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• Healthy human B-lymphopoiesis RNA-Seq reference using FACS sorted bone marrow aspirates

  To define a transcriptomic reference of human B lymphopoiesis, bone marrow aspirates were obtained from n=4 healthy donors (study registration DRKS00023583). After immunodensity cell separation, samples were FACS-sorted into 7 established lymphopoietic differentiation stages. RNA was extracted from 5,000-320,000 cells per differentiation stage and subjected to ultra-low-input RNA sequencing after generation of stranded sequencing libraries.

  Dataset EGAD00001010917

• RNAseq of human breast cancer tumors from the PEARL study

  Formalin fixed, paraffin-embedded human breast cancer tumor samples had RNA extracted using the Thermo Scientific KingFisher Flex instrument and the Applied Biosystems MagMAX FFPE DNA/RNA Ultra Kit; Total RNA libraries were created using the Bravo Automated Liquid-Handling Platform and the TruSeq Stranded Total RNA Library Prep Gold Kit; libraries were sequenced on the Illumina NovaSeq 6000 machine using a 2x50 bp paired-end configuration to target a read depth of 120 million clusters per library.

  Dataset EGAD00001015613

• RNA-Seq of human longitudinal whole blood samples from PCR-positive and PCR-negative recent household contacts of COVID-19 index cases.

  Little is known about the transcriptomic profile of individuals who are exposed to SARS-CoV-2 yet resist becoming PCR positive. To investigate this, longitudinal whole-blood samples were taken (0, 7, 14, and 28 days after enrolment) from PCR positive and PCR negative SARS-CoV-2-naïve household contacts who were recently exposed to a COVID-19 index. Samples were also taken from pre- and post-pandemic unexposed controls. Total RNA was extracted from PAXgene tubes before undergoing poly(A) selection followed by globin and rRNA depletion. DNA libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. All samples were then sequenced across 2 flowcells of an Illumina HiSeq 4000.

  Study EGAS50000000473

• Neoantigen Immunogenicity Landscapes and Evolution of Tumor Ecosystems During Immunotherapy with Nivolumab

  We performed Whole Exome (WXS) and RNASeq sequencing on samples obtained from the same site before and during therapy from our prospective clinical trial (CA209-153, NCT02066636) of nivolumab in advanced Non-small cell lung cancer (NSCLC) patients that progressed on chemotherapy. There are 58 pre and 42 on therapy WXS samples and 24 pre and 12 on therapy RNASeq samples. All WXS tumor samples have matching normal samples.

  Dataset EGAD00001011302

• Urothelial Cancer - Genomic Analysis to Improve Patient Outcomes and Research (UC-GENOME): A Bladder Cancer Advocacy Network (BCAN)-Led Collaborative Research Pilot Study

  UC-GENOME is a real-world cohort of patients with metastatic urothelial carcinoma (UC). The study consisted of two co-equal aims: 1) to provide targeted DNA sequencing for clinical decision making at no cost to patients; and 2) to create a resource for collaborative translational science including a clinically annotated biobank. The submitted data represents the foundational analysis of 218 patients accrued at 7 academic medical centers. The analysis includes 176 patients with both targeted DNA sequencing and RNA sequencing. The genomic data was combined with clinical variables to model response to chemotherapy and immune checkpoint inhibitors (ICI). Due to additional sharing restrictions, data from one site can be found in phs003094.

  Study phs003066

• Epidemiologic Architecture for Genes Linked to Environment (EAGLE) MetaboChip Study

  The Epidemiologic Architecture for Genes Linked to Environment (EAGLE) study is a study site of the larger Population Architecture using Genomics and Epidemiology (PAGE) I study.  EAGLE accessed two data resources during the course of study: the National Health and Nutrition Examination Surveys (NHANES) and BioVU, the Vanderbilt University Medical Center biorepository linked to de-identified electronic health records.The EAGLE MetaboChip Study, also known as EAGLE BioVU in the literature, is a data resource of Illumina MetaboChip genotypes for ~15,000 DNA samples from African American/Black, Hispanic, and Asian patients in BioVU (PMID: 26201699). Several EAGLE BioVU and PAGE I study phenotypes were extracted using structured and unstructured data available in de-identified electronic health records linked to the DNA samples. 

  Study phs002767

• Germline Whole-Exome Sequencing of Lung Cancer in EAGLE

  EAGLE is a large population-based case-control study designed and conducted to investigate the genetic and environmental determinants of lung cancer and smoking persistence using an integrative approach that allows combined analysis of genetic, environmental, clinical, and behavioral data. Here, we applied whole exome sequencing (WES) to EAGLE study, in a group of 2,777 Italian subjects (including 1,461 lung cancer cases and 1,316 healthy controls). We derived gene-level burden tests to explore the cumulative effect of deleterious rare variants within protein-coding genes and the lung cancer risk. Additionally, at this site we include WES datasets of 1259 healthy controls from 1054 PLCO (The Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial) subjects and 205 ACS (The American Cancer Society study) subjects.

  Study phs002496

• Cergentis FFPE-TLC

  In this study, formalin-fixed paraffin-embedded targeted locus capture (FFPE-TLC) sequencing is used as a novel technology for targeted detection of tumor-specific genomic structural variants (SVs) in the primary tumor of 29 colorectal cancer patients with metastatic disease. The tumor region was macrodissected and sequenced for 29 patients, and the "normal" region of the same slide was macrodissected and sequenced for 8 of these patients. SVs were found in the common fragile site (CFS)-associated genes MACROD2, PRKN, FHIT and WWOX as well as SVs caused by three LINE transposable elements. Tumor-specificity of selected SVs was independently verified by droplet digital PCR of tumor tissue DNA and their applicability as plasma circulating tumor DNA biomarkers was demonstrated.

  Study EGAS50000000427

• WGS Fastq files from the CPC-Gene project in support of PRAD-CA, DCC Release 26

  This dataset contains fastq files with Whole genome sequencing data for the CPC-Gene Project. Data from each sample was generated using multiple whole genome libraries and sequenced across multiple runs

  Dataset EGAD00001003761

• ICGC PCAWG Dataset: ORCA-IN_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: ORCA-IN.

  Dataset EGAD00001002120