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• DAC for study CMMRD–associated high-grade glioma

  This Data Access Committee (DAC) is responsible for de-identified, summarized somatic variant call data derived from paired tumor–blood Whole-exome sequencing of human samples in a glioma research study. Access requests are approved without additional restrictions and are granted solely for health-related research purposes.

  Dac EGAC50000000855

• ICGC PCAWG Dataset: MALY-DE_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: MALY-DE.

  Dataset EGAD00001002123

• ICGC PCAWG Dataset: MALY-DE_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: MALY-DE.

  Dataset EGAD00001003560

• ICGC PCAWG Dataset: MALY-DE_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: MALY-DE.

  Dataset EGAD00001003561

• PacBio HiFi sequencing of telobait-captured DNA from 48 patients

  PacBio HiFi sequencing was performed on 48 barcoded patients' genomic DNA after a telobait-capture protocol to enrich for telomeric regions. The sequencing reads of each patient were de-multiplexed and presented as patient-specific PacBio CCS BAM files.

  Dataset EGAD00001008626

• ICGC PCAWG Dataset: PBCA-DE_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PBCA-DE.

  Dataset EGAD00001002127

• ICGC PCAWG Dataset: EOPC-DE_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: EOPC-DE.

  Dataset EGAD00001002124

• Single cell RNA sequencing data of advanced melanoma patients treated with checkpoint inhibitor immunotherapy

  Single cell RNA libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 3’ v2 reagents. The samples were barcoded and each library were pooled with two samples at equimolar concentrations. The pooled libraries (n=4) were sequenced on the NextSeq 500 machine (Illumina) with paired-end sequencing and dual indexing as recommended in the manufacturer’s protocol; 26 and 98 cycles for the respective Read 1 and 2, and 8 cycles for i7 index.

  Dataset EGAD50000000493

• HERBY trial WES

  Whole exome sequencing of non-brainstem paediatric high grade glioma from the HERBY phase II randomised trial. DNA from 86 cases was subjected to Illumina paired end whole exome sequencing using a customised SureSelect Human All Exon V6 capture set. Germline DNA from whole blood was sequenced for 83 cases. 26 cases were sequenced from both fresh frozen tissue and FFPE material, 10 were sequenced from only fresh frozen material and 50 from only FFPE. Data is provided as bwa aligned BAM files

  Dataset EGAD00001004036

• CTSP: Clinical Trial Sequencing Project

  For the Clinical Trials Sequencing Project (CTSP), National Cancer Institute (NCI) will utilize whole genome sequencing and/or whole exome sequencing in conjunction with transcriptome sequencing to try to identify recurrent genetic alterations (mutations, deletions, amplifications, rearrangements) and/or gene expression signatures that would be important to the hypothesis(es) submitted by the investigators. The samples will be processed and submitted for genomic characterization using pipelines and procedures established within The Cancer Genome Analysis (TCGA) project. Data analysis will be performed as a collaboration between the National Clinical Trials Network (NCTN) Group and its investigators submitting the proposal. The investigators at the NCI-sponsored Genomic Data Analysis Center (GDAC) will characterize the samples. The NCTN Group will be responsible for providing the clinical data needed for the proposal to the open clinical system maintained by NCI CCG's Biospecimen Core Resource (BCR) at Nationwide Children's Hospital in Columbus, Ohio. The project team (Network Group/investigators and GDAC) will analyze the data together. Additionally, clinical and genomic data related to the analyses will also need to be registered by NCI and will be made available to qualified researchers via a controlled-access database (e.g., dbGaP) upon publication of the primary analysis described in the study proposal. A substudy description and its molecular data information are provided under its own page: phs001184 CTSP Diffuse Large B-Cell Lymphoma (DLBCL) CALGB 50303

  Study phs001175