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• ChIP sequencing from a collection of PFA tumors

  ChIP data from PFA (n = 10). Raw data provided as FASTQ. Data generated on Illumina NovaSeq 6000 PE50.

  Dataset EGAD00001009045

• WGS files for CIC paper data

  WGS files for CIC paper titled "Malignant progression of an ancestral bone marrow clone harboring a CIC-NUTM2A fusion in isolated myeloid sarcoma"

  Dataset EGAD00001009787

• Single-cell dissection of the immune response after a myocardial infarction

  38 STEMI patients at hospital admission, 24 hours (acute phase) and 6-8 weeks (chronic phase) after STEMI

  Dataset EGAD00001010064

• NiCOL Study Target-seq dataset

  10 samples sequenced in Target-sequencing of a panel of 571 genes (Illumina NovaSeq 6000) - Raw FASTQ data - Annotated VCF

  Dataset EGAD00001010911

• Exome sequencing of osteosarcoma, blood and saliva

  We profiled 31 osteosarcoma tumor patient samples, 18 blood and 1 saliva control samples by exome sequencing, for a total of 50 samples. The raw fastqs are provided.

  Dataset EGAD00001011370

• Minority Health Genomics and Translational Research Bio-Repository Database

  The Minority Health Genomics and Translational Research Bio-repository Database (MHGRID) Network infrastructure facilitated the collection of biospecimens and related multidimensional data elements within a consortium of minority-serving clinics. This initiative expands the diversity of ancestral groups in national genomic medicine datasets and promises to accelerate the translation of personalized medicine into minority communities. MHGRID has an observational case-control design with severe hypertension as primary outcome.

  Study phs001815

• Identification of Recurrent SMO and BRAF Mutations in Ameloblastomas

  RNA-seq data from two cases of ameloblastoma was analyzed for candidate gene fusions and point mutations. Recurrent point mutations identified in the RNA-seq data, as well as mutations identified with limited panel targeted deep sequencing, were validated as somatic. Expanding to a larger cohort of 28, one of two activating mutations was found in 80% of cases. No recurrent gene fusions events were identified.

  Study phs000739

• Interruption of BTK Inhibitor Improves Response to SARS-CoV-2 Booster Vaccination in Patients with Chronic Lymphocytic Leukemia

  This study investigates the effect of booster SARS-CoV-2 vaccination and Bruton tyrosine kinase inhibitor (BTKi) interruption on antibody response to vaccination. Patients with chronic lymphocytic leukemia (CLL) are immunocompromised, at increased risk of infection, and have historically poor response to immunization. BTKi therapy is a standard treatment for CLL in frontline and salvage settings and further suppresses antibody vaccine responses.

  Study phs003319

• Genomic-Enabled Medicine for Recurrent Glioblastoma

  In this prospective study, we performed genome-wide tumor/normal exome sequencing and tumor RNA-sequencing for recurrent glioblastoma patients. A subset of patients had both enhancing tumor and non-enhancing tissue sequenced to investigate spatial heterogeneity of this disease. Together, this information builds our understanding of the genomic underpinnings of glioblastoma, and contributes toward the knowledge base for identifying and developing more effective treatments for patients with glioblastoma.

  Study phs001460

• GUARDIAN: The Insulin Resistance Atherosclerosis Study (IRAS Classic)

  The Insulin Resistance Atherosclerosis Study (IRAS) was an epidemiologic cohort study designed to examine the relationship between insulin resistance and carotid atherosclerosis across a range of glucose tolerance. Individuals of self-reported Mexican-American ethnicity were recruited in San Antonio, TX and San Luis Valley, CO. Recruitment was balanced across age and glucose tolerance status. GUARDIAN includes 173 individuals from the IRAS. Insulin sensitivity was obtained by FSIGT.

  Study phs001014

• Phase IB/II Study of Bazedoxifene in Combination with Palbociclib in Patients with Endocrine Resistant Hormone Receptor-Positive Breast Cancer

  In this phase Ib/II clinical trial, the investigators evaluated the efficacy and safety of the combination of palbociclib with bazedoxifene in patients with a metastatic endocrine-resistant hormone receptor-positive, HER2-negative breast cancer. Furthermore, whole exome sequencing of cell-free tumor DNA was done on serial samples from these patients, revealing potential molecular changes associated with mechanisms of resistance.

  Study phs002802

• Pilot Sequencing Study: DNA Hydroxymethylation and Gene Expression in Peripheral Blood Mononuclear Cells in Healthy Human Aging

  This study was a pilot analysis of samples of human peripheral blood mononuclear cell (PBMCs) from 10 young (23-30 years) and 10 older (68-76 years) healthy Caucasian female volunteers. Whole genome sequencing was performed to assess multiple epigenetic mechanisms and gene expression, including 5hmC-capture sequencing and RNA-sequencing, followed by integrative analyses to identify regions and genes associated with age.

  Study phs001916

• Genomic sequencing of Ewing's Sarcoma

  The Ewing sarcoma family of tumors (EFT) is a group of malignant small round blue cell tumors that arise in bone or soft tissue. Ewing sarcoma (ES) is the second most common type of primary bone tumor to affect children and adolescents and accounts for 2.9% of all childhood cancers. This data set reports whole-genome sequencing of 6 primary Ewing's Sarcoma samples and matching germline samples.

  Study phs000768

• Epigenetic Mechanisms of Inflammation and Fatigue in Head and Neck Cancer

  This was a longitudinal observational study to examine the association between fatigue and DNA methylation as well as gene expression among patients with head and neck cancer. Demographic and clinical variables were collected before chemoradiotherapy and/or at follow-up visits as appropriate. Fatigue was assessed and biosamples (for DNA methylation and gene expression) were collected before, immediately after, and at six- and twelve-months post-chemoradiotherapy.

  Study phs002106

• Cellular Origins and Genetic Landscape of Cutaneous GD T Cell Lymphoma

  Cutaneous gamma-delta T cell lymphomas are a rare and aggressive subtype of cutaneous lymphoma. In the present study, we analyzed these cancers by DNA and RNA sequencing in order to illuminate the genetic landscape for this rare disease. We obtained tumor samples from multiple institutions, including Northwestern University (Chicago, IL), University of Chicago (Chicago, IL), University of Virginia (Charlottesville, VA), and Massachusetts General Hospital (Boston, MA).

  Study phs001969

• Genome-Wide Approach to Measure Variant-Based Heritability of Drug Outcome Phenotypes

  Current pharmacogenetic approaches often use a few large-effect alleles to predict drug outcomes. However, many drug outcome phenotypes are determined by complex pathways that may be influenced by common single-nucleotide variants (SNVs) across the genome. We ascertained how much variation in drug response is explained by common SNVs for pharmacokinetic (drug levels) and pharmacodynamic phenotypes (highest creatinine) for 4 drugs: vancomycin, gentamicin, cyclosporine and tacrolimus.

  Study phs002506

• Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma

  Lymphomas are a prevalent and heterogeneous family of cancers arising in cells of the immune system. Drivers of lymphomagenesis include genomic rearrangements that juxtapose active regulatory elements with specific oncogene targets, as well as mutations affecting specific transcription factors and chromatin regulatory proteins. This study seeks to combine genome-wide genetic and epigenetic datasets to better understand mechanisms of oncogene dysregulation across distinct lymphoma types.

  Study phs000939

• Collaborative Association Study of Psoriasis

  The goal of this collaborative study is to combine the resources and expertise of three groups with long-standing studies of psoriasis genetics in order to identify new genetic susceptibility factors for psoriasis, a common inflammatory skin disease that affects over 4 million Americans. Consent groups and participant set General research use (GRU): 1677 (950 cases, 692 controls, 35 others) Autoimmune disease (AD): 1198 (449 cases, 734 controls, 15 others)

  Study phs000019

• Dana-Farber Cancer Institute (DFCI) Brown Lab CLL Sequencing Study

  Chronic Lymphocytic Leukemia (CLL) is a hematological malignancy characterized by accumulation of CD5+CD19+ B cells in peripheral lymphoid organs, bone marrow and blood. In this study we analyze matched whole genome sequencing and RNA-seq data from CLL patients to characterize the mutational processes operative throughout tumor evolution. Source of tumor and normal DNA used is patient PBMC or B cells and saliva respectively.

  Study phs000879

• Non-Coding Mutations Cause Enhancer Targeting Resulting in Protein Synthesis Dysregulation During B-Cell Lymphoma Progression

  In this study, we performed whole-genome sequencing of longitudinal tumor pairs, representing transformation of follicular lymphoma (FL) to high grade B-cell lymphoma with MYC and BCL2 rearrangements (known as "double hit lymphoma" or DHL), a very aggressive class of non-Hodgkin B cell lymphoma (B-NHL). We identified coding and noncoding genomic alterations acquired during the course of lymphoma progression.

  Study phs003398

• Evolving Cell States and Oncogenic Drivers during the Progression of IDH-Mutant Gliomas

  The study aims to understand the changes in cell states during the progression of IDH mutant gliomas. We generated scATAC-seq data from tumor samples of patients with IDH mutant gliomas, ranging from grade 2 to grade 4, including both IDH mutant oligodendroglioma and IDH mutant astrocytoma samples. Additionally, we have generated scRNA-seq data from patient-derived organoids that were treated with a DNMT1 inhibitor.

  Study phs003697

• DAC for a single-cell multi-omic atlas of nodal B-cell non-Hodgkin lymphomas

  Nodal B-cell non-Hodgkin lymphomas (B-NHL) are a clinically diverse set of cancers thought to originate from distinct stages of B-cell maturation. To characterize intratumor heterogeneity across B-NHL entities, we performed CITE-Seq (cellular indexing of transcriptomes and epitopes) on 51 lymph node samples including mantle cell lymphoma (MCL, n = 8), follicular lymphoma (FL, n = 12), germinal center (GCB, n = 5) or activated B-cell (non-GCB/ABC, n = 7) diffuse large B-cell lymphoma (DLBCL) and marginal zone lymphoma (MZL, n = 11) tumors, in addition to non-malignant reactive lymph nodes (rLN, n = 8). We also performed 5 prime scRNA-seq with immune receptor profiling for 11 of these samples (2 rLN, 2 MCL, 3 FL, 2 DLBCL, and 2 MZL).

  Dac EGAC50000000226

• Analysis of genes associated with autistic spectrum disorder, schizophrenia, and bipolar disorder.

  Autism spectrum disorders (ASD) represent a heterogeneous group of neurodevelopmental disorders with strong genetic predispositions. Although an increasing number of genetic variants have been implicated in the pathogenesis of ASD, little is known about the relationship between ASD-associated genetic variants and individual ASD traits. We performed case-control association study of 32 Japanese children with ASD (mainly with high-functioning autism) and 36 with typical development.

  Study JGAS000731

• Childhood Cancer Data Initiative (CCDI): Texas Pediatric Patient Derived Xenograft 

  The DNA/RNA samples of patients for which PDX models were developed were from a population of children, adolescents, and young adults from South Texas. Consent was obtained for collection of malignant and non-malignant tissue samples for genetic analysis and for the development of models to study new ways to treat cancer. For additional details, please refer to these publications: PMID: 37915590; PMID: 37990009.

  Study phs003215

• Analysis of Large Cell Neuroendocrine Carcinoma Expressing HNF4alpha Using WGS

  Lung LCNEC (Large Cell Neuroendocrine Carcinoma) has a poor prognosis, and no effective treatment has yet been established. We have found that the gastrointestinal marker HNF4alpha is specifically expressed in some LCNEC cases. By performing Whole Genome Sequencing (WGS) on samples from 10 LCNEC patients, we aim to identify changes characteristic of LCNEC expressing HNF4alpha and explore new classifications and treatment options for LCNEC.

  Study JGAS000732