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• SLAMF7 Regulates Synovial Macrophages in Rheumatoid Arthritis

  The purpose of this study was to characterize the role of SLAMF7 on human macrophages. RNA-sequencing was performed on myeloid populations from blood of healthy controls or rheumatoid arthritis patients, or synovial fluid of rheumatoid arthritis patients, based on high or low expression of SLAMF7. Then, monocyte-derived macrophages from healthy controls were left untreated, or stimulated with anti-SLAMF7 or recombinant SLAMF7 protein, and transcriptional profile was defined after SLAMF7 engagement.

  Study phs002771

• Molecular genetic analysis of inherited kidney dysfunction

  Samples were chosen for sequencing from a set of probands from pedigrees with apparently inherited forms of focal segmental glomerulosclerosis (FSGS). Several genes have been identified which when mutated cause FSGS under both recessive and dominant inheritance patterns. These known genes are estimated to explain less than 50% of inherited FSGS. We chose samples from individuals in which previous analyses of known disease genes failed to identify likely disease-causing mutations.

  Study phs000484

• The Genomic Landscape of Juvenile Myelomonocytic Leukemia

  This study analyzed samples from 29 patients with juvenile myelomonocytic leukemia (JMML) using whole exome sequencing. Each patient had a paired germline tissue along with a diagnostic leukemia sample. Germline tissue types included buccal mucosa, cordblood, Epstein-Barr virus immortalized cell lines and fibroblasts from either skin or bone marrow. Leukemia samples were either blood or bone marrow. Seven of the 29 patients also had a relapsed leukemia sample available for exome analysis.

  Study phs000973

• Identification of Structural Variants Relevant to Autism by Pacific Biosciences HiFi Whole-Genome Sequencing

  The purpose of this research study was to perform long-read whole-genome sequencing on a family with autism. This family had no known genetic cause based on clinical array and whole-exome sequencing analysis. Utilizing PacBio HiFi long-read whole-genome sequencing, we identified a relevant missense variant in the KCNC2 gene. This variant was likely to be a germline mosaic in the paternal germline.

  Study phs002698

• ZRSR2 Mutant Myelodysplastic Syndromes

  Mutations in splicing factor genes are common in myelodysplastic syndromes but the reason for selection of these mutations remains incompletely understood. This study aimed to identify the effect of minor intron retention due to ZRSR2 mutations in myelodysplastic syndromes. Nine samples from patients with myelodysplastic syndromes bearing ZRSR2 mutations and ten samples from patients with myelodysplastic syndromes not bearing any splicing factor mutations were subjected to transcriptomic analysis for mis-splicing events after RNA-sequencing. 

  Study phs002212

• The PUWMa (

  The PUWMa GWAS of ADHD is a multi-site collaboration initiated to conduct a family-based association study from existing research samples. The source sample of ADHD families was ascertained at Massachusetts General Hospital (MGH, N=309 trios), Washington University at St. Louis (WASH-U, N=272 trios), and University of California at Los Angeles (UCLA, N=156 trios). All offspring met criteria for DSM-IV-TR attention-deficit hyperactivity disorder with childhood onset.

  Study phs000358

• Whole Genome Sequencing of Waldenstrom's Macroglobulinemia

  Whole genome sequencing was conducted on 10 tumor/germline paired samples along with 20 additional unpaired tumor samples from patients with Waldesntrom's macroglobulinemia. Tumor lymphoplasmacytic lymphoma cells were obtained from CD19+ selected bone marrow mononuclear cells. Germline tissue was obtained from CD19 depleted peripheral blood mononuclear cells. High molecular weight DNA was then submitted for whole genome sequencing with Complete Genomics and aligned to HG19/NCBI human reference build 37.

  Study phs000740

• Study of Cutaneous Biology of Cutaneous T Cell Lymphoma

  This study is designed to help us understand the biological factors that contribute to the development of Cutaneous T Cell Lymphoma (CTCL) through the use of single-cell -omics technologies. The data that will be available include single-cell RNAseq and paired single-cell TCRseq data from the primary lesions of CTCL patients.The number of consented subjects listed here is artificially inflated by one to account for the pooling of all subjects.

  Study phs002717

• Germline Sequencing for Aggressive Prostate Carcinoma

  This study aims to elucidate the genetic determinants of susceptibility to aggressive prostate carcinoma. To this end, germ line whole exome sequence has been generated from patients with aggressive prostate cancer. Whole genome sequence for a representative subset of tumors from patients whose cancer was resistant to primary therapy is included as well. This deep genomic interrogation will allow the identification of rare, functionally disruptive variants that may play a role in disease progession and response to treatment.

  Study phs000661

• Genome Sequencing of Familial Cholangiocarcinoma for the Identification of Germline Risk Alleles

  In this study, sequencing data (WES, WGS, linked-read WGS) was used to identify candidate causal germline variants in a family with inherited cholangiocarcinoma. Candidate causal SNVs and indels were identified from the germline WES data of eight siblings (four affected, four unaffected), then somatic second hits were identified from matched tumor/normal pairs. Second hits were verified using haplotype information derived from linked-read WGS of the tumor data.

  Study phs001593

• Breast Cancer Family Registry Early-onset Breast Cancer GWAS

  In order to enhance our understanding of the genetic etiology of breast cancer, this study analyzed 1,265,548 Hapmap3 single-nucleotide polymorphisms (SNP) among a discovery set of 3,523 EOBC incident cases and 2,702 age-matched population control women, all of whom were age 50 or younger at enrollment. Subjects were recruited from the eight sites, some of which oversampled cases with a personal or family history of breast cancer.

  Study phs001589

• Genetic Analysis of Syndromic Orofacial Clefting

  The goal of this study is to identify previously unknown genetic causes of human syndromic cleft lip/palate by using genome sequencing. Many previous studies have shown that isolated cleft lip and/or palate are not often likely to be monogenic or Mendelian diseases. We hope that by focusing on syndromic presentations, we will find novel causes of disorders which include orofacial clefting among their phenotype(s). Data provided will be fastq files from sequencing partners.

  Study phs002997

• High-Fidelity, Large-Scale Targeted Profiling of Microsatellites

  This study developed a novel method of targeted sequencing of microsatellites. We optimized every aspect of targeted hybridization capture geared towards minimizing artifacts that commonly occur in laboratory manipulation of microsatellite-containing DNA. This achieved a higher fidelity for microsatellite sequencing than standard targeted DNA sequencing. In the accompanying manuscript, we also introduce two computational tools for design of targeted microsatellite capture panels and for analyzing the resulting microsatellite sequencing data.

  Study phs003679

• Genetic Evaluation of Autoinflammatory Diseases

  Many pediatric patients with early-onset autoinflammatory disease (AID) phenotypes are mutation-negative for genetically known AIDs. Recent data suggest a role for Type-I interferon (IFN) dysregulation in causing AID phenotypes with clinical features that are distinct from those found in patients with IL-1 mediated AIDs. We screened patients for the presence of an IFN-response gene signature (IRS) to characterize their clinical phenotypes, IFN-related biomarkers, and genetic causes.

  Study phs001946

• LCM-isolated buccal epithelial cell sequencing

  Single buccal epithelial cells were dissected and collected on an adhesive cap with laser capture microdissection (LCM) with approximately 13-60 cells per cap. Each adhesive cap containing 13-60 cells was independently processed with QIAamp DNA micro kit (Qiagen) for DNA extraction. The NEBNext ultra II FS DNA library kit was used to prepare DNA libraries with low starting material. Paired-end whole genome sequencing reads were obtained with the NovaSeq.

  Study EGAS50000000098

• Systematic Identification of Minor Histocompatibility Antigens Informs Outcomes after Allogeneic Stem Cell Transplantation

  This study cohort is composed of 287 patients affected by myeloid disease (AML/MDS) who were subjected to allogeneic hematopoietic cell transplantation (allo-HCT) from an HLA-matched related donor. For each study subject, we have collected genomic DNA from both donor and recipient (D-R). Resulting germline whole exome sequencing from D-R pairs has formed the basis for applying an analytical pipeline to systematically predict minor histocompatibility antigens (mHAgs)

  Study phs003394

• Whole genome sequencing of pancreatic cystic fluid for early detection and diagnosis of pancreatic cancer

  Pancreatic cancer (PC) is a leading cause of cancer-related deaths globally. Accurate PC detection at early or premalignant stage, when surgery is effective, would increase survival rates and prevent unnecessary surgery or surveillance. Molecular diagnostic attempts using PCy fluid (PCyF), as a liquid biopsy, to analyze common mutations associated with PC development are yet to contribute to early diagnosis. Whole genome sequencing (WGS) is utilized in various cancers, PC inclusive, for detecting genetic changes associated with carcinogenesis, but not in PCyF due to technical limitations, including isolated DNA purity. The goal of the study was to achieve high quality of WGS from PCyF from 9 patients to enable development of signatures of malignancy. The WGS was performed using Illumina sequencing. Experimental design was at a 50x depth.

  Dataset EGAD50000000869

• Cas9-targeted-based long-read sequencing for genetic screening of RPE65 locus

  In order to compare sequencing performance of different technologies in a specific locus, we sequenced blood samples of five inherited retinal dystrophies (IRD) patients harboring a monoallelic variant in RPE65 that remained uncharacterized with: 1) Clinical exome targeted sequencing (CES), 2) whole genome sequencing (WGS), and 3) Long-read sequencing on a MinION platform where CRISPR-Cas9 guide RNA probes were designed to target a 31 kb region including the entire RPE65 locus.

  Study EGAS50000000596

• Patient-derived models of primary breast cancer for preclinical development of novel neoadjuvant therapies

  Generation of the first large-scale cohort of mouse intraductal patient-derived xenograft (MIND-PDX) models of primary invasive breast cancer (IBC) and a collection of matched PDX-derived organoids (PDXO) representing all molecular subtypes of IBC, including estrogen receptor (ER-) positive breast cancer. Furthermore, we show that our IBC-MIND cohort can serve as a platform to test experimental neoadjuvant treatment options in different molecular subtypes of breast cancer.

  Study EGAS50000000398

• Targeted Sequencing of 52 Genes for Severe COVID-19

  This dataset comprises targeted sequencing data of 52 genes previously implicated in severe COVID-19 outcomes. The study includes samples from 764 individuals with severe COVID-19 and 3,939 population-based controls from the GCAT cohort (Spain). Molecular Inversion Probes (MIPs) were utilized for cost-effective and precise sequencing of the selected genes. The targeted genes include: Inflammasome/IL-1/TNF Pathway: NLRP3, CASP1, CASP8, IL1B, TNF, RIPK1, RIPK3, MYD88, TNFRSF13B SARS-CoV-2 Entry/Replication: ACE2, TMPRSS2, FURIN, SLC6A20, DDX1, DDX58, TLR4, FYCO1, CTSB, CTSL, ADAM17 Complement System: MBL2, CFH, CFI, CFB, ADAM10, CD46 Interferon Signaling: TLR3, IFIH1, IFITM3, TBK1, TLR7, IL10RB, IFNAR1, IFNAR2, SIGLEC1, MYD88, IFNGR1 Chemokine Receptor Signaling: CCR1, CCR3, CCR2, CCR9, IL8, CXCL3, CXCL10, CXCR6, XCR1, CCL2, CCL20 Immunodeficiency Genes: CASP8, CD46, CFB, CFH, CFI, IFNAR1, IFNAR2, IFNGR1, IFIH1, MYD88, NLRP3, RIPK1, TBK1, TLR3, TLR7

  Dataset EGAD50000001378

• NCI's Collection of Studies for General Cancer Research

  This collection contains all of NCIs authorized individual-level genomic datasets currently in dbGaP that are approved for Cancer Research (DS-CA) use only and limitations outlined in the model Data Use Certification Agreement. Access to this study will include any additional authorized individual-level DS-CA datasets that become available. Renewal of this study is required annually. To request access to this study collection, select phs003967.v1.p1 in the dbGaP Authorized Access System.

  Study phs003967

• Predicting resistance to chemotherapy using chromosomal instability signatures

  The aim of this study is to assess whether three chromosomal instability signature biomarkers are capable of predicting resistance to standard chemotherapies, namely platins, taxanes and anthracyclines. As part of this study we compiled a proof of principle cohort of ovarian cancers treated with these therapies, profiled using the Illumina TSO500 panel. Analysis of these data demonstrated that accurate biomarker calling can be computed from these gene panel data.

  Study EGAS50000000992

• Single cell long read whole genome sequencing reveals somatic transposon activity in human brain

  The advent of single cell DNA sequencing revealed astonishing dynamics of genomic variability, but failed at characterizing smaller to mid size variants that on the germline level have a profound impact. In this work we discover novel dynamics in three brains utilizing single cell long-read sequencing. This provides key insights into the dynamic of the genomes of individual cells and further highlights brain specific activity of transposable elements.

  Study EGAS50000001156

• PTEN homozygous deletion is a negative prognostic factor in Tumor Treating Fields-treated glioblastoma, IDH wildtype patients

  This study investigates genomic determinants of outcome in glioblastoma, IDH-wildtype patients treated with Tumor Treating Fields (TTFields) in addition to standard radiochemotherapy. Tumor tissue from primary glioblastoma at initial diagnosis was profiled using the Illumina TruSight Oncology 500 (TSO500) targeted sequencing panel to characterise somatic alterations. The overarching goal is to provide exploration of genomic determinants of survival and treatment response in TTFields-treated glioblastoma, IDH-wildtype.

  Study EGAS50000001469

• Broad utility of ultrasensitive analysis of ctDNA dynamics across solid tumors treated with immunotherapy

  Plasma ctDNA sequencing data from samples collected from a pan-cancer cohort of patients with advanced-stage disease treated with IO therapies. This study highlights the broader applicability of ultrasensitive ctDNA as a biomarker across cancer types and immunotherapy modalities. Here, we applied a whole-genome, tumor-informed approach to study ctDNA in 202 advanced-stage cancer patients treated at VHIO. This study captures the plasma sequencing data from the project.

  Study EGAS50000001271