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• National Cancer Institute (NCI) Study of Lung Cancer and Smoking Phenotypes in African-American Cases and Controls

  This is a two-stage case-control study designed to evaluate the association between common genetic variants and the risk of lung cancer. The stage 1 studies included 1737 cases and 3602 controls from the following studies: MD Anderson Lung Cancer Epidemiology Study, The Multiethnic Cohort Study (MEC), NCI-MD Lung Cancer-Case Control Study, Northern California Lung Cancer Study, Project CHURCH (Creating a Higher Understanding of Cancer Research δ Community Health), Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO), Southern Community Cohort Study (SCCS), and the Karmanos Cancer Institute at Wayne State University (KCI/WSU). The stage 2 studies included an independent set of 866 cases and 796 controls from the following studies: The Black Women's Health Study (BWHS), The Harvard-MGH Lung Cancer Susceptibility Study (HLCS), MD Anderson Lung Cancer Epidemiology Study, MD Anderson/LBJ Hospital Biorepository, NCI-MD Lung Cancer Case-Control Study, Northern California Lung Cancer Study, Philadelphia Lung Cancer Study on Gene Environment Interactions (Plus-Gene), Southern Community Cohort Study (SCCS), and KCI/WSU.

  Study phs001210

• Integrated genomic analysis identifies driver genes and cisplatin-resistant progenitor phenotype in pediatric liver cancer

  Dataset EGAD00001007858

• Dual targeting of polyamine synthesis and uptake in diffuse intrinsic pontine gliomas

  Bulk RNA-seq data of tumour data.

  Dataset EGAD00001006794

• Whole-genome sequencing of gastric cancer 81 samples in the Japanese population.

  Genomic DNA of 81 cases from Japanese gastric cancer was extracted from tumor and matched normal tissues, and libraries with an insert size of 350–550 bp were prepared. The libraries were sequenced on a HiSeq 2500 instrument (Illumina) with paired-end reads of 101 bp. The read data are stored as FASTQ formatted files.

  Dataset EGAD00001008610

• MGHBoston_Molpheno_Closed

  This dataset contains Whole Genome Sequencing and, if available, RNA-sequencing and/or ATAC-sequencing data of 17 lymphoblastoid cell lines derived from patients with complex genomic rearrangements. Patients have phenotypes in category of intellectual disability and/or multiple congenital anomalies. Data access is closed.

  Dataset EGAD00001004866

• Covid19 WGS variants analysis

  483 samples were collected for WGS and aligned with GRCh38 human genome. The variants were called using GATK (Sentieon v. 201808.03) in GVCF and VCF format.

  Dataset EGAD00001010138

• UK10K_COHORT_ALSPAC REL-2011-12-01

  For information about this sample set, please contact the sample custodian Nic Timpson: N.J.Timpson@bristol.ac.uk

  Dataset EGAD00001000195

• Targeted and Whole Exome Sequencing for Validation of PGDx elio tissue complete

  This dataset consists of 116 tumor and normal samples analyzed with whole exome sequencing on the HiSeq2500 instruments with 100bp paired-end reads as well as 760 tumor and normal samples analyzed with the PGDx elio tissue complete assay. The PGDx elio tissue complete assay is a hybrid capture approach targeting 500+ genes with sequencing on the NextSeq instruments with 150bp paired-end reads. The bam files provided have been adapter masked and contain duplicate reads.

  Dataset EGAD00001008099

• RNA-Seq of 584 DLBCL Cases of Non-China Cohort from Phoenix Clinical Trial

  Standard RNA-Seq datasets. Check the associated paper for more details.

  Dataset EGAD00001008131

• Covid19 Transcriptomic Data analysis in Irish Population

  The Samples were collected from Saint James's Hospital, Dublin and after informed consent. RNA-Sequencing library preparation was performed using the Illumina TruSeq Stranded Total RNA Library Prep Globin kit (20020612) with an input amount of 100 – 1000 ng. Library preparation was automated and processed using a Hamilton NGS Star. Library quality was assessed using the Roche KAPA Library Quantification Kit (7960298001) and GX Caliper HS Assay (CLS760672, 760517), run on Roche Lightcycler 480 II and Perkin Elmer LabChip GX Touch analyser respectively. Libraries were pooled and sequenced (75bp PE) on an Illumina NovaSeq 6000 instrument using NovaSeq 6000 S2 Reagent Kit v1.5 (20028314) targeting 50M paired reads. Raw data (BCL format) were demultiplexed and converted to FASTQ format using BCL2FastQ (Illumina). Adapters were trimmed using Skewer (PMID: 24925680) and QC assessed using FASTQC. STAR (PMID: 23104886) was used to align reads to the reference genome (GRCh38/hg38) as well as to the transcriptome (GENCODE v. 25). Quality of the RNA alignment was assessed using Picard QC. Gene and isoform quantification was performed using RSEM (PMID: 21816040). The study shares expression data (gene.results) and chimeric.junction.out.

  Study EGAS00001007116