
      },
      {
        "family": "Storm",
        "given": "Phillip B."
      },
      {
        "family": "Barrett",
        "given": "David M."
      },
      {
        "family": "Resnick",
        "given": "Adam C."
      },
      {
        "family": "Maris",
        "given": "John M."
      },
      {
        "family": "Bosse",
        "given": "Kristopher R."
      }
    ],
    "accessed": {
      "date-parts": [
        [
          "2022",
          8,
          11
        ]
      ]
    },
    "issued": {
      "date-parts": [
        [
          "2021",
          7,
          7
        ]
      ]
    }
  },
  {
    "id": "biorxiv:10.1101/201178",
    "type": "article-journal",
    "container-title": "bioRxiv",
    "title": "Scaling accurate genetic variant discovery to tens of thousands of samples",
    "page": "201178",
    "DOI": "10.1101/201178",
    "language": "en",
    "abstract": "Comprehensive disease gene discovery in both common and rare diseases will require the efficient and accurate detection of all classes of genetic variation across tens to hundreds of thousands of human samples. We describe here a novel assembly-based approach to variant calling, the GATK HaplotypeCaller (HC) and Reference Confidence Model (RCM), that determines genotype likelihoods independently per-sample but performs joint calling across all samples within a project simultaneously. We show by calling over 90,000 samples from the Exome Aggregation Consortium (ExAC) that, in contrast to other algorithms, the HC-RCM scales efficiently to very large sample sizes without loss in accuracy; and that the accuracy of indel variant calling is superior in comparison to other algorithms. More importantly, the HC-RCM produces a fully squared-off matrix of genotypes across all samples at every genomic position being investigated. The HC-RCM is a novel, scalable, assembly-based algorithm with abundant applications for population genetics and clinical studies.",
    "source": "bioRxiv",
    "URL": "https://www.biorxiv.org/content/10.1101/201178v3",
    "author": [
      {
        "family": "Poplin",
        "given": "Ryan"
      },
      {
        "family": "Ruano-Rubio",
        "given": "Valentin"
      },
      {
        "family": "DePristo",
        "given": "Mark A."
      },
      {
        "family": "Fennell",
        "given": "Tim J."
      },
      {
        "family": "Carneiro",
        "given": "Mauricio O."
      },
      {
        "family": "Auwera",
        "given": "Geraldine A. Van",
        "dropping-particle": "der"
      },
      {
        "family": "Kling",
        "given": "David E."
      },
      {
        "family": "Gauthier",
        "given": "Laura D."
      },
      {
        "family": "Levy-Moonshine",
        "given": "Ami"
      },
      {
        "family": "Roazen",
        "given": "David"
      },
      {
        "family": "Shakir",
        "given": "Khalid"
      },
      {
        "family": "Thibault",
        "given": "Joel"
      },
      {
        "family": "Chandran",
        "given": "Sheila"
      },
      {
        "family": "Whelan",
        "given": "Chris"
      },
      {
        "family": "Lek",
        "given": "Monkol"
      },
      {
        "family": "Gabriel",
        "given": "Stacey"
      },
      {
        "family": "Daly",
        "given": "Mark J."
      },
      {
        "family": "Neale",
        "given": "Ben"
      },
      {
        "family": "MacArthur",
        "given": "Daniel G."
      },
      {
        "family": "Banks",
        "given": "Eric"
      }
    ],
    "accessed": {
      "date-parts": [
        [
          "2022",
          8,
          11
        ]
      ]
    },
    "issued": {
      "date-parts": [
        [
          "2018",
          7,
          24
        ]
      ]
    }
  },
  {
    "id": "biorxiv:10.1101/861054",
    "type": "article-journal",
    "container-title": "bioRxiv",
    "title": "Calling Somatic SNVs and Indels with Mutect2",
    "page": "861054",
    "DOI": "10.1101/861054",
    "abstract": "Mutect2 is a somatic variant caller that uses local assembly and realignment to detect SNVs and indels. Assembly implies whole haplotypes and read pairs, rather than single bases, as the atomic units of biological variation and sequencing evidence, improving variant calling. Beyond local assembly and alignment, Mutect2 is based on several probabilistic models for genotyping and filtering that work well with and without a matched normal sample and for all sequencing depths.",
    "language": "en",
    "source": "bioRxiv",
    "URL": "https://www.biorxiv.org/content/10.1101/861054v1",
    "author": [
      {
        "family": "Benjamin",
        "given": "David"
      },
      {
        "family": "Sato",
        "given": "Takuto"
      },
      {
        "family": "Cibulskis",
        "given": "Kristian"
      },
      {
        "family": "Getz",
        "given": "Gad"
      },
      {
        "family": "Stewart",
        "given": "Chip"
      },
      {
        "family": "Lichtenstein",
        "given": "Lee"
      }
    ],
    "accessed": {
      "date-parts": [
        [
          "2022",
          8,
          11
        ]
      ]
    },
    "issued": {
      "date-parts": [
        [
          "2019",
          12,
          2
        ]
      ]
    }
  },
  {
    "id": "biorxiv:10.1101/120295",
    "type": "article-journal",
    "container-title": "bioRxiv",
    "abstract": "Motivation Fusion genes created by genomic rearrangements can be potent drivers of tumorigenesis. However, accurate identification of functionally fusion genes from genomic sequencing requires whole genome sequencing, since exonic sequencing alone is often insufficient. Transcriptome sequencing provides a direct, highly effective alternative for capturing molecular evidence of expressed fusions in the precision medicine pipeline, but current methods tend to be inefficient or insufficiently accurate, lacking in sensitivity or predicting large numbers of false positives. Here, we describe STAR-Fusion, a method that is both fast and accurate in identifying fusion transcripts from RNA-Seq data.\nResults We benchmarked STAR-Fusion’s fusion detection accuracy using both simulated and genuine Illumina paired-end RNA-Seq data, and show that it has superior performance compared to popular alternative fusion detection methods.\nAvailability and implementation STAR-Fusion is implemented in Perl, freely available as open source software at http://star-fusion.github.io, and supported on Linux.\nContact bhaas{at}broadinstitute.org",
    "language": "en",
    "page": "120295",
    "DOI": "10.1101/120295",
    "source": "bioRxiv",
    "title": "STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq",
    "title-short": "STAR-Fusion",
    "URL": "https://www.biorxiv.org/content/10.1101/120295v1",
    "author": [
      {
        "family": "Haas",
        "given": "Brian J."
      },
      {
        "family": "Dobin",
        "given": "Alex"
      },
      {
        "family": "Stransky",
        "given": "Nicolas"
      },
      {
        "family": "Li",
        "given": "Bo"
      },
      {
        "family": "Yang",
        "given": "Xiao"
      },
      {
        "family": "Tickle",
        "given": "Timothy"
      },
      {
        "family": "Bankapur",
        "given": "Asma"
      },
      {
        "family": "Ganote",
        "given": "Carrie"
      },
      {
        "family": "Doak",
        "given": "Thomas G."
      },
      {
        "family": "Pochet",
        "given": "Nathalie"
      },
      {
        "family": "Sun",
        "given": "Jing"
      },
      {
        "family": "Wu",
        "given": "Catherine J."
      },
      {
        "family": "Gingeras",
        "given": "Thomas R."
      },
      {
        "family": "Regev",
        "given": "Aviv"
      }
    ],
    "accessed": {
      "date-parts": [
        [
          "2022",
          8,
          11
        ]
      ]
    },
    "issued": {
      "date-parts": [
        [
          "2017",
          3,
          24
        ]
      ]
    }
  },
  {
    "id": "pubmed:26389418",
    "type": "chapter",
    "title": "Childhood Medulloblastoma and Other Central Nervous System Embryonal Tumors Treatment (PDQ®): Health Professional Version",
    "container-title": "PDQ Cancer Information Summaries",
    "URL": "https://www.cancer.gov/types/brain/hp/child-cns-embryonal-treatment-pdq",
    "author":[
      {
        "literal": "PDQ® Pediatric Treatment Editorial Board"
      }
    ],
    "publisher": "National Cancer Institute",
    "publisher-place": "Bethesda, MD",
    "PMID": "26389418",
    "updated": {
      "date-parts": [
        [
          "2022",
          3,
          30
        ]
      ]
    },
    "accessed": {
      "date-parts": [
        [
          "2022",
          8,
          11
        ]
      ]
    }
  },
  {
    "id": "doi:10.7287/peerj.preprints.3210v1",
    "type": "article-journal",
    "container-title": "PeerJ Preprints",
    "abstract": "Traditionally, statistical training has focused primarily on mathematical derivations and proofs of statistical tests. The process of developing the technical artifact—that is, the paper, dashboard, or other deliverable—is much less frequently taught, presumably because of an aversion to cookbookery or prescribing specific software choices. In this paper I argue that it’s critical to teach analysts how to go about developing an analysis in order to maximize the probability that their analysis is reproducible, accurate, and collaborative. A critical component of this is adopting a blameless postmortem culture. By encouraging the use of and fluency in tooling that implements these opinions, as well as a blameless way of correcting course as analysts encounter errors, we as a community can foster the growth of processes that fail the practitioners as infrequently as possible.",
    "language": "en",
    "page": "e3210v1",
    "DOI": "10.7287/peerj.preprints.3210v1",
    "publisher": "PeerJ Preprints",
    "source": "peerj.com",
    "title": "Opinionated analysis development",
    "URL": "https://peerj.com/preprints/3210",
    "author": [
      {
        "family": "Parker",
        "given": "Hilary"
      }
    ],
    "accessed": {
      "date-parts": [
        [
          "2022",
          8,
          17
        ]
      ]
    },
    "issued": {
      "date-parts": [
        [
          "2017",
          8,
          31
        ]
      ]
    }
  },
  {
    "id": "url:https://www.fda.gov/about-fda/oncology-center-excellence/pediatric-oncology-drug-approvals",
    "type": "website",
    "abstract": "Pediatric Oncology Drug Approvals",
    "language": "en",
    "source": "www.fda.gov",
    "publisher": "U.S. Food and Drug Administration",
    "title": "Pediatric Oncology Drug Approvals",
    "URL": "https://www.fda.gov/about-fda/oncology-center-excellence/pediatric-oncology-drug-approvals",
    "author": [
      {
        "literal": "Oncology Center of Excellence, U.S. Food and Drug Administration"
      }
    ],
    "accessed": {
      "date-parts": [
        [
          "2022",
          8,
          17
        ]
      ]
    },
    "issued": {
      "date-parts": [
        [
          "2022",
          6,
          29
        ]
      ]
    }
  },
  {
    "id": "doi:10.1101/cshperspect.a026187",
    "publisher": "Cold Spring Harbor Laboratory",
    "issue": "4",
    "DOI": "10.1101/cshperspect.a026187",
    "type": "article-journal",
    "page": "a026187",
    "source": "Crossref",
    "title": "Inherited TP53 Mutations and the Li–Fraumeni Syndrome",
    "volume": "7",
    "author": [
      {
        "given": "Tanya",
        "family": "Guha"
      },
      {
        "given": "David",
        "family": "Malkin"
      }
    ],
    "container-title": "Cold Spring Harbor Perspectives in Medicine",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2017,
          3,
          7
        ]
      ]
    },
    "URL": "https://doi.org/f9s4h3",
    "container-title-short": "Cold Spring Harb Perspect Med",
    "PMCID": "PMC5378014",
    "PMID": "28270529"
  },
  {
    "id": "doi:10.1111/nan.12626",
    "publisher": "Wiley",
    "issue": "5",
    "DOI": "10.1111/nan.12626",
    "type": "article-journal",
    "page": "506-509",
    "source": "Crossref",
    "title": "A polyphenotypic malignant paediatric brain tumour presenting a MN1‐PATZ1 fusion, no epigenetic similarities with CNS High‐Grade Neuroepithelial Tumour with MN1 Alteration (CNS HGNET‐MN1) and related to PATZ1‐fused sarcomas",
    "volume": "46",
    "author": [
      {
        "given": "F.",
        "family": "Burel‐Vandenbos"
      },
      {
        "given": "G.",
        "family": "Pierron"
      },
      {
        "given": "C.",
        "family": "Thomas"
      },
      {
        "given": "S.",
        "family": "Reynaud"
      },
      {
        "given": "V.",
        "family": "Gregoire"
      },
      {
        "given": "G.",
        "family": "Duhil de Benaze"
      },
      {
        "given": "S.",
        "family": "Croze"
      },
      {
        "given": "N.",
        "family": "Chivoret"
      },
      {
        "given": "M.",
        "family": "Honavar"
      },
      {
        "given": "D.",
        "family": "Figarella‐Branger"
      },
      {
        "given": "C.‐A.",
        "family": "Maurage"
      },
      {
        "given": "F.",
        "family": "Pedeutour"
      },
      {
        "given": "M.",
        "family": "Hasselblatt"
      },
      {
        "given": "C.",
        "family": "Godfraind"
      }
    ],
    "container-title": "Neuropathology and Applied Neurobiology",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2020,
          6,
          3
        ]
      ]
    },
    "URL": "https://doi.org/gmndph",
    "container-title-short": "Neuropathol Appl Neurobiol",
    "PMID": "32397004"
  },
  {
    "id": "doi:10.1200/jco.2010.31.1670",
    "publisher": "American Society of Clinical Oncology (ASCO)",
    "issue": "35",
    "abstract": "<jats:sec><jats:title>Purpose</jats:title><jats:p> The role of TP53 mutations in the tumorigenesis of sporadic medulloblastoma (MB) and the value of TP53 mutation status as a prognostic marker are not yet definitely elucidated. A recent report identified TP53 mutations in MB as an adverse prognostic marker. Hence, the current study was conducted to validate the prognostic role of TP53 mutation in MB and to understand its contribution to tumorigenesis. </jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p> A comprehensive genetic analysis of 310 MB samples was performed by screening for TP53 mutations and further relating the TP53 mutation status to p53 immunostaining, cytogenetic aberrations, and clinical variables. </jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p> Mutation analysis of TP53 revealed mutations in 21 (6.8%) of 310 samples. Germline TP53 mutations were found in two patients with a history suggestive of a hereditary cancer syndrome. TP53 mutation status was not associated with unfavorable prognosis (P = .63) and was not linked to 17p allelic loss but was over-represented in the prognostically favorable WNT subgroup of MB as defined by CTNNB1 mutation (seven of 35 TP53-mutated tumors v 14 of 271 TP53 wild-type tumors; P = .005) and in tumors carrying high-level MYCN amplification (seven of 21 TP53-mutated tumors v 14 of 282 TP53 wild-type tumors; P = .001). </jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p> The contradictory results in the recent literature concerning the prognostic value of TP53 mutation might be explained by different frequencies of WNT MBs, different frequencies of patients with Li-Fraumeni syndrome, and different cumulative doses of alkylating drugs applied in these studies. </jats:p></jats:sec>",
    "DOI": "10.1200/jco.2010.31.1670",
    "type": "article-journal",
    "page": "5188-5196",
    "source": "Crossref",
    "title": "TP53 Mutation Is Frequently Associated With CTNNB1 Mutation or MYCN Amplification and Is Compatible With Long-Term Survival in Medulloblastoma",
    "volume": "28",
    "author": [
      {
        "given": "Elke",
        "family": "Pfaff"
      },
      {
        "given": "Marc",
        "family": "Remke"
      },
      {
        "given": "Dominik",
        "family": "Sturm"
      },
      {
        "given": "Axel",
        "family": "Benner"
      },
      {
        "given": "Hendrik",
        "family": "Witt"
      },
      {
        "given": "Till",
        "family": "Milde"
      },
      {
        "given": "André O.",
        "family": "von Bueren"
      },
      {
        "given": "Andrea",
        "family": "Wittmann"
      },
      {
        "given": "Anna",
        "family": "Schöttler"
      },
      {
        "given": "Norbert",
        "family": "Jorch"
      },
      {
        "given": "Norbert",
        "family": "Graf"
      },
      {
        "given": "Andreas E.",
        "family": "Kulozik"
      },
      {
        "given": "Olaf",
        "family": "Witt"
      },
      {
        "given": "Wolfram",
        "family": "Scheurlen"
      },
      {
        "given": "Andreas",
        "family": "von Deimling"
      },
      {
        "given": "Stefan",
        "family": "Rutkowski"
      },
      {
        "given": "Michael D.",
        "family": "Taylor"
      },
      {
        "given": "Uri",
        "family": "Tabori"
      },
      {
        "given": "Peter",
        "family": "Lichter"
      },
      {
        "given": "Andrey",
        "family": "Korshunov"
      },
      {
        "given": "Stefan M.",
        "family": "Pfister"
      }
    ],
    "container-title": "Journal of Clinical Oncology",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2010,
          12,
          10
        ]
      ]
    },
    "URL": "https://doi.org/dpd6hh",
    "container-title-short": "JCO",
    "PMID": "21060032"
  },
  {
    "id": "doi:10.1002/gcc.22110",
    "publisher": "Wiley",
    "issue": "12",
    "DOI": "10.1002/gcc.22110",
    "type": "article-journal",
    "page": "1150-1166",
    "source": "Crossref",
    "title": "Recurrent pre-existing and acquired DNA copy number alterations, including focal TERT gains, in neuroblastoma central nervous system metastases",
    "volume": "52",
    "author": [
      {
        "given": "David",
        "family": "Cobrinik"
      },
      {
        "given": "Irina",
        "family": "Ostrovnaya"
      },
      {
        "given": "Maryam",
        "family": "Hassimi"
      },
      {
        "given": "Satish K.",
        "family": "Tickoo"
      },
      {
        "given": "Irene Y.",
        "family": "Cheung"
      },
      {
        "given": "Nai-Kong V.",
        "family": "Cheung"
      }
    ],
    "container-title": "Genes, Chromosomes and Cancer",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2013,
          10,
          10
        ]
      ]
    },
    "URL": "https://doi.org/f5gd94",
    "container-title-short": "Genes Chromosomes Cancer",
    "PMID": "24123354"
  },
  {
    "id": "doi:10.1073/pnas.1300252110",
    "publisher": "Proceedings of the National Academy of Sciences",
    "issue": "20",
    "abstract": "<jats:p>\n            Pediatric low-grade gliomas (PLGGs) are among the most common solid tumors in children but, apart from\n            <jats:italic>BRAF</jats:italic>\n            kinase mutations or duplications in specific subclasses, few genetic driver events are known. Diffuse PLGGs comprise a set of uncommon subtypes that exhibit invasive growth and are therefore especially challenging clinically. We performed high-resolution copy-number analysis on 44 formalin-fixed, paraffin-embedded diffuse PLGGs to identify recurrent alterations. Diffuse PLGGs exhibited fewer such alterations than adult low-grade gliomas, but we identified several significantly recurrent events. The most significant event, 8q13.1 gain, was observed in 28% of diffuse astrocytoma grade IIs and resulted in partial duplication of the transcription factor\n            <jats:italic>MYBL1</jats:italic>\n            with truncation of its C-terminal negative-regulatory domain. A similar recurrent deletion-truncation breakpoint was identified in two angiocentric gliomas in the related gene\n            <jats:italic>v-myb avian myeloblastosis viral oncogene homolog</jats:italic>\n            (\n            <jats:italic>MYB</jats:italic>\n            ) on 6q23.3. Whole-genome sequencing of a\n            <jats:italic>MYBL1</jats:italic>\n            -rearranged diffuse astrocytoma grade II demonstrated\n            <jats:italic>MYBL1</jats:italic>\n            tandem duplication and few other events. Truncated\n            <jats:italic>MYBL1</jats:italic>\n            transcripts identified in this tumor induced anchorage-independent growth in 3T3 cells and tumor formation in nude mice. Truncated transcripts were also expressed in two additional tumors with\n            <jats:italic>MYBL1</jats:italic>\n            partial duplication. Our results define clinically relevant molecular subclasses of diffuse PLGGs and highlight a potential role for the MYB family in the biology of low-grade gliomas.\n          </jats:p>",
    "DOI": "10.1073/pnas.1300252110",
    "type": "article-journal",
    "page": "8188-8193",
    "source": "Crossref",
    "title": "Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent oncogenic truncating rearrangements in the transcription factor\n            <i>MYBL1</i>",
    "volume": "110",
    "author": [
      {
        "given": "Lori A.",
        "family": "Ramkissoon"
      },
      {
        "given": "Peleg M.",
        "family": "Horowitz"
      },
      {
        "given": "Justin M.",
        "family": "Craig"
      },
      {
        "given": "Shakti H.",
        "family": "Ramkissoon"
      },
      {
        "given": "Benjamin E.",
        "family": "Rich"
      },
      {
        "given": "Steven E.",
        "family": "Schumacher"
      },
      {
        "given": "Aaron",
        "family": "McKenna"
      },
      {
        "given": "Michael S.",
        "family": "Lawrence"
      },
      {
        "given": "Guillaume",
        "family": "Bergthold"
      },
      {
        "given": "Priscilla K.",
        "family": "Brastianos"
      },
      {
        "given": "Barbara",
        "family": "Tabak"
      },
      {
        "given": "Matthew D.",
        "family": "Ducar"
      },
      {
        "given": "Paul",
        "family": "Van Hummelen"
      },
      {
        "given": "Laura E.",
        "family": "MacConaill"
      },
      {
        "given": "Tina",
        "family": "Pouissant-Young"
      },
      {
        "given": "Yoon-Jae",
        "family": "Cho"
      },
      {
        "given": "Hala",
        "family": "Taha"
      },
      {
        "given": "Madeha",
        "family": "Mahmoud"
      },
      {
        "given": "Daniel C.",
        "family": "Bowers"
      },
      {
        "given": "Linda",
        "family": "Margraf"
      },
      {
        "given": "Uri",
        "family": "Tabori"
      },
      {
        "given": "Cynthia",
        "family": "Hawkins"
      },
      {
        "given": "Roger J.",
        "family": "Packer"
      },
      {
        "given": "D. Ashley",
        "family": "Hill"
      },
      {
        "given": "Scott L.",
        "family": "Pomeroy"
      },
      {
        "given": "Charles G.",
        "family": "Eberhart"
      },
      {
        "given": "Ian F.",
        "family": "Dunn"
      },
      {
        "given": "Liliana",
        "family": "Goumnerova"
      },
      {
        "given": "Gad",
        "family": "Getz"
      },
      {
        "given": "Jennifer A.",
        "family": "Chan"
      },
      {
        "given": "Sandro",
        "family": "Santagata"
      },
      {
        "given": "William C.",
        "family": "Hahn"
      },
      {
        "given": "Charles D.",
        "family": "Stiles"
      },
      {
        "given": "Azra H.",
        "family": "Ligon"
      },
      {
        "given": "Mark W.",
        "family": "Kieran"
      },
      {
        "given": "Rameen",
        "family": "Beroukhim"
      },
      {
        "given": "Keith L.",
        "family": "Ligon"
      }
    ],
    "container-title": "Proceedings of the National Academy of Sciences",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2013,
          4,
          30
        ]
      ]
    },
    "URL": "https://doi.org/f42gg4",
    "container-title-short": "Proc. Natl. Acad. Sci. U.S.A.",
    "PMCID": "PMC3657784",
    "PMID": "23633565"
  },
  {
    "id": "doi:10.1093/bioinformatics/btu314",
    "publisher": "Oxford University Press (OUP)",
    "issue": "17",
    "abstract": "<jats:p>Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the requirement to read, write, sort and compress large BAM files multiple times.</jats:p>\n               <jats:p>Results: We present SAMBLASTER, a tool that reduces the number of times such costly operations are performed. SAMBLASTER is designed to mark duplicates in read-sorted SAM files as a piped post-pass on DNA aligner output before it is compressed to BAM. In addition, it can simultaneously output into separate files the discordant read-pairs and/or split-read mappings used for structural variant calling. As an alignment post-pass, its own runtime overhead is negligible, while dramatically reducing overall pipeline complexity and runtime. As a stand-alone duplicate marking tool, it performs significantly better than PICARD or SAMBAMBA in terms of both speed and memory usage, while achieving nearly identical results.</jats:p>\n               <jats:p>Availability and implementation: SAMBLASTER is open-source C++ code and freely available for download from https://github.com/GregoryFaust/samblaster.</jats:p>\n               <jats:p>Contact:  imh4y@virginia.edu</jats:p>",
    "DOI": "10.1093/bioinformatics/btu314",
    "type": "article-journal",
    "page": "2503-2505",
    "source": "Crossref",
    "title": "SAMBLASTER: fast duplicate marking and structural variant read extraction",
    "volume": "30",
    "author": [
      {
        "given": "Gregory G.",
        "family": "Faust"
      },
      {
        "given": "Ira M.",
        "family": "Hall"
      }
    ],
    "container-title": "Bioinformatics",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2014,
          5,
          7
        ]
      ]
    },
    "URL": "https://doi.org/f6kft3",
    "PMCID": "PMC4147885",
    "PMID": "24812344"
  },
  {
    "id": "doi:10.1093/neuonc/noaa251",
    "publisher": "Oxford University Press (OUP)",
    "issue": "1",
    "abstract": "<jats:title>Abstract</jats:title>\n               <jats:sec>\n                  <jats:title>Background</jats:title>\n                  <jats:p>Malignant astrocytic gliomas in children show a remarkable biological and clinical diversity. Small in-frame insertions or missense mutations in the epidermal growth factor receptor gene (EGFR) have recently been identified in a distinct subset of pediatric-type bithalamic gliomas with a unique DNA methylation pattern.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Methods</jats:title>\n                  <jats:p>Here, we investigated an epigenetically homogeneous cohort of malignant gliomas (n = 58) distinct from other subtypes and enriched for pediatric cases and thalamic location, in comparison with this recently identified subtype of pediatric bithalamic gliomas.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Results</jats:title>\n                  <jats:p>EGFR gene amplification was detected in 16/58 (27%) tumors, and missense mutations or small in-frame insertions in EGFR were found in 20/30 tumors with available sequencing data (67%; 5 of them co-occurring with EGFR amplification). Additionally, 8 of the 30 tumors (27%) harbored an H3.1 or H3.3 K27M mutation (6 of them with a concomitant EGFR alteration). All tumors tested showed loss of H3K27me3 staining, with evidence of overexpression of the EZH inhibitory protein (EZHIP) in the H3 wildtype cases. Although some tumors indeed showed a bithalamic growth pattern, a significant proportion of tumors occurred in the unilateral thalamus or in other (predominantly midline) locations.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions</jats:title>\n                  <jats:p>Our findings present a distinct molecular class of pediatric-type malignant gliomas largely overlapping with the recently reported bithalamic gliomas characterized by EGFR alteration, but additionally showing a broader spectrum of EGFR alterations and tumor localization. Global H3K27me3 loss in this group appears to be mediated by either H3 K27 mutation or EZHIP overexpression. EGFR inhibition may represent a potential therapeutic strategy in these highly aggressive gliomas.</jats:p>\n               </jats:sec>",
    "DOI": "10.1093/neuonc/noaa251",
    "type": "article-journal",
    "page": "34-43",
    "source": "Crossref",
    "title": "A subset of pediatric-type thalamic gliomas share a distinct DNA methylation profile, H3K27me3 loss and frequent alteration of <i>EGFR</i>",
    "volume": "23",
    "author": [
      {
        "given": "Philipp",
        "family": "Sievers"
      },
      {
        "given": "Martin",
        "family": "Sill"
      },
      {
        "given": "Daniel",
        "family": "Schrimpf"
      },
      {
        "given": "Damian",
        "family": "Stichel"
      },
      {
        "given": "David E",
        "family": "Reuss"
      },
      {
        "given": "Dominik",
        "family": "Sturm"
      },
      {
        "given": "Jürgen",
        "family": "Hench"
      },
      {
        "given": "Stephan",
        "family": "Frank"
      },
      {
        "given": "Lenka",
        "family": "Krskova"
      },
      {
        "given": "Ales",
        "family": "Vicha"
      },
      {
        "given": "Michal",
        "family": "Zapotocky"
      },
      {
        "given": "Brigitte",
        "family": "Bison"
      },
      {
        "given": "David",
        "family": "Castel"
      },
      {
        "given": "Jacques",
        "family": "Grill"
      },
      {
        "given": "Marie-Anne",
        "family": "Debily"
      },
      {
        "given": "Patrick N",
        "family": "Harter"
      },
      {
        "given": "Matija",
        "family": "Snuderl"
      },
      {
        "given": "Christof M",
        "family": "Kramm"
      },
      {
        "given": "Guido",
        "family": "Reifenberger"
      },
      {
        "given": "Andrey",
        "family": "Korshunov"
      },
      {
        "given": "Nada",
        "family": "Jabado"
      },
      {
        "given": "Pieter",
        "family": "Wesseling"
      },
      {
        "given": "Wolfgang",
        "family": "Wick"
      },
      {
        "given": "David A",
        "family": "Solomon"
      },
      {
        "given": "Arie",
        "family": "Perry"
      },
      {
        "given": "Thomas S",
        "family": "Jacques"
      },
      {
        "given": "Chris",
        "family": "Jones"
      },
      {
        "given": "Olaf",
        "family": "Witt"
      },
      {
        "given": "Stefan M",
        "family": "Pfister"
      },
      {
        "given": "Andreas",
        "family": "von Deimling"
      },
      {
        "given": "David T W",
        "family": "Jones"
      },
      {
        "given": "Felix",
        "family": "Sahm"
      }
    ],
    "container-title": "Neuro-Oncology",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2020,
          11,
          1
        ]
      ]
    },
    "URL": "https://doi.org/gnxj54",
    "PMCID": "PMC7850075",
    "PMID": "33130881"
  },
  {
    "id": "doi:10.1073/pnas.1300252110",
    "publisher": "Proceedings of the National Academy of Sciences",
    "issue": "20",
    "abstract": "<jats:p>\n            Pediatric low-grade gliomas (PLGGs) are among the most common solid tumors in children but, apart from\n            <jats:italic>BRAF</jats:italic>\n            kinase mutations or duplications in specific subclasses, few genetic driver events are known. Diffuse PLGGs comprise a set of uncommon subtypes that exhibit invasive growth and are therefore especially challenging clinically. We performed high-resolution copy-number analysis on 44 formalin-fixed, paraffin-embedded diffuse PLGGs to identify recurrent alterations. Diffuse PLGGs exhibited fewer such alterations than adult low-grade gliomas, but we identified several significantly recurrent events. The most significant event, 8q13.1 gain, was observed in 28% of diffuse astrocytoma grade IIs and resulted in partial duplication of the transcription factor\n            <jats:italic>MYBL1</jats:italic>\n            with truncation of its C-terminal negative-regulatory domain. A similar recurrent deletion-truncation breakpoint was identified in two angiocentric gliomas in the related gene\n            <jats:italic>v-myb avian myeloblastosis viral oncogene homolog</jats:italic>\n            (\n            <jats:italic>MYB</jats:italic>\n            ) on 6q23.3. Whole-genome sequencing of a\n            <jats:italic>MYBL1</jats:italic>\n            -rearranged diffuse astrocytoma grade II demonstrated\n            <jats:italic>MYBL1</jats:italic>\n            tandem duplication and few other events. Truncated\n            <jats:italic>MYBL1</jats:italic>\n            transcripts identified in this tumor induced anchorage-independent growth in 3T3 cells and tumor formation in nude mice. Truncated transcripts were also expressed in two additional tumors with\n            <jats:italic>MYBL1</jats:italic>\n            partial duplication. Our results define clinically relevant molecular subclasses of diffuse PLGGs and highlight a potential role for the MYB family in the biology of low-grade gliomas.\n          </jats:p>",
    "DOI": "10.1073/pnas.1300252110",
    "type": "article-journal",
    "page": "8188-8193",
    "source": "Crossref",
    "title": "Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent oncogenic truncating rearrangements in the transcription factor MYBL1",
    "volume": "110",
    "author": [
      {
        "given": "Lori A.",
        "family": "Ramkissoon"
      },
      {
        "given": "Peleg M.",
        "family": "Horowitz"
      },
      {
        "given": "Justin M.",
        "family": "Craig"
      },
      {
        "given": "Shakti H.",
        "family": "Ramkissoon"
      },
      {
        "given": "Benjamin E.",
        "family": "Rich"
      },
      {
        "given": "Steven E.",
        "family": "Schumacher"
      },
      {
        "given": "Aaron",
        "family": "McKenna"
      },
      {
        "given": "Michael S.",
        "family": "Lawrence"
      },
      {
        "given": "Guillaume",
        "family": "Bergthold"
      },
      {
        "given": "Priscilla K.",
        "family": "Brastianos"
      },
      {
        "given": "Barbara",
        "family": "Tabak"
      },
      {
        "given": "Matthew D.",
        "family": "Ducar"
      },
      {
        "given": "Paul",
        "family": "Van Hummelen"
      },
      {
        "given": "Laura E.",
        "family": "MacConaill"
      },
      {
        "given": "Tina",
        "family": "Pouissant-Young"
      },
      {
        "given": "Yoon-Jae",
        "family": "Cho"
      },
      {
        "given": "Hala",
        "family": "Taha"
      },
      {
        "given": "Madeha",
        "family": "Mahmoud"
      },
      {
        "given": "Daniel C.",
        "family": "Bowers"
      },
      {
        "given": "Linda",
        "family": "Margraf"
      },
      {
        "given": "Uri",
        "family": "Tabori"
      },
      {
        "given": "Cynthia",
        "family": "Hawkins"
      },
      {
        "given": "Roger J.",
        "family": "Packer"
      },
      {
        "given": "D. Ashley",
        "family": "Hill"
      },
      {
        "given": "Scott L.",
        "family": "Pomeroy"
      },
      {
        "given": "Charles G.",
        "family": "Eberhart"
      },
      {
        "given": "Ian F.",
        "family": "Dunn"
      },
      {
        "given": "Liliana",
        "family": "Goumnerova"
      },
      {
        "given": "Gad",
        "family": "Getz"
      },
      {
        "given": "Jennifer A.",
        "family": "Chan"
      },
      {
        "given": "Sandro",
        "family": "Santagata"
      },
      {
        "given": "William C.",
        "family": "Hahn"
      },
      {
        "given": "Charles D.",
        "family": "Stiles"
      },
      {
        "given": "Azra H.",
        "family": "Ligon"
      },
      {
        "given": "Mark W.",
        "family": "Kieran"
      },
      {
        "given": "Rameen",
        "family": "Beroukhim"
      },
      {
        "given": "Keith L.",
        "family": "Ligon"
      }
    ],
    "container-title": "Proceedings of the National Academy of Sciences",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2013,
          4,
          30
        ]
      ]
    },
    "URL": "https://doi.org/f42gg4",
    "container-title-short": "Proc. Natl. Acad. Sci. U.S.A.",
    "PMCID": "PMC3657784",
    "PMID": "23633565"
  },
  {
    "id": "doi:10.1093/neuonc/noaa251",
    "publisher": "Oxford University Press (OUP)",
    "issue": "1",
    "abstract": "<jats:title>Abstract</jats:title>\n               <jats:sec>\n                  <jats:title>Background</jats:title>\n                  <jats:p>Malignant astrocytic gliomas in children show a remarkable biological and clinical diversity. Small in-frame insertions or missense mutations in the epidermal growth factor receptor gene (EGFR) have recently been identified in a distinct subset of pediatric-type bithalamic gliomas with a unique DNA methylation pattern.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Methods</jats:title>\n                  <jats:p>Here, we investigated an epigenetically homogeneous cohort of malignant gliomas (n = 58) distinct from other subtypes and enriched for pediatric cases and thalamic location, in comparison with this recently identified subtype of pediatric bithalamic gliomas.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Results</jats:title>\n                  <jats:p>EGFR gene amplification was detected in 16/58 (27%) tumors, and missense mutations or small in-frame insertions in EGFR were found in 20/30 tumors with available sequencing data (67%; 5 of them co-occurring with EGFR amplification). Additionally, 8 of the 30 tumors (27%) harbored an H3.1 or H3.3 K27M mutation (6 of them with a concomitant EGFR alteration). All tumors tested showed loss of H3K27me3 staining, with evidence of overexpression of the EZH inhibitory protein (EZHIP) in the H3 wildtype cases. Although some tumors indeed showed a bithalamic growth pattern, a significant proportion of tumors occurred in the unilateral thalamus or in other (predominantly midline) locations.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions</jats:title>\n                  <jats:p>Our findings present a distinct molecular class of pediatric-type malignant gliomas largely overlapping with the recently reported bithalamic gliomas characterized by EGFR alteration, but additionally showing a broader spectrum of EGFR alterations and tumor localization. Global H3K27me3 loss in this group appears to be mediated by either H3 K27 mutation or EZHIP overexpression. EGFR inhibition may represent a potential therapeutic strategy in these highly aggressive gliomas.</jats:p>\n               </jats:sec>",
    "DOI": "10.1093/neuonc/noaa251",
    "type": "article-journal",
    "page": "34-43",
    "source": "Crossref",
    "title": "A subset of pediatric-type thalamic gliomas share a distinct DNA methylation profile, H3K27me3 loss and frequent alteration of EGFR",
    "volume": "23",
    "author": [
      {
        "given": "Philipp",
        "family": "Sievers"
      },
      {
        "given": "Martin",
        "family": "Sill"
      },
      {
        "given": "Daniel",
        "family": "Schrimpf"
      },
      {
        "given": "Damian",
        "family": "Stichel"
      },
      {
        "given": "David E",
        "family": "Reuss"
      },
      {
        "given": "Dominik",
        "family": "Sturm"
      },
      {
        "given": "Jürgen",
        "family": "Hench"
      },
      {
        "given": "Stephan",
        "family": "Frank"
      },
      {
        "given": "Lenka",
        "family": "Krskova"
      },
      {
        "given": "Ales",
        "family": "Vicha"
      },
      {
        "given": "Michal",
        "family": "Zapotocky"
      },
      {
        "given": "Brigitte",
        "family": "Bison"
      },
      {
        "given": "David",
        "family": "Castel"
      },
      {
        "given": "Jacques",
        "family": "Grill"
      },
      {
        "given": "Marie-Anne",
        "family": "Debily"
      },
      {
        "given": "Patrick N",
        "family": "Harter"
      },
      {
        "given": "Matija",
        "family": "Snuderl"
      },
      {
        "given": "Christof M",
        "family": "Kramm"
      },
      {
        "given": "Guido",
        "family": "Reifenberger"
      },
      {
        "given": "Andrey",
        "family": "Korshunov"
      },
      {
        "given": "Nada",
        "family": "Jabado"
      },
      {
        "given": "Pieter",
        "family": "Wesseling"
      },
      {
        "given": "Wolfgang",
        "family": "Wick"
      },
      {
        "given": "David A",
        "family": "Solomon"
      },
      {
        "given": "Arie",
        "family": "Perry"
      },
      {
        "given": "Thomas S",
        "family": "Jacques"
      },
      {
        "given": "Chris",
        "family": "Jones"
      },
      {
        "given": "Olaf",
        "family": "Witt"
      },
      {
        "given": "Stefan M",
        "family": "Pfister"
      },
      {
        "given": "Andreas",
        "family": "von Deimling"
      },
      {
        "given": "David T W",
        "family": "Jones"
      },
      {
        "given": "Felix",
        "family": "Sahm"
      }
    ],
    "container-title": "Neuro-Oncology",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2020,
          11,
          1
        ]
      ]
    },
    "URL": "https://doi.org/gnxj54",
    "PMCID": "PMC7850075",
    "PMID": "33130881"
  },
  {
    "id": "arxiv:1303.3997",
    "type": "article",
    "abstract": "Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads and performs chimeric alignment. The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases. For mapping 100bp sequences, BWA-MEM shows better performance than several state-of-art read aligners to date. Availability and implementation: BWA-MEM is implemented as a component of BWA, which is available at http://github.com/lh3/bwa. Contact: hengli@broadinstitute.org",
    "DOI": "10.48550/arXiv.1303.3997",
    "publisher": "arXiv",
    "source": "arXiv.org",
    "container-title": "arXiv",
    "page": "1303.3997",
    "title": "Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM",
    "URL": "http://arxiv.org/abs/1303.3997",
    "author": [
      {
        "family": "Li",
        "given": "Heng"
      }
    ],
    "accessed": {
      "date-parts": [
        [
          "2023",
          4,
          24
        ]
      ]
    },
    "issued": {
      "date-parts": [
        [
          "2013",
          5,
          26
        ]
      ]
    }
  },
  {
    "id": "doi:10.1136/jitc-2021-004012",
    "publisher": "BMJ",
    "issue": "2",
    "abstract": "<jats:sec><jats:title>Background</jats:title><jats:p>Programmed cell death protein-1 (PD-1) expression has been associated with activation and exhaustion of both the CD4 and CD8 populations in advanced non-small cell lung cancer (aNSCLC). Nevertheless, the impact of the balance between circulating CD8<jats:sup>+</jats:sup>PD-1<jats:sup>+</jats:sup> and CD4<jats:sup>+</jats:sup>PD-1<jats:sup>+</jats:sup> in patients treated with immune checkpoint blockers (ICB) is unknown.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>The CD8<jats:sup>+</jats:sup>PD-1<jats:sup>+</jats:sup> to CD4<jats:sup>+</jats:sup>PD-1<jats:sup>+</jats:sup> ratio (PD-1-Expressing Ratio on Lymphocytes in a Systemic blood sample, or ‘PERLS’) was determined by cytometry in fresh whole blood from patients with aNSCLC before treatment with single-agent ICB targeting PD-1 or programmed cell death-ligand 1 (PD-L1 (discovery cohort). A PERLS cut-off was identified by log-rank maximization. Patients treated with ICB (validation cohort) or polychemotherapy (control cohort) were classified as PERLS+/− (above/below cut-off). Circulating immune cell phenotype and function were correlated with PERLS. A composite score (good, intermediate and poor) was determined using the combination of PERLS and senescent immune phenotype as previously described in aNSCLC.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>In the discovery cohort (N=75), the PERLS cut-off was 1.91, and 11% of patients were PERLS+. PERLS + correlated significantly with median progression-free survival (PFS) of 9.63 months (95% CI 7.82 to not reached (NR)) versus 2.69 months (95% CI 1.81 to 5.52; p=0.03). In an independent validation cohort (N=36), median PFS was NR (95% CI 7.9 to NR) versus 2.00 months (95% CI 1.3 to 4.5; p=0.04) for PERLS + and PERLS−, respectively; overall survival (OS) followed a similar but non-significant trend. In the pooled cohort (N=111), PERLS + correlated significantly with PFS and OS. PERLS did not correlate with outcome in the polychemotherapy cohort. PERLS did not correlate with clinical characteristics but was significantly associated with baseline circulating naïve CD4<jats:sup>+</jats:sup> T cells and the increase of memory T cells post-ICB treatment. Accumulation of memory T cells during treatment was linked to CD4<jats:sup>+</jats:sup> T cell polyfunctionality. The composite score was evaluated in the pooled cohort (N=68). The median OS for good, intermediate and poor composite scores was NR (95% CI NR to NR), 8.54 months (95% CI 4.96 to NR) and 2.42 months (95% CI 1.97 to 15.5; p=0.001), respectively. The median PFS was 12.60 months (95% CI 9.63 to NR), 2.58 months (95% CI 1.74 to 7.29) and 1.76 months (95% CI 1.31 to 4.57; p&lt;0.0001), respectively.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>Elevated PERLS, determined from a blood sample before immunotherapy, was correlated with benefit from PD-(L)1 blockers in aNSCLC.</jats:p></jats:sec>",
    "DOI": "10.1136/jitc-2021-004012",
    "type": "article-journal",
    "page": "e004012",
    "source": "Crossref",
    "title": "CD8⁺PD-1⁺ to CD4⁺PD-1⁺ ratio (PERLS) is associated with prognosis of patients with advanced NSCLC treated with PD-(L)1 blockers",
    "volume": "10",
    "author": [
      {
        "given": "Boris",
        "family": "Duchemann"
      },
      {
        "given": "Marie",
        "family": "Naigeon"
      },
      {
        "given": "Edouard",
        "family": "Auclin"
      },
      {
        "given": "Roberto",
        "family": "Ferrara"
      },
      {
        "given": "Lydie",
        "family": "Cassard"
      },
      {
        "given": "Jean-Mehdi",
        "family": "Jouniaux"
      },
      {
        "given": "Lisa",
        "family": "Boselli"
      },
      {
        "given": "Jonathan",
        "family": "Grivel"
      },
      {
        "given": "Aude",
        "family": "Desnoyer"
      },
      {
        "given": "François-Xavier",
        "family": "Danlos"
      },
      {
        "given": "Laura",
        "family": "Mezquita"
      },
      {
        "given": "Caroline",
        "family": "Caramella"
      },
      {
        "given": "Aurelien",
        "family": "Marabelle"
      },
      {
        "given": "Benjamin",
        "family": "Besse"
      },
      {
        "given": "Nathalie",
        "family": "Chaput"
      }
    ],
    "container-title": "Journal for ImmunoTherapy of Cancer",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2022,
          2
        ]
      ]
    },
    "URL": "https://doi.org/gqc4j2",
    "container-title-short": "J Immunother Cancer",
    "PMCID": "PMC8823243",
    "PMID": "35131864"
  },
  {
    "publisher": "Oxford University Press (OUP)",
    "abstract": "<jats:title>Abstract</jats:title>\n               <jats:sec>\n                  <jats:title>Background</jats:title>\n                  <jats:p>To achieve replicative immortality, most cancers develop a telomere maintenance mechanism, such as reactivation of telomerase or alternative lengthening of telomeres (ALT). There are limited data on the prevalence and clinical significance of ALT in pediatric brain tumors, and ALT-directed therapy is not available.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Methods</jats:title>\n                  <jats:p>We performed C-circle analysis (CCA) on 579 pediatric brain tumors that had corresponding tumor/normal whole genome sequencing through the Open Pediatric Brain Tumor Atlas (OpenPBTA). We detected ALT in 6.9% (n = 40/579) of these tumors and completed additional validation by ultrabright telomeric foci in situ on a subset of these tumors. We used CCA to validate TelomereHunter for computational prediction of ALT status and focus subsequent analyses on pediatric high-grade gliomas (pHGGs) Finally, we examined whether ALT is associated with recurrent somatic or germline alterations.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Results</jats:title>\n                  <jats:p>ALT is common in pHGGs (n = 24/63, 38.1%), but occurs infrequently in other pediatric brain tumors (&amp;lt;3%). Somatic ATRX mutations occur in 50% of ALT+ pHGGs and in 30% of ALT− pHGGs. Rare pathogenic germline variants in mismatch repair (MMR) genes are significantly associated with an increased occurrence of ALT.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions</jats:title>\n                  <jats:p>We demonstrate that ATRX is mutated in only a subset of ALT+ pHGGs, suggesting other mechanisms of ATRX loss of function or alterations in other genes may be associated with the development of ALT in these patients. We show that germline variants in MMR are associated with the development of ALT in patients with pHGG.</jats:p>\n               </jats:sec>",
    "DOI": "10.1093/neuonc/noac278",
    "type": "article-journal",
    "source": "Crossref",
    "title": "Alternative lengthening of telomeres (ALT) in pediatric high-grade gliomas can occur without ATRX mutation and is enriched in patients with pathogenic germline mismatch repair (MMR) variants",
    "author": [
      {
        "given": "Jennifer L",
        "family": "Stundon"
      },
      {
        "given": "Heba",
        "family": "Ijaz"
      },
      {
        "given": "Krutika S",
        "family": "Gaonkar"
      },
      {
        "given": "Rebecca S",
        "family": "Kaufman"
      },
      {
        "given": "Run",
        "family": "Jin"
      },
      {
        "given": "Anastasios",
        "family": "Karras"
      },
      {
        "given": "Zalman",
        "family": "Vaksman"
      },
      {
        "given": "Jung",
        "family": "Kim"
      },
      {
        "given": "Ryan J",
        "family": "Corbett"
      },
      {
        "given": "Matthew R",
        "family": "Lueder"
      },
      {
        "given": "Daniel P",
        "family": "Miller"
      },
      {
        "given": "Yiran",
        "family": "Guo"
      },
      {
        "given": "Mariarita",
        "family": "Santi"
      },
      {
        "given": "Marilyn",
        "family": "Li"
      },
      {
        "given": "Gonzalo",
        "family": "Lopez"
      },
      {
        "given": "Phillip B",
        "family": "Storm"
      },
      {
        "given": "Adam C",
        "family": "Resnick"
      },
      {
        "given": "Angela J",
        "family": "Waanders"
      },
      {
        "given": "Suzanne P",
        "family": "MacFarland"
      },
      {
        "given": "Douglas R",
        "family": "Stewart"
      },
      {
        "given": "Sharon J",
        "family": "Diskin"
      },
      {
        "given": "Jo Lynne",
        "family": "Rokita"
      },
      {
        "given": "Kristina A",
        "family": "Cole"
      }
    ],
    "container-title": "Neuro-Oncology",
    "page": "noac278",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2022,
          12,
          20
        ]
      ]
    },
    "URL": "https://doi.org/grnc33",
    "PMID": "36541551",
    "id": "doi:10.1093/neuonc/noac278"
  },
  {
    "id": "arxiv:1710.03675",
    "type": "article",
    "abstract": "We describe the Rocker project, which provides a widely-used suite of Docker images with customized R environments for particular tasks. We discuss how this suite is organized, and how these tools can increase portability, scaling, reproducibility, and convenience of R users and developers.",
    "DOI": "10.48550/arXiv.1710.03675",
    "publisher": "arXiv",
    "source": "arXiv.org",
    "container-title": "arXiv",
    "page": "1710.03675",
    "title": "An Introduction to Rocker: Docker Containers for R",
    "title-short": "An Introduction to Rocker",
    "URL": "http://arxiv.org/abs/1710.03675",
    "author": [
      {
        "family": "Boettiger",
        "given": "Carl"
      },
      {
        "family": "Eddelbuettel",
        "given": "Dirk"
      }
    ],
    "accessed": {
      "date-parts": [
        [
          "2023",
          4,
          24
        ]
      ]
    },
    "issued": {
      "date-parts": [
        [
          "2017",
          10,
          10
        ]
      ]
    }
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "DOI": "10.1186/s13029-016-0053-y",
    "type": "article-journal",
    "source": "Crossref",
    "title": "MM2S: personalized diagnosis of medulloblastoma patients and model systems",
    "volume": "11",
    "page": "6",
    "author": [
      {
        "given": "Deena M.A.",
        "family": "Gendoo"
      },
      {
        "given": "Benjamin",
        "family": "Haibe-Kains"
      }
    ],
    "container-title": "Source Code for Biology and Medicine",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2016,
          4,
          11
        ]
      ]
    },
    "URL": "https://doi.org/ghcqf2",
    "container-title-short": "Source Code Biol Med",
    "PMCID": "PMC4827218",
    "PMID": "27069505",
    "id": "doi:10.1186/s13029-016-0053-y"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "page": "30",
    "abstract": "<jats:title>Abstract</jats:title><jats:p>Low grade gliomas are the most frequent brain tumors in children and encompass a spectrum of histologic entities which are currently assigned World Health Organisation grades I and II. They differ substantially from their adult counterparts in both their underlying genetic alterations and in the infrequency with which they transform to higher grade tumors. Nonetheless, children with low grade glioma are a therapeutic challenge due to the heterogeneity in their clinical behavior – in particular, those with incomplete surgical resection often suffer repeat progressions with resultant morbidity and, in some cases, mortality. The identification of up-regulation of the RAS–mitogen-activated protein kinase (RAS/MAPK) pathway as a near universal feature of these tumors has led to the development of targeted therapeutics aimed at improving responses while mitigating patient morbidity. Here, we review how molecular information can help to further define the entities which fall under the umbrella of pediatric-type low-grade glioma. In doing so we discuss the specific molecular drivers of pediatric low grade glioma and how to effectively test for them, review the newest therapeutic agents and their utility in treating this disease, and propose a risk-based stratification system that considers both clinical and molecular parameters to aid clinicians in making treatment decisions.</jats:p>",
    "DOI": "10.1186/s40478-020-00902-z",
    "type": "article-journal",
    "source": "Crossref",
    "title": "Pediatric low-grade glioma in the era of molecular diagnostics",
    "volume": "8",
    "author": [
      {
        "given": "Scott",
        "family": "Ryall"
      },
      {
        "given": "Uri",
        "family": "Tabori"
      },
      {
        "given": "Cynthia",
        "family": "Hawkins"
      }
    ],
    "container-title": "Acta Neuropathologica Communications",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2020,
          3,
          12
        ]
      ]
    },
    "URL": "https://doi.org/gm3kst",
    "container-title-short": "acta neuropathol commun",
    "PMCID": "PMC7066826",
    "PMID": "32164789",
    "id": "doi:10.1186/s40478-020-00902-z"
  },{
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "abstract": "<jats:title>Abstract</jats:title><jats:p>Four molecular types of rare central nervous system (CNS) tumors have been recently identified by gene methylation profiling: CNS Neuroblastoma with <jats:italic>FOXR2</jats:italic> activation (CNS NB-FOXR2), CNS Ewing Sarcoma Family Tumor with <jats:italic>CIC</jats:italic> alteration (CNS EFT-CIC), CNS high grade neuroepithelial tumor with <jats:italic>MN1</jats:italic> alteration (CNS HGNET-MN1) and CNS high grade neuroepithelial tumor with <jats:italic>BCOR</jats:italic> alteration (CNS HGNET-BCOR). Although they are not represented in 2016 updated WHO classification of CNS tumors, their diagnostic recognition is important because of clinical consequences. We have introduced a diagnostic method based on transcription profiling of tumor specific signature genes from formalin-fixed, paraffin-embedded tumor blocks using NanoString nCounter Technology. Altogether, 14 out of 187 (7.4%) high grade pediatric brain tumors were diagnosed with either of four new CNS categories. Histopathological examination of the tumors confirmed, that they demonstrate a spectrum of morphology mimicking other CNS high grade tumors. However, they also exhibit some suggestive histopathological and immunohistochemical features that allow for a presumptive diagnosis prior to molecular assessment. Clinical characteristics of patients corroborated with the previous findings for CNS EFT-CIC, CNS NB-FOXR2 and CNS HGNET-MN1 patients, with a favorable survival rate for the latter two groups. Among six CNS HGNET-BCOR patients, three patients are long term survivors, suggesting possible heterogeneity within this molecular category of tumors. In summary, we confirmed the effectiveness of NanoString method using a single, multi-gene tumor specific signature and recommend this novel approach for identification of either one of the four newly described CNS tumor entities.</jats:p>",
    "DOI": "10.1186/s40478-020-00984-9",
    "type": "article-journal",
    "source": "Crossref",
    "title": "Molecular identification of CNS NB-FOXR2, CNS EFT-CIC, CNS HGNET-MN1 and CNS HGNET-BCOR pediatric brain tumors using tumor-specific signature genes",
    "volume": "8",
    "page": "105",
    "author": [
      {
        "given": "Maria",
        "family": "Łastowska"
      },
      {
        "given": "Joanna",
        "family": "Trubicka"
      },
      {
        "given": "Anna",
        "family": "Sobocińska"
      },
      {
        "given": "Bartosz",
        "family": "Wojtas"
      },
      {
        "given": "Magdalena",
        "family": "Niemira"
      },
      {
        "given": "Anna",
        "family": "Szałkowska"
      },
      {
        "given": "Adam",
        "family": "Krętowski"
      },
      {
        "given": "Agnieszka",
        "family": "Karkucińska-Więckowska"
      },
      {
        "given": "Magdalena",
        "family": "Kaleta"
      },
      {
        "given": "Maria",
        "family": "Ejmont"
      },
      {
        "given": "Marta",
        "family": "Perek-Polnik"
      },
      {
        "given": "Bożenna",
        "family": "Dembowska-Bagińska"
      },
      {
        "given": "Wiesława",
        "family": "Grajkowska"
      },
      {
        "given": "Ewa",
        "family": "Matyja"
      }
    ],
    "container-title": "Acta Neuropathologica Communications",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2020,
          7,
          10
        ]
      ]
    },
    "URL": "https://doi.org/gm3q3p",
    "container-title-short": "acta neuropathol commun",
    "PMCID": "PMC7350623",
    "PMID": "32650833",
    "id": "doi:10.1186/s40478-020-00984-9"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "DOI": "10.1186/s40478-020-00905-w",
    "type": "article-journal",
    "source": "Crossref",
    "title": "Diffuse intrinsic pontine glioma-like tumor with EZHIP expression and molecular features of PFA ependymoma",
    "volume": "8",
    "page": "37",
    "author": [
      {
        "given": "Drew",
        "family": "Pratt"
      },
      {
        "given": "Martha",
        "family": "Quezado"
      },
      {
        "given": "Zied",
        "family": "Abdullaev"
      },
      {
        "given": "Debra",
        "family": "Hawes"
      },
      {
        "given": "Fusheng",
        "family": "Yang"
      },
      {
        "given": "Hugh J. L.",
        "family": "Garton"
      },
      {
        "given": "Alexander R.",
        "family": "Judkins"
      },
      {
        "given": "Rajen",
        "family": "Mody"
      },
      {
        "given": "Arul",
        "family": "Chinnaiyan"
      },
      {
        "given": "Kenneth",
        "family": "Aldape"
      },
      {
        "given": "Carl",
        "family": "Koschmann"
      },
      {
        "given": "Sriram",
        "family": "Venneti"
      }
    ],
    "container-title": "Acta Neuropathologica Communications",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2020,
          3,
          20
        ]
      ]
    },
    "URL": "https://doi.org/gm3ksv",
    "container-title-short": "acta neuropathol commun",
    "PMCID": "PMC7083001",
    "PMID": "32197665",
    "id": "doi:10.1186/s40478-020-00905-w"
  },
  {
    "publisher": "Oxford University Press (OUP)",
    "issue": "12",
    "abstract": "<jats:title>Abstract</jats:title><jats:p>Dysembryoplastic neuroepithelial tumors (DNT) lacking key diagnostic criteria are challenging to diagnose and sometimes fall into the broader category of mixed neuronal-glial tumors (MNGT) or the recently described polymorphous low-grade neuroepithelial tumor of the young (PLNTY). We examined 41 patients with DNT, MNGT, or PLNTY for histologic features, genomic findings, and progression-free survival (PFS). Genomic analysis included sequence and copy number variants and RNA-sequencing. Classic DNT (n = 26) was compared with those with diffuse growth without cortical nodules (n = 15), 6 of which exhibited impressive CD34 staining classifying them as PLNTY. Genomic analysis was complete in 33, with sequence alterations recurrently identified in BRAF, FGFR1, NF1, and PDGFRA, as well as 7 fusion genes involving FGFR2, FGFR1, NTRK2, and BRAF. Genetic alterations did not distinguish between MNGTs, DNTs, or PLNTYs; however, FGFR1 alterations were confined to DNT, and PLNTYs contained BRAF V600E or FGFR2 fusion genes. Analysis of PFS showed no significant difference by histology or genetic alteration; however, numbers were small and follow-up time short. Further molecular characterization of a PLNTY-related gene fusion, FGFR2-CTNNA3, demonstrated oncogenic potential via MAPK/PI3K/mTOR pathway activation. Overall, DNT-MNGT spectrum tumors exhibit diverse genomic alterations, with more than half (19/33) leading to MAPK/PI3K pathway alterations.</jats:p>",
    "DOI": "10.1093/jnen/nlz101",
    "type": "article-journal",
    "page": "1100-1111",
    "source": "Crossref",
    "title": "Genomic Analysis of Dysembryoplastic Neuroepithelial Tumor Spectrum Reveals a Diversity of Molecular Alterations Dysregulating the MAPK and PI3K/mTOR Pathways",
    "volume": "78",
    "author": [
      {
        "given": "Lea F",
        "family": "Surrey"
      },
      {
        "given": "Payal",
        "family": "Jain"
      },
      {
        "given": "Bo",
        "family": "Zhang"
      },
      {
        "given": "Joshua",
        "family": "Straka"
      },
      {
        "given": "Xiaonan",
        "family": "Zhao"
      },
      {
        "given": "Brian N",
        "family": "Harding"
      },
      {
        "given": "Adam C",
        "family": "Resnick"
      },
      {
        "given": "Phillip B",
        "family": "Storm"
      },
      {
        "given": "Anna Maria",
        "family": "Buccoliero"
      },
      {
        "given": "Lorenzo",
        "family": "Genitori"
      },
      {
        "given": "Marilyn M",
        "family": "Li"
      },
      {
        "given": "Angela J",
        "family": "Waanders"
      },
      {
        "given": "Mariarita",
        "family": "Santi"
      }
    ],
    "container-title": "Journal of Neuropathology & Experimental Neurology",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2019,
          9,
          26
        ]
      ]
    },
    "URL": "https://doi.org/gpnm3p",
    "PMID": "31617914",
    "id": "doi:10.1093/jnen/nlz101"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "abstract": "<jats:title>Abstract</jats:title><jats:p>The<jats:italic>FGFR1</jats:italic>gene encoding fibroblast growth factor receptor 1 has emerged as a frequently altered oncogene in the pathogenesis of multiple low-grade neuroepithelial tumor (LGNET) subtypes including pilocytic astrocytoma, dysembryoplastic neuroepithelial tumor (DNT), rosette-forming glioneuronal tumor (RGNT), and extraventricular neurocytoma (EVN). These activating<jats:italic>FGFR1</jats:italic>alterations in LGNET can include tandem duplication of the exons encoding the intracellular tyrosine kinase domain, in-frame gene fusions most often with<jats:italic>TACC1</jats:italic>as the partner, or hotspot missense mutations within the tyrosine kinase domain (either at p.N546 or p.K656). However, the specificity of these different<jats:italic>FGFR1</jats:italic>events for the various LGNET subtypes and accompanying genetic alterations are not well defined. Here we performed comprehensive genomic and epigenomic characterization on a diverse cohort of 30 LGNET with<jats:italic>FGFR1</jats:italic>alterations. We identified that RGNT harbors a distinct epigenetic signature compared to other LGNET with<jats:italic>FGFR1</jats:italic>alterations, and is uniquely characterized by<jats:italic>FGFR1</jats:italic>kinase domain hotspot missense mutations in combination with either<jats:italic>PIK3CA</jats:italic>or<jats:italic>PIK3R1</jats:italic>mutation, often with accompanying<jats:italic>NF1</jats:italic>or<jats:italic>PTPN11</jats:italic>mutation. In contrast, EVN harbors its own distinct epigenetic signature and is characterized by<jats:italic>FGFR1</jats:italic>-<jats:italic>TACC1</jats:italic>fusion as the solitary pathogenic alteration. Additionally, DNT and pilocytic astrocytoma are characterized by either kinase domain tandem duplication or hotspot missense mutations, occasionally with accompanying<jats:italic>NF1</jats:italic>or<jats:italic>PTPN11</jats:italic>mutation, but lacking the accompanying<jats:italic>PIK3CA</jats:italic>or<jats:italic>PIK3R1</jats:italic>mutation that characterizes RGNT. The glial component of LGNET with<jats:italic>FGFR1</jats:italic>alterations typically has a predominantly oligodendroglial morphology, and many of the pilocytic astrocytomas with<jats:italic>FGFR1</jats:italic>alterations lack the biphasic pattern, piloid processes, and Rosenthal fibers that characterize pilocytic astrocytomas with<jats:italic>BRAF</jats:italic>mutation or fusion. Together, this analysis improves the classification and histopathologic stratification of LGNET with<jats:italic>FGFR1</jats:italic>alterations.</jats:p>",
    "DOI": "10.1186/s40478-020-01027-z",
    "type": "article-journal",
    "source": "Crossref",
    "title": "Comprehensive analysis of diverse low-grade neuroepithelial tumors with FGFR1 alterations reveals a distinct molecular signature of rosette-forming glioneuronal tumor",
    "volume": "8",
    "page": "151",
    "author": [
      {
        "given": "Calixto-Hope G.",
        "family": "Lucas"
      },
      {
        "given": "Rohit",
        "family": "Gupta"
      },
      {
        "given": "Pamela",
        "family": "Doo"
      },
      {
        "given": "Julieann C.",
        "family": "Lee"
      },
      {
        "given": "Cathryn R.",
        "family": "Cadwell"
      },
      {
        "given": "Biswarathan",
        "family": "Ramani"
      },
      {
        "given": "Jeffrey W.",
        "family": "Hofmann"
      },
      {
        "given": "Emily A.",
        "family": "Sloan"
      },
      {
        "given": "Bette K.",
        "family": "Kleinschmidt-DeMasters"
      },
      {
        "given": "Han S.",
        "family": "Lee"
      },
      {
        "given": "Matthew D.",
        "family": "Wood"
      },
      {
        "given": "Marjorie",
        "family": "Grafe"
      },
      {
        "given": "Donald",
        "family": "Born"
      },
      {
        "given": "Hannes",
        "family": "Vogel"
      },
      {
        "given": "Shahriar",
        "family": "Salamat"
      },
      {
        "given": "Diane",
        "family": "Puccetti"
      },
      {
        "given": "David",
        "family": "Scharnhorst"
      },
      {
        "given": "David",
        "family": "Samuel"
      },
      {
        "given": "Tabitha",
        "family": "Cooney"
      },
      {
        "given": "Elaine",
        "family": "Cham"
      },
      {
        "given": "Lee-way",
        "family": "Jin"
      },
      {
        "given": "Ziad",
        "family": "Khatib"
      },
      {
        "given": "Ossama",
        "family": "Maher"
      },
      {
        "given": "Gabriel",
        "family": "Chamyan"
      },
      {
        "given": "Carole",
        "family": "Brathwaite"
      },
      {
        "given": "Serguei",
        "family": "Bannykh"
      },
      {
        "given": "Sabine",
        "family": "Mueller"
      },
      {
        "given": "Cassie N.",
        "family": "Kline"
      },
      {
        "given": "Anu",
        "family": "Banerjee"
      },
      {
        "given": "Alyssa",
        "family": "Reddy"
      },
      {
        "given": "Jennie W.",
        "family": "Taylor"
      },
      {
        "given": "Jennifer L.",
        "family": "Clarke"
      },
      {
        "given": "Nancy Ann",
        "family": "Oberheim Bush"
      },
      {
        "given": "Nicholas",
        "family": "Butowski"
      },
      {
        "given": "Nalin",
        "family": "Gupta"
      },
      {
        "given": "Kurtis I.",
        "family": "Auguste"
      },
      {
        "given": "Peter P.",
        "family": "Sun"
      },
      {
        "given": "Jarod L.",
        "family": "Roland"
      },
      {
        "given": "Corey",
        "family": "Raffel"
      },
      {
        "given": "Manish K.",
        "family": "Aghi"
      },
      {
        "given": "Philip",
        "family": "Theodosopoulos"
      },
      {
        "given": "Edward",
        "family": "Chang"
      },
      {
        "given": "Shawn",
        "family": "Hervey-Jumper"
      },
      {
        "given": "Joanna J.",
        "family": "Phillips"
      },
      {
        "given": "Melike",
        "family": "Pekmezci"
      },
      {
        "given": "Andrew W.",
        "family": "Bollen"
      },
      {
        "given": "Tarik",
        "family": "Tihan"
      },
      {
        "given": "Susan",
        "family": "Chang"
      },
      {
        "given": "Mitchel S.",
        "family": "Berger"
      },
      {
        "given": "Arie",
        "family": "Perry"
      },
      {
        "given": "David A.",
        "family": "Solomon"
      }
    ],
    "container-title": "Acta Neuropathologica Communications",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2020,
          8,
          28
        ]
      ]
    },
    "URL": "https://doi.org/gpnmx5",
    "container-title-short": "acta neuropathol commun",
    "PMCID": "PMC7456392",
    "PMID": "32859279",
    "id": "doi:10.1186/s40478-020-01027-z"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "abstract": "<jats:title>Abstract</jats:title><jats:p>Active telomerase is essential for stem cells and most cancers to maintain telomeres. The enzymatic activity of telomerase is related but not equivalent to the expression of TERT, the catalytic subunit of the complex. Here we show that telomerase enzymatic activity can be robustly estimated from the expression of a 13-gene signature. We demonstrate the validity of the expression-based approach, named EXTEND, using cell lines, cancer samples, and non-neoplastic samples. When applied to over 9,000 tumors and single cells, we find a strong correlation between telomerase activity and cancer stemness. This correlation is largely driven by a small population of proliferating cancer cells that exhibits both high telomerase activity and cancer stemness. This study establishes a computational framework for quantifying telomerase enzymatic activity and provides new insights into the relationships among telomerase, cancer proliferation, and stemness.</jats:p>",
    "DOI": "10.1038/s41467-020-20474-9",
    "type": "article-journal",
    "source": "Crossref",
    "title": "Integrated analysis of telomerase enzymatic activity unravels an association with cancer stemness and proliferation",
    "volume": "12",
    "page": "139",
    "author": [
      {
        "given": "Nighat",
        "family": "Noureen"
      },
      {
        "given": "Shaofang",
        "family": "Wu"
      },
      {
        "given": "Yingli",
        "family": "Lv"
      },
      {
        "given": "Juechen",
        "family": "Yang"
      },
      {
        "given": "W. K.",
        "family": "Alfred Yung"
      },
      {
        "given": "Jonathan",
        "family": "Gelfond"
      },
      {
        "given": "Xiaojing",
        "family": "Wang"
      },
      {
        "given": "Dimpy",
        "family": "Koul"
      },
      {
        "given": "Andrew",
        "family": "Ludlow"
      },
      {
        "given": "Siyuan",
        "family": "Zheng"
      }
    ],
    "container-title": "Nature Communications",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2021,
          1,
          8
        ]
      ]
    },
    "URL": "https://doi.org/gmfxxd",
    "container-title-short": "Nat Commun",
    "PMCID": "PMC7794223",
    "PMID": "33420056",
    "id": "doi:10.1038/s41467-020-20474-9"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "3",
    "DOI": "10.1007/s12032-016-0736-x",
    "type": "article-journal",
    "source": "Crossref",
    "title": "Telomerase activity in breast cancer patients: association with poor prognosis and more aggressive phenotype",
    "volume": "33",
    "page": "23",
    "author": [
      {
        "given": "Ana",
        "family": "Kulić"
      },
      {
        "given": "Natalija Dedić",
        "family": "Plavetić"
      },
      {
        "given": "Stjepan",
        "family": "Gamulin"
      },
      {
        "given": "Jasminka",
        "family": "Jakić-Razumović"
      },
      {
        "given": "Damir",
        "family": "Vrbanec"
      },
      {
        "given": "Maja",
        "family": "Sirotković-Skerlev"
      }
    ],
    "container-title": "Medical Oncology",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2016,
          1,
          30
        ]
      ]
    },
    "URL": "https://doi.org/f8ck55",
    "container-title-short": "Med Oncol",
    "PMID": "26833480",
    "id": "doi:10.1007/s12032-016-0736-x"
  },
  {
    "publisher": "Oxford University Press (OUP)",
    "issue": "1",
    "abstract": "<jats:title>Abstract</jats:title>\n               <jats:p>Vestibular schwannomas are tumors arising from the vestibulocochlear nerve at the cerebellopontine angle. Their proximity to eloquent brainstem structures means that the pathology itself and the treatment thereof can be associated with significant morbidity. The vast majority of these tumors are sporadic, with the remainder arising as a result of the genetic syndrome Neurofibromatosis Type 2 or, more rarely, LZTR1-related schwannomatosis. The natural history of these tumors is extremely variable, with some tumors not displaying any evidence of growth, others demonstrating early, persistent growth and a small number growing following an extended period of indolence. Emerging evidence now suggests that far from representing Schwann cell proliferation only, the tumor microenvironment is complex, with inflammation proposed to play a key role in their growth. In this review, we provide an overview of this new evidence, including the role played by immune cell infiltration, the underlying molecular pathways involved, and biomarkers for detecting this inflammation in vivo. Given the limitations of current treatments, there is a pressing need for novel therapies to aid in the management of this condition, and we conclude by proposing areas for future research that could lead to the development of therapies targeted toward inflammation in vestibular schwannoma.</jats:p>",
    "DOI": "10.1093/noajnl/vdaa023",
    "type": "article-journal",
    "source": "Crossref",
    "title": "The inflammatory microenvironment in vestibular schwannoma",
    "volume": "2",
    "page": "vdaa023",
    "author": [
      {
        "given": "Cathal John",
        "family": "Hannan"
      },
      {
        "given": "Daniel",
        "family": "Lewis"
      },
      {
        "given": "Claire",
        "family": "O’Leary"
      },
      {
        "given": "Carmine A",
        "family": "Donofrio"
      },
      {
        "given": "Dafydd Gareth",
        "family": "Evans"
      },
      {
        "given": "Federico",
        "family": "Roncaroli"
      },
      {
        "given": "David",
        "family": "Brough"
      },
      {
        "given": "Andrew Thomas",
        "family": "King"
      },
      {
        "given": "David",
        "family": "Coope"
      },
      {
        "given": "Omar Nathan",
        "family": "Pathmanaban"
      }
    ],
    "container-title": "Neuro-Oncology Advances",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2020,
          2,
          27
        ]
      ]
    },
    "URL": "https://doi.org/gpwh65",
    "PMCID": "PMC7212860",
    "PMID": "32642684",
    "id": "doi:10.1093/noajnl/vdaa023"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "DOI": "10.1186/s40478-018-0553-x",
    "type": "article-journal",
    "source": "Crossref",
    "title": "Non-inflammatory tumor microenvironment of diffuse intrinsic pontine glioma",
    "volume": "6",
    "page": "51",
    "author": [
      {
        "given": "Grant L.",
        "family": "Lin"
      },
      {
        "given": "Surya",
        "family": "Nagaraja"
      },
      {
        "given": "Mariella G.",
        "family": "Filbin"
      },
      {
        "given": "Mario L.",
        "family": "Suvà"
      },
      {
        "given": "Hannes",
        "family": "Vogel"
      },
      {
        "given": "Michelle",
        "family": "Monje"
      }
    ],
    "container-title": "Acta Neuropathologica Communications",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2018,
          6,
          28
        ]
      ]
    },
    "URL": "https://doi.org/gp2nq6",
    "container-title-short": "acta neuropathol commun",
    "PMCID": "PMC6022714",
    "PMID": "29954445",
    "id": "doi:10.1186/s40478-018-0553-x"
  },
  {
    "title": "The Inflammatory Milieu of Adamantinomatous Craniopharyngioma and Its Implications for Treatment.",
    "volume": "9",
    "issue": "2",
    "page": "519",
    "container-title": "Journal of clinical medicine",
    "container-title-short": "J Clin Med",
    "ISSN": "2077-0383",
    "issued": {
      "date-parts": [
        [
          2020,
          2,
          14
        ]
      ]
    },
    "author": [
      {
        "given": "Ros",
        "family": "Whelan"
      },
      {
        "given": "Eric",
        "family": "Prince"
      },
      {
        "given": "Ahmed",
        "family": "Gilani"
      },
      {
        "given": "Todd",
        "family": "Hankinson"
      }
    ],
    "PMID": "32075140",
    "PMCID": "PMC7074265",
    "DOI": "10.3390/jcm9020519",
    "abstract": "Pediatric Adamantinomatous Craniopharyngiomas (ACPs) are histologically benign brain tumors that often follow an aggressive clinical course. Their suprasellar location leaves them in close proximity to critical neurological and vascular structures and often results in significant neuroendocrine morbidity. Current treatment paradigms, involving surgical resection and radiotherapy, confer significant morbidity to patients and there is an obvious need to discover effective and safe alternative treatments. Recent years have witnessed significant efforts to fully detail the genomic, transcriptomic and proteomic make-up of these tumors, in an attempt to identify potential therapeutic targets. These studies have resulted in ever mounting evidence that inflammatory processes and the immune response play a critical role in the pathogenesis of both the solid and cystic portion of ACPs. Several inflammatory and immune markers have been identified in both the cyst fluid and solid tumor tissue of ACP. Due to the existence of effective agents that target them, IL-6 and immune checkpoint inhibitors seem to present the most likely immediate candidates for clinical trials of targeted immune-related therapy in ACP. If effective, such agents may result in a paradigm shift in treatment that ultimately reduces morbidity and results in better outcomes for our patients.",
    "URL": "https://www.ncbi.nlm.nih.gov/pubmed/32075140",
    "type": "article-journal",
    "id": "pubmed:32075140"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "abstract": "<jats:title>Abstract</jats:title><jats:sec>\n                <jats:title>Background</jats:title>\n                <jats:p>Gene fusion events are significant sources of somatic variation across adult and pediatric cancers and are some of the most clinically-effective therapeutic targets, yet low consensus of RNA-Seq fusion prediction algorithms makes therapeutic prioritization difficult. In addition, events such as polymerase read-throughs, mis-mapping due to gene homology, and fusions occurring in healthy normal tissue require informed filtering, making it difficult for researchers and clinicians to rapidly discern gene fusions that might be true underlying oncogenic drivers of a tumor and in some cases, appropriate targets for therapy.</jats:p>\n              </jats:sec><jats:sec>\n                <jats:title>Results</jats:title>\n                <jats:p>We developed <jats:italic>annoFuse</jats:italic>, an R package, and <jats:italic>shinyFuse</jats:italic>, a companion web application, to annotate, prioritize, and explore biologically-relevant expressed gene fusions, downstream of fusion calling. We validated <jats:italic>annoFuse</jats:italic> using a random cohort of TCGA RNA-Seq samples (N = 160) and achieved a 96% sensitivity for retention of high-confidence fusions (N = 603). <jats:italic>annoFuse</jats:italic> uses FusionAnnotator annotations to filter non-oncogenic and/or artifactual fusions. Then, fusions are prioritized if previously reported in TCGA and/or fusions containing gene partners that are known oncogenes, tumor suppressor genes, COSMIC genes, and/or transcription factors. We applied <jats:italic>annoFuse</jats:italic> to fusion calls from pediatric brain tumor RNA-Seq samples (N = 1028) provided as part of the Open Pediatric Brain Tumor Atlas (OpenPBTA) Project to determine recurrent fusions and recurrently-fused genes within different brain tumor histologies. <jats:italic>annoFuse</jats:italic> annotates protein domains using the PFAM database, assesses reciprocality, and annotates gene partners for kinase domain retention. As a standard function, <jats:italic>reportFuse</jats:italic> enables generation of a reproducible R Markdown report to summarize filtered fusions, visualize breakpoints and protein domains by transcript, and plot recurrent fusions within cohorts. Finally, we created <jats:italic>shinyFuse</jats:italic> for algorithm-agnostic interactive exploration and plotting of gene fusions.</jats:p>\n              </jats:sec><jats:sec>\n                <jats:title>Conclusions</jats:title>\n                <jats:p><jats:italic>annoFuse</jats:italic> provides standardized filtering and annotation for gene fusion calls from STAR-Fusion and Arriba by merging, filtering, and prioritizing putative oncogenic fusions across large cancer datasets, as demonstrated here with data from the OpenPBTA project. We are expanding the package to be widely-applicable to other fusion algorithms and expect <jats:italic>annoFuse</jats:italic> to provide researchers a method for rapidly evaluating, prioritizing, and translating fusion findings in patient tumors.</jats:p>\n              </jats:sec>",
    "DOI": "10.1186/s12859-020-03922-7",
    "type": "article-journal",
    "source": "Crossref",
    "title": "annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions",
    "volume": "21",
    "page": "577",
    "author": [
      {
        "given": "Krutika S.",
        "family": "Gaonkar"
      },
      {
        "given": "Federico",
        "family": "Marini"
      },
      {
        "given": "Komal S.",
        "family": "Rathi"
      },
      {
        "given": "Payal",
        "family": "Jain"
      },
      {
        "given": "Yuankun",
        "family": "Zhu"
      },
      {
        "given": "Nicholas A.",
        "family": "Chimicles"
      },
      {
        "given": "Miguel A.",
        "family": "Brown"
      },
      {
        "given": "Ammar S.",
        "family": "Naqvi"
      },
      {
        "given": "Bo",
        "family": "Zhang"
      },
      {
        "given": "Phillip B.",
        "family": "Storm"
      },
      {
        "given": "John M.",
        "family": "Maris"
      },
      {
        "given": "Pichai",
        "family": "Raman"
      },
      {
        "given": "Adam C.",
        "family": "Resnick"
      },
      {
        "given": "Konstantin",
        "family": "Strauch"
      },
      {
        "given": "Jaclyn N.",
        "family": "Taroni"
      },
      {
        "given": "Jo Lynne",
        "family": "Rokita"
      }
    ],
    "container-title": "BMC Bioinformatics",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2020,
          12,
          14
        ]
      ]
    },
    "URL": "https://doi.org/gm84mh",
    "container-title-short": "BMC Bioinformatics",
    "PMCID": "PMC7737294",
    "PMID": "33317447",
    "id": "doi:10.1186/s12859-020-03922-7"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "abstract": "<jats:title>Abstract</jats:title><jats:p>Reliable detection of somatic variations is of critical importance in cancer research. Here we present Lancet, an accurate and sensitive somatic variant caller, which detects SNVs and indels by jointly analyzing reads from tumor and matched normal samples using colored de Bruijn graphs. We demonstrate, through extensive experimental comparison on synthetic and real whole-genome sequencing datasets, that Lancet has better accuracy, especially for indel detection, than widely used somatic callers, such as MuTect, MuTect2, LoFreq, Strelka, and Strelka2. Lancet features a reliable variant scoring system, which is essential for variant prioritization, and detects low-frequency mutations without sacrificing the sensitivity to call longer insertions and deletions empowered by the local-assembly engine. In addition to genome-wide analysis, Lancet allows inspection of somatic variants in graph space, which augments the traditional read alignment visualization to help confirm a variant of interest. Lancet is available as an open-source program at <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"https://github.com/nygenome/lancet\">https://github.com/nygenome/lancet</jats:ext-link>.</jats:p>",
    "DOI": "10.1038/s42003-018-0023-9",
    "type": "article-journal",
    "source": "Crossref",
    "title": "Genome-wide somatic variant calling using localized colored de Bruijn graphs",
    "volume": "1",
    "page": "20",
    "author": [
      {
        "given": "Giuseppe",
        "family": "Narzisi"
      },
      {
        "given": "André",
        "family": "Corvelo"
      },
      {
        "given": "Kanika",
        "family": "Arora"
      },
      {
        "given": "Ewa A.",
        "family": "Bergmann"
      },
      {
        "given": "Minita",
        "family": "Shah"
      },
      {
        "given": "Rajeeva",
        "family": "Musunuri"
      },
      {
        "given": "Anne-Katrin",
        "family": "Emde"
      },
      {
        "given": "Nicolas",
        "family": "Robine"
      },
      {
        "given": "Vladimir",
        "family": "Vacic"
      },
      {
        "given": "Michael C.",
        "family": "Zody"
      }
    ],
    "container-title": "Communications Biology",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2018,
          3,
          22
        ]
      ]
    },
    "URL": "https://doi.org/gfcfr8",
    "container-title-short": "Commun Biol",
    "PMCID": "PMC6123722",
    "PMID": "30271907",
    "id": "doi:10.1038/s42003-018-0023-9"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "abstract": "<jats:title>Abstract</jats:title><jats:p>To test the performance of a new sequencing platform, develop an updated somatic calling pipeline and establish a reference for future benchmarking experiments, we performed whole-genome sequencing of 3 common cancer cell lines (COLO-829, HCC-1143 and HCC-1187) along with their matched normal cell lines to great sequencing depths (up to 278x coverage) on both Illumina HiSeqX and NovaSeq sequencing instruments. Somatic calling was generally consistent between the two platforms despite minor differences at the read level. We designed and implemented a novel pipeline for the analysis of tumor-normal samples, using multiple variant callers. We show that coupled with a high-confidence filtering strategy, the use of combination of tools improves the accuracy of somatic variant calling. We also demonstrate the utility of the dataset by creating an artificial purity ladder to evaluate the somatic pipeline and benchmark methods for estimating purity and ploidy from tumor-normal pairs. The data and results of the pipeline are made accessible to the cancer genomics community.</jats:p>",
    "DOI": "10.1038/s41598-019-55636-3",
    "type": "article-journal",
    "source": "Crossref",
    "title": "Deep whole-genome sequencing of 3 cancer cell lines on 2 sequencing platforms",
    "volume": "9",
    "page": "19123",
    "author": [
      {
        "given": "Kanika",
        "family": "Arora"
      },
      {
        "given": "Minita",
        "family": "Shah"
      },
      {
        "given": "Molly",
        "family": "Johnson"
      },
      {
        "given": "Rashesh",
        "family": "Sanghvi"
      },
      {
        "given": "Jennifer",
        "family": "Shelton"
      },
      {
        "given": "Kshithija",
        "family": "Nagulapalli"
      },
      {
        "given": "Dayna M.",
        "family": "Oschwald"
      },
      {
        "given": "Michael C.",
        "family": "Zody"
      },
      {
        "given": "Soren",
        "family": "Germer"
      },
      {
        "given": "Vaidehi",
        "family": "Jobanputra"
      },
      {
        "given": "Jade",
        "family": "Carter"
      },
      {
        "given": "Nicolas",
        "family": "Robine"
      }
    ],
    "container-title": "Scientific Reports",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2019,
          12,
          13
        ]
      ]
    },
    "URL": "https://doi.org/gqm73w",
    "container-title-short": "Sci Rep",
    "PMCID": "PMC6911065",
    "PMID": "31836783",
    "id": "doi:10.1038/s41598-019-55636-3"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "DOI": "10.1186/s13059-016-0974-4",
    "type": "article-journal",
    "source": "Crossref",
    "title": "The Ensembl Variant Effect Predictor",
    "volume": "17",
    "page": "122",
    "author": [
      {
        "given": "William",
        "family": "McLaren"
      },
      {
        "given": "Laurent",
        "family": "Gil"
      },
      {
        "given": "Sarah E.",
        "family": "Hunt"
      },
      {
        "given": "Harpreet Singh",
        "family": "Riat"
      },
      {
        "given": "Graham R. S.",
        "family": "Ritchie"
      },
      {
        "given": "Anja",
        "family": "Thormann"
      },
      {
        "given": "Paul",
        "family": "Flicek"
      },
      {
        "given": "Fiona",
        "family": "Cunningham"
      }
    ],
    "container-title": "Genome Biology",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2016,
          6,
          6
        ]
      ]
    },
    "URL": "https://doi.org/gdz75c",
    "container-title-short": "Genome Biol",
    "PMCID": "PMC4893825",
    "PMID": "27268795",
    "id": "doi:10.1186/s13059-016-0974-4"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "4",
    "DOI": "10.1186/gb-2011-12-4-r41",
    "type": "article-journal",
    "source": "Crossref",
    "title": "GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers",
    "volume": "12",
    "page": "R41",
    "author": [
      {
        "given": "Craig H",
        "family": "Mermel"
      },
      {
        "given": "Steven E",
        "family": "Schumacher"
      },
      {
        "given": "Barbara",
        "family": "Hill"
      },
      {
        "given": "Matthew L",
        "family": "Meyerson"
      },
      {
        "given": "Rameen",
        "family": "Beroukhim"
      },
      {
        "given": "Gad",
        "family": "Getz"
      }
    ],
    "container-title": "Genome Biology",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2011,
          4
        ]
      ]
    },
    "URL": "https://doi.org/dzhjqh",
    "container-title-short": "Genome Biol",
    "PMCID": "PMC3218867",
    "PMID": "21527027",
    "id": "doi:10.1186/gb-2011-12-4-r41"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "DOI": "10.1038/ncomms3612",
    "type": "article-journal",
    "source": "Crossref",
    "title": "Inferring tumour purity and stromal and immune cell admixture from expression data",
    "volume": "4",
    "page": "2612",
    "author": [
      {
        "given": "Kosuke",
        "family": "Yoshihara"
      },
      {
        "given": "Maria",
        "family": "Shahmoradgoli"
      },
      {
        "given": "Emmanuel",
        "family": "Martínez"
      },
      {
        "given": "Rahulsimham",
        "family": "Vegesna"
      },
      {
        "given": "Hoon",
        "family": "Kim"
      },
      {
        "given": "Wandaliz",
        "family": "Torres-Garcia"
      },
      {
        "given": "Victor",
        "family": "Treviño"
      },
      {
        "given": "Hui",
        "family": "Shen"
      },
      {
        "given": "Peter W.",
        "family": "Laird"
      },
      {
        "given": "Douglas A.",
        "family": "Levine"
      },
      {
        "given": "Scott L.",
        "family": "Carter"
      },
      {
        "given": "Gad",
        "family": "Getz"
      },
      {
        "given": "Katherine",
        "family": "Stemke-Hale"
      },
      {
        "given": "Gordon B.",
        "family": "Mills"
      },
      {
        "given": "Roel G.W.",
        "family": "Verhaak"
      }
    ],
    "container-title": "Nature Communications",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2013,
          10,
          11
        ]
      ]
    },
    "URL": "https://doi.org/gbd4jn",
    "container-title-short": "Nat Commun",
    "PMCID": "PMC3826632",
    "PMID": "24113773",
    "id": "doi:10.1038/ncomms3612"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "DOI": "10.1186/s13073-019-0638-6",
    "type": "article-journal",
    "source": "Crossref",
    "title": "Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data",
    "volume": "11",
    "page": "34",
    "author": [
      {
        "given": "Francesca",
        "family": "Finotello"
      },
      {
        "given": "Clemens",
        "family": "Mayer"
      },
      {
        "given": "Christina",
        "family": "Plattner"
      },
      {
        "given": "Gerhard",
        "family": "Laschober"
      },
      {
        "given": "Dietmar",
        "family": "Rieder"
      },
      {
        "given": "Hubert",
        "family": "Hackl"
      },
      {
        "given": "Anne",
        "family": "Krogsdam"
      },
      {
        "given": "Zuzana",
        "family": "Loncova"
      },
      {
        "given": "Wilfried",
        "family": "Posch"
      },
      {
        "given": "Doris",
        "family": "Wilflingseder"
      },
      {
        "given": "Sieghart",
        "family": "Sopper"
      },
      {
        "given": "Marieke",
        "family": "Ijsselsteijn"
      },
      {
        "given": "Thomas P.",
        "family": "Brouwer"
      },
      {
        "given": "Douglas",
        "family": "Johnson"
      },
      {
        "given": "Yaomin",
        "family": "Xu"
      },
      {
        "given": "Yu",
        "family": "Wang"
      },
      {
        "given": "Melinda E.",
        "family": "Sanders"
      },
      {
        "given": "Monica V.",
        "family": "Estrada"
      },
      {
        "given": "Paula",
        "family": "Ericsson-Gonzalez"
      },
      {
        "given": "Pornpimol",
        "family": "Charoentong"
      },
      {
        "given": "Justin",
        "family": "Balko"
      },
      {
        "given": "Noel Filipe da Cunha Carvalho",
        "family": "de Miranda"
      },
      {
        "given": "Zlatko",
        "family": "Trajanoski"
      }
    ],
    "container-title": "Genome Medicine",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2019,
          5,
          24
        ]
      ]
    },
    "URL": "https://doi.org/gf5jwc",
    "container-title-short": "Genome Med",
    "PMCID": "PMC6534875",
    "PMID": "31126321",
    "id": "doi:10.1186/s13073-019-0638-6"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "abstract": "<jats:title>Abstract</jats:title>\n          <jats:sec>\n            <jats:title>Background</jats:title>\n            <jats:p>Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise and dimension reduction, as well as greater biological interpretability. As molecular profiling experiments move beyond simple case-control studies, robust and flexible GSE methodologies are needed that can model pathway activity within highly heterogeneous data sets.</jats:p>\n          </jats:sec>\n          <jats:sec>\n            <jats:title>Results</jats:title>\n            <jats:p>To address this challenge, we introduce Gene Set Variation Analysis (GSVA), a GSE method that estimates variation of pathway activity over a sample population in an unsupervised manner. We demonstrate the robustness of GSVA in a comparison with current state of the art sample-wise enrichment methods. Further, we provide examples of its utility in differential pathway activity and survival analysis. Lastly, we show how GSVA works analogously with data from both microarray and RNA-seq experiments.</jats:p>\n          </jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions</jats:title>\n            <jats:p>GSVA provides increased power to detect subtle pathway activity changes over a sample population in comparison to corresponding methods. While GSE methods are generally regarded as end points of a bioinformatic analysis, GSVA constitutes a starting point to build pathway-centric models of biology. Moreover, GSVA contributes to the current need of GSE methods for RNA-seq data. GSVA is an open source software package for R which forms part of the Bioconductor project and can be downloaded at <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"http://www.bioconductor.org\" ext-link-type=\"uri\">http://www.bioconductor.org</jats:ext-link>.</jats:p>\n          </jats:sec>",
    "DOI": "10.1186/1471-2105-14-7",
    "type": "article-journal",
    "source": "Crossref",
    "title": "GSVA: gene set variation analysis for microarray and RNA-Seq data",
    "volume": "14",
    "page": "7",
    "author": [
      {
        "given": "Sonja",
        "family": "Hänzelmann"
      },
      {
        "given": "Robert",
        "family": "Castelo"
      },
      {
        "given": "Justin",
        "family": "Guinney"
      }
    ],
    "container-title": "BMC Bioinformatics",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2013,
          1,
          16
        ]
      ]
    },
    "URL": "https://doi.org/gb8vx5",
    "container-title-short": "BMC Bioinformatics",
    "PMCID": "PMC3618321",
    "PMID": "23323831",
    "id": "doi:10.1186/1471-2105-14-7"
  },
  {
    "id": "url:https://doi.org/10.48550/arXiv.1802.03426",
    "type": "article",
    "abstract": "UMAP (Uniform Manifold Approximation and Projection) is a novel manifold learning technique for dimension reduction. UMAP is constructed from a theoretical framework based in Riemannian geometry and algebraic topology. The result is a practical scalable algorithm that applies to real world data. The UMAP algorithm is competitive with t-SNE for visualization quality, and arguably preserves more of the global structure with superior run time performance. Furthermore, UMAP has no computational restrictions on embedding dimension, making it viable as a general purpose dimension reduction technique for machine learning.",
    "DOI": "10.48550/arXiv.1802.03426",
    "publisher": "arXiv",
    "container-title": "arXiv",
    "page": "1802.03426",
    "source": "arXiv.org",
    "title": "UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction",
    "title-short": "UMAP",
    "URL": "http://arxiv.org/abs/1802.03426",
    "author": [
      {
        "family": "McInnes",
        "given": "Leland"
      },
      {
        "family": "Healy",
        "given": "John"
      },
      {
        "family": "Melville",
        "given": "James"
      }
    ],
    "accessed": {
      "date-parts": [
        [
          "2023",
          4,
          24
        ]
      ]
    },
    "issued": {
      "date-parts": [
        [
          "2020",
          9,
          17
        ]
      ]
    }
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "2",
    "DOI": "10.1007/s11910-017-0722-5",
    "type": "article-journal",
    "source": "Crossref",
    "title": "New Molecular Considerations for Glioma: IDH, ATRX, BRAF, TERT, H3 K27M",
    "volume": "17",
    "page": "19",
    "author": [
      {
        "given": "Michael",
        "family": "Karsy"
      },
      {
        "given": "Jian",
        "family": "Guan"
      },
      {
        "given": "Adam L.",
        "family": "Cohen"
      },
      {
        "given": "Randy L.",
        "family": "Jensen"
      },
      {
        "given": "Howard",
        "family": "Colman"
      }
    ],
    "container-title": "Current Neurology and Neuroscience Reports",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2017,
          2
        ]
      ]
    },
    "URL": "https://doi.org/ggdhk2",
    "container-title-short": "Curr Neurol Neurosci Rep",
    "PMID": "28271343",
    "id": "doi:10.1007/s11910-017-0722-5"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "abstract": "<jats:title>Abstract</jats:title><jats:p>During implantation, cytotrophoblasts undergo epithelial-to-mesenchymal transition (EMT) as they differentiate into invasive extravillous trophoblasts (EVTs). The primate-specific microRNA cluster on chromosome 19 (C19MC) is exclusively expressed in the placenta, embryonic stem cells and certain cancers however, its role in EMT gene regulation is unknown. <jats:italic>In situ</jats:italic> hybridization for miR-517a/c, a C19MC cistron microRNA, in first trimester human placentas displayed strong expression in villous trophoblasts and a gradual decrease from proximal to distal cell columns as cytotrophoblasts differentiate into invasive EVTs. To investigate the role of C19MC in the regulation of EMT genes, we employed the CRISPR/dCas9 Synergistic Activation Mediator (SAM) system, which induced robust transcriptional activation of the entire C19MC cistron and resulted in suppression of EMT associated genes. Exposure of human iPSCs to hypoxia or differentiation of iPSCs into either cytotrophoblast-stem-like cells or EVT-like cells under hypoxia reduced C19MC expression and increased EMT genes. Furthermore, transcriptional activation of the C19MC cistron induced the expression of OCT4 and FGF4 and accelerated cellular reprogramming. This study establishes the CRISPR/dCas9 SAM as a powerful tool that enables activation of the entire C19MC cistron and uncovers its novel role in suppressing EMT genes critical for maintaining the epithelial cytotrophoblasts stem cell phenotype.</jats:p>",
    "DOI": "10.1038/s41598-020-59812-8",
    "type": "article-journal",
    "source": "Crossref",
    "title": "Chromosome 19 microRNA cluster enhances cell reprogramming by inhibiting epithelial-to-mesenchymal transition",
    "volume": "10",
    "page": "3029",
    "author": [
      {
        "given": "Ezinne F.",
        "family": "Mong"
      },
      {
        "given": "Ying",
        "family": "Yang"
      },
      {
        "given": "Kemal M.",
        "family": "Akat"
      },
      {
        "given": "John",
        "family": "Canfield"
      },
      {
        "given": "Jeffrey",
        "family": "VanWye"
      },
      {
        "given": "John",
        "family": "Lockhart"
      },
      {
        "given": "John C. M.",
        "family": "Tsibris"
      },
      {
        "given": "Frederick",
        "family": "Schatz"
      },
      {
        "given": "Charles J.",
        "family": "Lockwood"
      },
      {
        "given": "Thomas",
        "family": "Tuschl"
      },
      {
        "given": "Umit A.",
        "family": "Kayisli"
      },
      {
        "given": "Hana",
        "family": "Totary-Jain"
      }
    ],
    "container-title": "Scientific Reports",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2020,
          2,
          20
        ]
      ]
    },
    "URL": "https://doi.org/gg329d",
    "container-title-short": "Sci Rep",
    "PMCID": "PMC7033247",
    "PMID": "32080251",
    "id": "doi:10.1038/s41598-020-59812-8"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "abstract": "<jats:title>Abstract</jats:title><jats:p>High-grade meningiomas frequently recur and are associated with high rates of morbidity and mortality. To determine the factors that promote the development and evolution of these tumors, we analyzed the genomes of 134 high-grade meningiomas and compared this information with data from 595 previously published meningiomas. High-grade meningiomas had a higher mutation burden than low-grade meningiomas but did not harbor any significantly mutated genes aside from <jats:italic>NF2</jats:italic>. High-grade meningiomas also possessed significantly elevated rates of chromosomal gains and losses, especially among tumors with monosomy 22. Meningiomas previously treated with adjuvant radiation had significantly more copy number alterations than radiation-induced or radiation-naïve meningiomas. Across serial recurrences, genomic disruption preceded the emergence of nearly all mutations, remained largely uniform across time, and when present in low-grade meningiomas correlated with subsequent progression to a higher grade. In contrast to the largely stable copy number alterations, mutations were strikingly heterogeneous across tumor recurrences, likely due to extensive geographic heterogeneity in the primary tumor. While high-grade meningiomas harbored significantly fewer overtly targetable alterations than low-grade meningiomas, they contained numerous mutations that are predicted to be neoantigens, suggesting that immunologic targeting may be of therapeutic value.</jats:p>",
    "DOI": "10.1038/s41525-017-0014-7",
    "type": "article-journal",
    "source": "Crossref",
    "title": "Genomic landscape of high-grade meningiomas",
    "volume": "2",
    "page": "15",
    "author": [
      {
        "given": "Wenya Linda",
        "family": "Bi"
      },
      {
        "given": "Noah F.",
        "family": "Greenwald"
      },
      {
        "given": "Malak",
        "family": "Abedalthagafi"
      },
      {
        "given": "Jeremiah",
        "family": "Wala"
      },
      {
        "given": "Will J.",
        "family": "Gibson"
      },
      {
        "given": "Pankaj K.",
        "family": "Agarwalla"
      },
      {
        "given": "Peleg",
        "family": "Horowitz"
      },
      {
        "given": "Steven E.",
        "family": "Schumacher"
      },
      {
        "given": "Ekaterina",
        "family": "Esaulova"
      },
      {
        "given": "Yu",
        "family": "Mei"
      },
      {
        "given": "Aaron",
        "family": "Chevalier"
      },
      {
        "given": "Matthew",
        "family": "A. Ducar"
      },
      {
        "given": "Aaron R.",
        "family": "Thorner"
      },
      {
        "given": "Paul",
        "family": "van Hummelen"
      },
      {
        "given": "Anat",
        "family": "O. Stemmer-Rachamimov"
      },
      {
        "given": "Maksym",
        "family": "Artyomov"
      },
      {
        "given": "Ossama",
        "family": "Al-Mefty"
      },
      {
        "given": "Gavin P.",
        "family": "Dunn"
      },
      {
        "given": "Sandro",
        "family": "Santagata"
      },
      {
        "given": "Ian F.",
        "family": "Dunn"
      },
      {
        "given": "Rameen",
        "family": "Beroukhim"
      }
    ],
    "container-title": "npj Genomic Medicine",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2017,
          4,
          26
        ]
      ]
    },
    "URL": "https://doi.org/gbnhbw",
    "container-title-short": "npj Genomic Med",
    "PMCID": "PMC5506858",
    "PMID": "28713588",
    "id": "doi:10.1038/s41525-017-0014-7"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "DOI": "10.1186/s40478-020-01056-8",
    "type": "article-journal",
    "source": "Crossref",
    "title": "EZHIP is a specific diagnostic biomarker for posterior fossa ependymomas, group PFA and diffuse midline gliomas H3-WT with EZHIP overexpression",
    "volume": "8",
    "page": "183",
    "author": [
      {
        "given": "C.",
        "family": "Antin"
      },
      {
        "given": "A.",
        "family": "Tauziède-Espariat"
      },
      {
        "given": "M.-A.",
        "family": "Debily"
      },
      {
        "given": "D.",
        "family": "Castel"
      },
      {
        "given": "J.",
        "family": "Grill"
      },
      {
        "given": "M.",
        "family": "Pagès"
      },
      {
        "given": "O.",
        "family": "Ayrault"
      },
      {
        "given": "F.",
        "family": "Chrétien"
      },
      {
        "given": "A.",
        "family": "Gareton"
      },
      {
        "given": "F.",
        "family": "Andreiuolo"
      },
      {
        "given": "E.",
        "family": "Lechapt"
      },
      {
        "given": "P.",
        "family": "Varlet"
      }
    ],
    "container-title": "Acta Neuropathologica Communications",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2020,
          11,
          5
        ]
      ]
    },
    "URL": "https://doi.org/gm3q3q",
    "container-title-short": "acta neuropathol commun",
    "PMCID": "PMC7643397",
    "PMID": "33153494",
    "id": "doi:10.1186/s40478-020-01056-8"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "DOI": "10.1186/s13059-016-0893-4",
    "type": "article-journal",
    "source": "Crossref",
    "title": "deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution",
    "volume": "17",
    "page": "31",
    "author": [
      {
        "given": "Rachel",
        "family": "Rosenthal"
      },
      {
        "given": "Nicholas",
        "family": "McGranahan"
      },
      {
        "given": "Javier",
        "family": "Herrero"
      },
      {
        "given": "Barry S.",
        "family": "Taylor"
      },
      {
        "given": "Charles",
        "family": "Swanton"
      }
    ],
    "container-title": "Genome Biology",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2016,
          2,
          22
        ]
      ]
    },
    "URL": "https://doi.org/f8bdsq",
    "container-title-short": "Genome Biol",
    "PMCID": "PMC4762164",
    "PMID": "26899170",
    "id": "doi:10.1186/s13059-016-0893-4"
  },
  {
    "title": "Embryonal Tumors of the Central Nervous System in Children: The Era of Targeted Therapeutics.",
    "volume": "5",
    "issue": "4",
    "page": "78",
    "container-title": "Bioengineering (Basel, Switzerland)",
    "container-title-short": "Bioengineering (Basel)",
    "ISSN": "2306-5354",
    "issued": {
      "date-parts": [
        [
          2018,
          9,
          23
        ]
      ]
    },
    "author": [
      {
        "given": "David E",
        "family": "Kram"
      },
      {
        "given": "Jacob J",
        "family": "Henderson"
      },
      {
        "given": "Muhammad",
        "family": "Baig"
      },
      {
        "given": "Diya",
        "family": "Chakraborty"
      },
      {
        "given": "Morgan A",
        "family": "Gardner"
      },
      {
        "given": "Subhasree",
        "family": "Biswas"
      },
      {
        "given": "Soumen",
        "family": "Khatua"
      }
    ],
    "PMID": "30249036",
    "PMCID": "PMC6315657",
    "DOI": "10.3390/bioengineering5040078",
    "abstract": "Embryonal tumors (ET) of the central nervous system (CNS) in children encompass a wide clinical spectrum of aggressive malignancies. Until recently, the overlapping morphological features of these lesions posed a diagnostic challenge and undermined discovery of optimal treatment strategies. However, with the advances in genomic technology and the outpouring of biological data over the last decade, clear insights into the molecular heterogeneity of these tumors are now well delineated. The major subtypes of ETs of the CNS in children include medulloblastoma, atypical teratoid rhabdoid tumor (ATRT), and embryonal tumors with multilayered rosettes (ETMR), which are now biologically and clinically characterized as different entities. These important developments have paved the way for treatments guided by risk stratification as well as novel targeted therapies in efforts to improve survival and reduce treatment burden.",
    "URL": "https://www.ncbi.nlm.nih.gov/pubmed/30249036",
    "type": "article-journal",
    "id": "pubmed:30249036"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "DOI": "10.1186/s12859-016-1031-8",
    "type": "article-journal",
    "source": "Crossref",
    "title": "ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data",
    "volume": "17",
    "page": "188",
    "author": [
      {
        "given": "Navin",
        "family": "Rustagi"
      },
      {
        "given": "Oliver A",
        "family": "Hampton"
      },
      {
        "given": "Jie",
        "family": "Li"
      },
      {
        "given": "Liu",
        "family": "Xi"
      },
      {
        "given": "Richard A.",
        "family": "Gibbs"
      },
      {
        "given": "Sharon E.",
        "family": "Plon"
      },
      {
        "given": "Marek",
        "family": "Kimmel"
      },
      {
        "given": "David A.",
        "family": "Wheeler"
      }
    ],
    "container-title": "BMC Bioinformatics",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2016,
          4,
          27
        ]
      ]
    },
    "URL": "https://doi.org/gmndpj",
    "container-title-short": "BMC Bioinformatics",
    "PMCID": "PMC4847212",
    "PMID": "27121965",
    "id": "doi:10.1186/s12859-016-1031-8"
  },
  {
    "publisher": "Springer Science and Business Media LLC",
    "issue": "1",
    "abstract": "<jats:title>Abstract</jats:title><jats:sec>\n                <jats:title>Background</jats:title>\n                <jats:p>RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms of the same gene. A second significant issue is the design of RNA-Seq experiments, in terms of the number of reads, read length, and whether reads come from one or both ends of cDNA fragments.</jats:p>\n              </jats:sec><jats:sec>\n                <jats:title>Results</jats:title>\n                <jats:p>We present RSEM, an user-friendly software package for quantifying gene and isoform abundances from single-end or paired-end RNA-Seq data. RSEM outputs abundance estimates, 95% credibility intervals, and visualization files and can also simulate RNA-Seq data. In contrast to other existing tools, the software does not require a reference genome. Thus, in combination with a de novo transcriptome assembler, RSEM enables accurate transcript quantification for species without sequenced genomes. On simulated and real data sets, RSEM has superior or comparable performance to quantification methods that rely on a reference genome. Taking advantage of RSEM's ability to effectively use ambiguously-mapping reads, we show that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads. On the other hand, estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired-end reads, depending on the number of possible splice forms for each gene.</jats:p>\n              </jats:sec><jats:sec>\n                <jats:title>Conclusions</jats:title>\n                <jats:p>RSEM is an accurate and user-friendly software tool for quantifying transcript abundances from RNA-Seq data. As it does not rely on the existence of a reference genome, it is particularly useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable guidance for cost-efficient design of quantification experiments with RNA-Seq, which is currently relatively expensive.</jats:p>\n              </jats:sec>",
    "DOI": "10.1186/1471-2105-12-323",
    "type": "article-journal",
    "source": "Crossref",
    "title": "RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome",
    "volume": "12",
    "page": "323",
    "author": [
      {
        "given": "Bo",
        "family": "Li"
      },
      {
        "given": "Colin N",
        "family": "Dewey"
      }
    ],
    "container-title": "BMC Bioinformatics",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2011,
          8,
          4
        ]
      ]
    },
    "URL": "https://doi.org/cwg8n5",
    "container-title-short": "BMC Bioinformatics",
    "PMCID": "PMC3163565",
    "PMID": "21816040",
    "id": "doi:10.1186/1471-2105-12-323"
  },
  {
    "publisher": "American Association for Cancer Research (AACR)",
    "issue": "18",
    "abstract": "<jats:title>Abstract</jats:title>\n               <jats:sec>\n                  <jats:title>Purpose:</jats:title>\n                  <jats:p>PNOC003 is a multicenter precision medicine trial for children and young adults with newly diagnosed diffuse intrinsic pontine glioma (DIPG).</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Patients and Methods:</jats:title>\n                  <jats:p>Patients (3–25 years) were enrolled on the basis of imaging consistent with DIPG. Biopsy tissue was collected for whole-exome and mRNA sequencing. After radiotherapy (RT), patients were assigned up to four FDA-approved drugs based on molecular tumor board recommendations. H3K27M-mutant circulating tumor DNA (ctDNA) was longitudinally measured. Tumor tissue and matched primary cell lines were characterized using whole-genome sequencing and DNA methylation profiling. When applicable, results were verified in an independent cohort from the Children's Brain Tumor Network (CBTN).</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Results:</jats:title>\n                  <jats:p>Of 38 patients enrolled, 28 patients (median 6 years, 10 females) were reviewed by the molecular tumor board. Of those, 19 followed treatment recommendations. Median overall survival (OS) was 13.1 months [95% confidence interval (CI), 11.2–18.4] with no difference between patients who followed recommendations and those who did not. H3K27M-mutant ctDNA was detected at baseline in 60% of cases tested and associated with response to RT and survival. Eleven cell lines were established, showing 100% fidelity of key somatic driver gene alterations in the primary tumor. In H3K27-altered DIPGs, TP53 mutations were associated with worse OS (TP53mut 11.1 mo; 95% CI, 8.7–14; TP53wt 13.3 mo; 95% CI, 11.8–NA; P = 3.4e−2), genome instability (P = 3.1e−3), and RT resistance (P = 6.4e−4). The CBTN cohort confirmed an association between TP53 mutation status, genome instability, and clinical outcome.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions:</jats:title>\n                  <jats:p>Upfront treatment-naïve biopsy provides insight into clinically relevant molecular alterations and prognostic biomarkers for H3K27-altered DIPGs.</jats:p>\n               </jats:sec>",
    "DOI": "10.1158/1078-0432.ccr-22-0803",
    "type": "article-journal",
    "page": "3965-3978",
    "source": "Crossref",
    "title": "Upfront Biology-Guided Therapy in Diffuse Intrinsic Pontine Glioma: Therapeutic, Molecular, and Biomarker Outcomes from PNOC003",
    "volume": "28",
    "author": [
      {
        "given": "Cassie",
        "family": "Kline"
      },
      {
        "given": "Payal",
        "family": "Jain"
      },
      {
        "given": "Lindsay",
        "family": "Kilburn"
      },
      {
        "given": "Erin R.",
        "family": "Bonner"
      },
      {
        "given": "Nalin",
        "family": "Gupta"
      },
      {
        "given": "John R.",
        "family": "Crawford"
      },
      {
        "given": "Anu",
        "family": "Banerjee"
      },
      {
        "given": "Roger J.",
        "family": "Packer"
      },
      {
        "given": "Javier",
        "family": "Villanueva-Meyer"
      },
      {
        "given": "Tracy",
        "family": "Luks"
      },
      {
        "given": "Yalan",
        "family": "Zhang"
      },
      {
        "given": "Madhuri",
        "family": "Kambhampati"
      },
      {
        "given": "Jie",
        "family": "Zhang"
      },
      {
        "given": "Sridevi",
        "family": "Yadavilli"
      },
      {
        "given": "Bo",
        "family": "Zhang"
      },
      {
        "given": "Krutika S.",
        "family": "Gaonkar"
      },
      {
        "given": "Jo Lynne",
        "family": "Rokita"
      },
      {
        "given": "Adam",
        "family": "Kraya"
      },
      {
        "given": "John",
        "family": "Kuhn"
      },
      {
        "given": "Winnie",
        "family": "Liang"
      },
      {
        "given": "Sara",
        "family": "Byron"
      },
      {
        "given": "Michael",
        "family": "Berens"
      },
      {
        "given": "Annette",
        "family": "Molinaro"
      },
      {
        "given": "Michael",
        "family": "Prados"
      },
      {
        "given": "Adam",
        "family": "Resnick"
      },
      {
        "given": "Sebastian M.",
        "family": "Waszak"
      },
      {
        "given": "Javad",
        "family": "Nazarian"
      },
      {
        "given": "Sabine",
        "family": "Mueller"
      }
    ],
    "container-title": "Clinical Cancer Research",
    "container-title-short": "Clin Cancer Res",
    "language": "en",
    "issued": {
      "date-parts": [
        [
          2022,
          7,
          19
        ]
      ]
    },
    "URL": "https://doi.org/gqh9gb",
    "PMCID": "PMC9475246",
    "PMID": "35852795",
    "id": "doi:10.1158/1078-0432.ccr-22-0803"
  },
  {
    "title": "Telomerase activity in human development is regulated by human telomerase reverse transcriptase (hTERT) transcription and by alternate splicing of hTERT transcripts.",
    "volume": "58",
    "issue": "18",
    "page": "4168-4172",
    "container-title": "Cancer research",
    "container-title-short": "Cancer Res",
    "ISSN": "0008-5472",
    "issued": {
      "date-parts": [
        [
          1998,
          9,
          15
        ]
      ]
    },
    "author": [
      {
        "given": "Gary A.",
        "family": "Ulaner"
      },
      {
        "given": "Ji-Fan",
        "family": "Hu"
      },
      {
        "given": "Tanh H.",
        "family": "Vu"
      },
      {
        "given": "Linda C.",
        "family": "Giudice"
      },
      {
        "given": "Andrew R.",
        "family": "Hoffman"
      }
    ],
    "PMID": "9751630",
    "abstract": "The correlation between telomerase activity, telomere lengths, and cellular replicative capacity has led to the theory that maintenance of telomere lengths by telomerase acts as a molecular clock to control replicative capacity and senescence. Regulation of this molecular clock may have applications in the treatment of cell aging and tumorigenesis, although little is presently known about the regulation of telomerase activity. To investigate possible mechanisms of regulation, we examined telomerase activity and the expression of the human telomerase RNA subunit and the human telomerase reverse transcriptase protein (hTERT) during human fetal heart, liver, and kidney development. The human telomerase RNA subunit is expressed in all three tissues at all gestational ages examined. hTERT expression correlates with telomerase activity in the liver, where both are expressed at all ages surveyed, and in the heart, where both are present until the 11th gestational week but not thereafter. However, although telomerase activity in the kidney is suppressed after the 15th gestational week, the hTERT transcript can be detected until at least the 21st week. Reverse transcription-PCR using primers within the reverse transcriptase domain of hTERT show the presence of multiple alternately spliced transcripts in these tissues, corresponding to full-length message as well as spliced messages with critical reverse transcriptase motifs deleted. Of note, telomerase activity in the kidney is only present at those gestational ages when full-length hTERT message is expressed (until approximately week 15), with spliced transcripts continuing to be expressed at later stages of development. The tissue-specific and gestational-age dependent expression of hTERT mRNA seen in human development suggests the presence of at least two regulatory mechanisms controlling the activity of telomerase: transcriptional control of the hTERT gene and alternate splicing of hTERT transcripts.",
    "URL": "https://www.ncbi.nlm.nih.gov/pubmed/9751630",
    "type": "article-journal",
    "id": "pubmed:9751630"
  },
  {
    "title": "The WHO classification of tumors of the nervous system.",
    "volume": "61",
    "issue": "3",
    "page": "215-25; discussion 226-9",
    "container-title": "Journal of neuropathology and experimental neurology",
    "container-title-short": "J Neuropathol Exp Neurol",
    "ISSN": "0022-3069",
    "issued": {
      "date-parts": [
        [
          2002,
          3
        ]
      ]
    },
    "author": [
      {
        "given": "Paul",
        "family": "Kleihues"
      },
      {
        "given": "David N",
        "family": "Louis"
      },
      {
        "given": "Bernd W",
        "family": "Scheithauer"
      },
      {
        "given": "Lucy B",
        "family": "Rorke"
      },
      {
        "given": "Guido",
        "family": "Reifenberger"
      },
      {
        "given": "Peter C",
        "family": "Burger"
      },
      {
        "given": "Webster K",
        "family": "Cavenee"
      }
    ],
    "PMID": "11895036",
    "DOI": "10.1093/jnen/61.3.215",
    "abstract": "The new World Health Organization (WHO) classification of nervous system tumors, published in 2000, emerged from a 1999 international consensus conference of neuropathologists. New entities include chordoid glioma of the third ventricle, cerebellar liponeurocytoma, atypical teratoid/rhabdoid tumor, and perineurioma. Several histological variants were added, including tanycytic ependymoma, large cell medulloblastoma, and rhabdoid meningioma. The WHO grading scheme was updated and, for meningiomas, extensively revised. In recognition of the emerging role of molecular diagnostic approaches to tumor classification, genetic profiles have been emphasized, as in the distinct subtypes of glioblastoma and the already clinically useful 1p and 19q markers for oligodendroglioma and 22q/INI1 for atypical teratoid/rhabdoid tumors. In accord with the new WHO Blue Book series, the actual classification is accompanied by extensive descriptions and illustrations of clinicopathological characteristics of each tumor type, including molecular genetic features, predictive factors, and separate chapters on inherited tumor syndromes. The 2000 WHO classification of nervous system tumors aims at being used and implemented by the neuro-oncology and biomedical research communities worldwide.",
    "URL": "https://www.ncbi.nlm.nih.gov/pubmed/11895036",
    "type": "article-journal",
    "id": "pubmed:11895036"
  },
  {
    "title": "Myc requires distinct E2F activities to induce S phase and apoptosis.",
    "volume": "8",
    "issue": "1",
    "page": "105-13",
    "container-title": "Molecular cell",
    "container-title-short": "Mol Cell",
    "ISSN": "1097-2765",
    "issued": {
      "date-parts": [
        [
          2001,
          7
        ]
      ]
    },
    "author": [
      {
        "given": "G",
        "family": "Leone"
      },
      {
        "given": "R",
        "family": "Sears"
      },
      {
        "given": "E",
        "family": "Huang"
      },
      {
        "given": "R",
        "family": "Rempel"
      },
      {
        "given": "F",
        "family": "Nuckolls"
      },
      {
        "given": "C H",
        "family": "Park"
      },
      {
        "given": "P",
        "family": "Giangrande"
      },
      {
        "given": "L",
        "family": "Wu"
      },
      {
        "given": "H I",
        "family": "Saavedra"
      },
      {
        "given": "S J",
        "family": "Field"
      },
      {
        "given": "M A",
        "family": "Thompson"
      },
      {
        "given": "H",
        "family": "Yang"
      },
      {
        "given": "Y",
        "family": "Fujiwara"
      },
      {
        "given": "M E",
        "family": "Greenberg"
      },
      {
        "given": "S",
        "family": "Orkin"
      },
      {
        "given": "C",
        "family": "Smith"
      },
      {
        "given": "J R",
        "family": "Nevins"
      }
    ],
    "PMID": "11511364",
    "DOI": "10.1016/s1097-2765(01)00275-1",
    "abstract": "Previous work has shown that the Myc transcription factor induces transcription of the E2F1, E2F2, and E2F3 genes. Using primary mouse embryo fibroblasts deleted for individual E2F genes, we now show that Myc-induced S phase and apoptosis requires distinct E2F activities. The ability of Myc to induce S phase is impaired in the absence of either E2F2 or E2F3 but not E2F1 or E2F4. In contrast, the ability of Myc to induce apoptosis is markedly reduced in cells deleted for E2F1 but not E2F2 or E2F3. From this data, we propose that the induction of specific E2F activities is an essential component in the Myc pathways that control cell proliferation and cell fate decisions.",
    "URL": "https://www.ncbi.nlm.nih.gov/pubmed/11511364",
    "type": "article-journal",
    "id": "pubmed:11511364"
  },
  {
    "title": "A Novel Immune Classification for Predicting Immunotherapy Responsiveness in Patients With Adamantinomatous Craniopharyngioma.",
    "volume": "12",
    "page": "704130",
    "container-title": "Frontiers in neurology",
    "container-title-short": "Front Neurol",
    "ISSN": "1664-2295",
    "issued": {
      "date-parts": [
        [
          2021,
          12,
          13
        ]
      ]
    },
    "author": [
      {
        "given": "Feng",
        "family": "Yuan"
      },
      {
        "given": "Xiangming",
        "family": "Cai"
      },
      {
        "given": "Junhao",
        "family": "Zhu"
      },
      {
        "given": "Lei",
        "family": "Yuan"
      },
      {
        "given": "Yingshuai",
        "family": "Wang"
      },
      {
        "given": "Chao",
        "family": "Tang"
      },
      {
        "given": "Zixiang",
        "family": "Cong"
      },
      {
        "given": "Chiyuan",
        "family": "Ma"
      }
    ],
    "PMID": "34966342",
    "PMCID": "PMC8710480",
    "DOI": "10.3389/fneur.2021.704130",
    "abstract": "Adamantinomatous craniopharyngioma (ACP) is the most common tumor of the sellar region in children. The aggressive behavior of ACP challenges the treatment for it. However, immunotherapy is rarely studied in ACP. In this research, we performed unsupervised cluster analysis on the 725 immune-related genes and arrays of 39 patients with ACP patients in GSE60815 and GSE94349 databases. Two novel immune subtypes were identified, namely immune resistance (IR) subtype and immunogenic (IG) subtype. Interestingly, we found that the ACPs with IG subtype (34.78%, 8/23) were more likely to respond to immunotherapy than the ACPs with IR subtype (6.25%, 1/16) ",
    "URL": "https://www.ncbi.nlm.nih.gov/pubmed/34966342",
    "type": "article-journal",
    "id": "pubmed:34966342"
  },
  {
    "title": "Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology.",
    "volume": "35",
    "issue": "14",
    "page": "i436-i445",
    "container-title": "Bioinformatics (Oxford, England)",
    "container-title-short": "Bioinformatics",
    "ISSN": "1367-4811",
    "issued": {
      "date-parts": [
        [
          2019,
          7,
          15
        ]
      ]
    },
    "author": [
      {
        "given": "Gregor",
        "family": "Sturm"
      },
      {
        "given": "Francesca",
        "family": "Finotello"
      },
      {
        "given": "Florent",
        "family": "Petitprez"
      },
      {
        "given": "Jitao David",
        "family": "Zhang"
      },
      {
        "given": "Jan",
        "family": "Baumbach"
      },
      {
        "given": "Wolf H",
        "family": "Fridman"
      },
      {
        "given": "Markus",
        "family": "List"
      },
      {
        "given": "Tatsiana",
        "family": "Aneichyk"
      }
    ],
    "PMID": "31510660",
    "PMCID": "PMC6612828",
    "DOI": "10.1093/bioinformatics/btz363",
    "abstract": "The composition and density of immune cells in the tumor microenvironment (TME) profoundly influence tumor progression and success of anti-cancer therapies. Flow cytometry, immunohistochemistry staining or single-cell sequencing are often unavailable such that we rely on computational methods to estimate the immune-cell composition from bulk RNA-sequencing (RNA-seq) data. Various methods have been proposed recently, yet their capabilities and limitations have not been evaluated systematically. A general guideline leading the research community through cell type deconvolution is missing.",
    "URL": "https://www.ncbi.nlm.nih.gov/pubmed/31510660",
    "type": "article-journal",
    "id": "pubmed:31510660"
  },
  {
    "title": "H3 K27M mutations are extremely rare in posterior fossa group A ependymoma.",
    "volume": "33",
    "issue": "7",
    "page": "1047-1051",
    "container-title": "Child's nervous system : ChNS : official journal of the International Society for Pediatric Neurosurgery",
    "container-title-short": "Childs Nerv Syst",
    "ISSN": "1433-0350",
    "issued": {
      "date-parts": [
        [
          2017,
          6,
          16
        ]
      ]
    },
    "author": [
      {
        "given": "Scott",
        "family": "Ryall"
      },
      {
        "given": "Miguel",
        "family": "Guzman"
      },
      {
        "given": "Samer K",
        "family": "Elbabaa"
      },
      {
        "given": "Betty",
        "family": "Luu"
      },
      {
        "given": "Stephen C",
        "family": "Mack"
      },
      {
        "given": "Michal",
        "family": "Zapotocky"
      },
      {
        "given": "Michael D",
        "family": "Taylor"
      },
      {
        "given": "Cynthia",
        "family": "Hawkins"
      },
      {
        "given": "Vijay",
        "family": "Ramaswamy"
      }
    ],
    "PMID": "28623522",
    "DOI": "10.1007/s00381-017-3481-3",
    "abstract": "Mutations in the tail of histone H3 (K27M) are frequently found in pediatric midline high-grade glioma's but have rarely been reported in other malignancies. Recently, recurrent somatic nucleotide variants in histone H3 (H3 K27M) have been reported in group A posterior fossa ependymoma (EPN_PFA), an entity previously described to have no recurrent mutations. However, the true incidence of H3 K27M mutations in EPN_PFA is unknown.",
    "URL": "https://www.ncbi.nlm.nih.gov/pubmed/28623522",
    "type": "article-journal",
    "id": "pubmed:28623522"
  },
  {
    "title": "Craniopharyngiomas of adamantinomatous type harbor beta-catenin gene mutations.",
    "volume": "161",
    "issue": "6",
    "page": "1997-2001",
    "container-title": "The American journal of pathology",
    "container-title-short": "Am J Pathol",
    "ISSN": "0002-9440",
    "issued": {
      "date-parts": [
        [
          2002,
          12
        ]
      ]
    },
    "author": [
      {
        "given": "Shigeki",
        "family": "Sekine"
      },
      {
        "given": "Tatsuhiro",
        "family": "Shibata"
      },
      {
        "given": "Akiko",
        "family": "Kokubu"
      },
      {
        "given": "Yukio",
        "family": "Morishita"
      },
      {
        "given": "Masayuki",
        "family": "Noguchi"
      },
      {
        "given": "Yukihiro",
        "family": "Nakanishi"
      },
      {
        "given": "Michiie",
        "family": "Sakamoto"
      },
      {
        "given": "Setsuo",
        "family": "Hirohashi"
      }
    ],
    "PMID": "12466115",
    "PMCID": "PMC1850925",
    "DOI": "10.1016/s0002-9440(10)64477-x",
    "abstract": "Craniopharyngioma is a rare tumor occurring in the sellar region comprising 3% of all intracranial tumors. To elucidate the contribution of beta-catenin gene mutation to tumorigenesis, we examined genetic alterations and expression of beta-catenin in 10 cases of adamantinomatous and 6 cases of papillary craniopharyngiomas. Beta-catenin gene mutations were found in all of the adamantinomatous and none of the papillary craniopharyngiomas. Immunohistochemically, all cases of adamantinomatous craniopharyngioma showed cytoplasmic and nuclear expression of beta-catenin. In contrast, papillary craniopharyngiomas showed exclusively membranous expression. The results suggest that adamantinomatous- and papillary-type craniopharyngiomas are not only clinicopathologically, but also genetically, distinctive variants. Mutation of the beta-catenin gene therefore seems to play an important role in the tumorigenesis of adamantinomatous craniopharyngioma. Among the adamantinomatous-type tumors, beta-catenin-positive mesenchymal cells were observed in two cases. Microdissection-based mutational analysis revealed that these mesenchymal cells also harbor the same beta-catenin gene mutations as those of epithelial cells, suggesting their tumorous nature. Thus, at least a subset of adamantinomatous craniopharyngioma is considered to be biphasic.",
    "URL": "https://www.ncbi.nlm.nih.gov/pubmed/12466115",
    "type": "article-journal",
    "id": "pubmed:12466115"
  },
  {
    "title": "The Sequence Alignment/Map format and SAMtools.",
    "volume": "25",
    "issue": "16",
    "page": "2078-9",
    "container-title": "Bioinformatics (Oxford, England)",
    "container-title-short": "Bioinformatics",
    "ISSN": "1367-4811",
    "issued": {
      "date-parts": [
        [
          2009,
          6,
          8
        ]
      ]
    },
    "author": [
      {
        "given": "Heng",
        "family": "Li"
      },
      {
        "given": "Bob",
        "family": "Handsaker"
      },
      {
        "given": "Alec",
        "family": "Wysoker"
      },
      {
        "given": "Tim",
        "family": "Fennell"
      },
      {
        "given": "Jue",
        "family": "Ruan"
      },
      {
        "given": "Nils",
        "family": "Homer"
      },
      {
        "given": "Gabor",
        "family": "Marth"
      },
      {
        "given": "Goncalo",
        "family": "Abecasis"
      },
      {
        "given": "Richard",
        "family": "Durbin"
      },
      {}
    ],
    "PMID": "19505943",
    "PMCID": "PMC2723002",
    "DOI": "10.1093/bioinformatics/btp352",
    "abstract": "The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.",
    "URL": "https://www.ncbi.nlm.nih.gov/pubmed/19505943",
    "type": "article-journal",
    "id": "pubmed:19505943"
  },
  {
    "title": "Evaluation of survival data and two new rank order statistics arising in its consideration.",
    "volume": "50",
    "issue": "3",
    "page": "163-70",
    "container-title": "Cancer chemotherapy reports",
    "container-title-short": "Cancer Chemother Rep",
    "ISSN": "0069-0112",
    "issued": {
      "date-parts": [
        [
          1966,
          3
        ]
      ]
    },
    "author": [
      {
        "given": "N",
        "family": "Mantel"
      }
    ],
    "PMID": "5910392",
    "URL": "https://www.ncbi.nlm.nih.gov/pubmed/5910392",
    "type": "article-journal",
    "id": "pubmed:5910392"
  }
]