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• Integrated Genomic Analyses of Cutaneous T Cell Lymphomas Reveal the Molecular Bases for Disease Heterogeneity

  Cutaneous T cell lymphomas (CTCLs) are a clinically diverse collection of lymphomas of the skin-homing T cell. In the present study, we performed DNA and RNA sequencing on a cohort of CTCLs with representative samples from varying disease subtypes and stages. We characterized the landscape of putative driver genes, identified genetic relationships between CTCLs across disease stages, and inferred molecular subtypes in patients with stage-matched leukemic disease. Collectively, our findings clarify CTCL genetics and provide novel insights into pathways that drive diverse disease phenotypes. DNA and RNA sequencing was performed on 114 and 96 samples respectively. Tumor samples were obtained from University of Chicago (Chicago, IL), Northwestern University (Chicago, IL) and Yale University (New Haven, CT). 

  Study phs002456

• Development of Computational Approaches for Cell Hashing in scRNA-Seq

  As a test of cell overloading after cell hashing, a sample of peripheral blood mononuclear cells (PBMC) from a single subject was separated into naive T cells, memory T cells, and non-T cell PBMC populations using fluorescence activated cell sorting (FACS). Each population was separated into two technical replicates, then stained with BioLegend TotalSeq-A antibodies. All 6 samples were pooled, then loaded into 6 wells of a 10X Genomics Chromium 3' RNA-seq v3 chip at increasing cell counts: 16,000 (k), 24k, 32k, 48k, 64, and 80k cells per well. We also included a single sample that was not hashed or pooled, as well as a single sample that was stained with hashing antibodies, but not pooled in two separate wells.

  Study phs002695

• Solve RD data - Short-Read Whole-Genome Sequencing, raw data, tuh-kounap_group samples

  Solve-RD SR-WGS data generated for 3 samples provided by the group tuh-kounap

  Dataset EGAD00001015514

• Single-cell profiling of neoantigen-specific T cells in lung cancers treated with neoadjuvant PD-1 blockade

  This dataset includes 406 samples from non small cell lung cancer patients treated with neoadjuvant anti-PD-1. The Single Cell 5’ V(D)J and 5’ DGE kits (10X Genomics) were used to capture immune repertoire information and gene expression from the same cell in an emulsion-based protocol at the single cell level. Libraries were generated and sequenced on an Illumina NovaSeq instrument using 2x150bp paired end sequencing.

  Dataset EGAD00001007728

• Whole genome sequencing of breast cancer and related clones

  Paired WGA (whole-genome amplificated) samples from 65 single cell-derived organoids and six fresh single cell-derived organoid samples both of which were established from normal mammary epithelial cells, 84 FFPE LCM (laser-capture microdissection) samples of breast cancer and related clones, 79 fresh-frozen LCM samples of non-cancer lobules of breast cancer patients, and 36 matched germline controls were subjected to whole genome sequencing using NovaSeq 6000 system (Illumina) or DNBSEQ-G400RS (MGI Tech).

  Dataset EGAD00001010833

• Establishment and Genomic Validation of Novel Patient-Derived Xenograft Models for Drug Discovery in Gastrointestinal Stromal Tumor

  This dataset contains targeted next-generation sequencing data generated with the Illumina TruSight Oncology 500 (TSO500) assay from six gastrointestinal stromal tumors (GIST) and matched patient-derived xenograft (PDX) models established at Fox Chase Cancer Center (Philadelphia, PA). GIST are most commonly driven by activating mutations in KIT or PDGFRA, and this study focused on KIT-mutant tumors. All PDXs were derived from metastatic patient tumors previously treated with one or more tyrosine kinase inhibitors (TKIs). PDXs were maintained through series of passages and represents in vivo models of differential TKI sensitivity. The dataset represents a detailed comparison of mutational profiles between primary tumors and corresponding PDXs across passages, enabling studies of genomic stability, resistance mechanisms, and the evaluation of novel therapeutic strategies in GIST.

  Study phs004185

• NuGen Targeted Sequencing of 574 DLBCL Cases of Non-China Cohort from Phoenix Clinical Trial

  NuGen 99-Gene-Panel Targeted Sequencing of 574 DLBCL Cases of Non-China Cohort from Phoenix Clinical Trial. Check the Associated Publication for More Experimental Details.

  Dataset EGAD00001008132

• WXS and RNA-seq raw sequence data for TG project

  WXS sequence data from 112 samples, RNA-seq sequence data from 117 samples, all sequence data are raw sequence data in fastq format, sequenced by Illumina platform.

  Dataset EGAD00001007989

• WGS dataset for Genomic rearrangements in Pediatric Cancer

  Dataset EGAD00001008272

• sWGS of core biopsies from localized breast cancer patients

  Paired end shallow whole genome sequencing (sWGS) data for the identification of genomewide somatic copy number alterations (SCNA) and the estimation of tumor fractions.

  Dataset EGAD00001008397