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• Targeted analysis of cell-free circulating tumor DNA is suitable for early relapse and actionable target detection in patients with neuroblastoma

  Study EGAS00001006027

• Jackson Heart Study (JHS-BioLINCC)

  Accessing Data: Please refer to “Authorized Access” below regarding accessing data through the BioData Catalyst ecosystem. The data from this accession is not available for download through dbGaP.Related Studies: Other Jackson Heart Study data available include: Imaging studies (JHS-Imaging), Genetics and genomics (The Jackson Heart Study, phs000286.v7.p2), and Collaborative Cohort of Cohorts for COVID-19 Research (C4R-JHS, phs002907.v1.p1): Jackson Heart Study (phs002907.v1.p1).Available Data: Data available for request include Jackson Heart Study visit 1-3 examination cycles, collated annual follow-up communication data through 2016, and follow-up for mortality, heart disease, and stroke events through 2014.Objectives: The objectives of the Jackson Heart Study are to: 1) investigate the associations of biological, psychosocial, and behavioral factors with the incidence atherosclerotic events and health outcomes in an African American cohort; and 2) increase access to and the participation of African American populations and scientists in biomedical research and professions.Background: It has long been recognized that African Americans share a disproportionate burden of deleterious health outcomes including diabetes, hypertension, kidney disease and early onset of cardiovascular disease. The Jackson Heart Study was initiated in 2000 to explore potential mechanisms and mediators of health outcomes in a large African American cohort. In addition, the JHS conducts a variety of community education and outreach activities to promote healthy lifestyles to reduce disease risk burden and student training programs to promote and support public health research.Participants: African American men and women, age 35-84 at entry. Of the 5306 cohort members enrolled in the study, the data repository contains data from 3,883 that provided informed consent to share their data with investigators not affiliated with the study.Design: Participants were enrolled in the study from 2000-2004 from urban and rural areas of three counties (Hinds, Madison and Rankin) in the Jackson, MS metropolitan statistical area. Participants were enrolled from each of 4 recruitment pools: a random sample component (17%), volunteer component (30%), currently enrolled in the Atherosclerosis Risk in Communities (ARIC) Study (31%), and secondary family members (22%). Recruitment was limited to non-institutionalized adult African Americans age 35-84 years, except in the family cohort where those age ≥21 years were eligible. The final cohort of 5,306 participants includes 6.59% of all African American residents aged 35-84 (N=76,426, US Census 2000). Data collection at the baseline exam included a medical history, physical examination, blood/urine analytes and interview questions on areas such as: physical activity; stress, coping and spirituality; racism and discrimination; socioeconomic status; and health care access.The current release of the Jackson Heart Study includes data collected at baseline, exam 2 (2005-2008), and exam 3 (2009-2013). Annual follow-up and surveillance of clinical cardiovascular events is ongoing.

  Study phs003740

• Paediatric Hepatic International Tumour Trial (JPLT2: PHITT)

  Hepatoblastoma (HBL) is the most common primary liver tumor in children. Despite their diversity in histopathological phenotype and clinical outcome, the underlying molecular aberrations have not been fully understood. Here we describe a comprehensive landscape of genomic, epigenomic, and transcriptomic heterogeneity among the 163 cases of HBLs and transitional liver cell tumors (TLCTs) collected in the multicenter clinical trial JPLT-2. The total numbers of mutational events in HBLs are very few (0.52 SNVs/Mb on exonic regions) but show a positive correlation with the age of onset. While dysregulation of Wnt-pathway related genes was observed (somatic deletion or mutations of CTNNB1 and germline or somatic mutations of APC) in 83.6% of the HBL cases, TERT promoter mutations are mainly in the elderly HBLs (> 8 years old), meeting with the proposed criteria of TLCT. These TLCT cases are clustered in the hypermethylated epigenotype in promoter and enhancer regions. Copy number analyses also revealed recurrent 11p15.5 UPD/LOHs including the IGF2/H19 region (31.6%), focal deletions in 4q35 (15.8%) and focal amplifications in 2q24.3 (7.0%) predominantly in the child and infant HBLs. Motif enrichment analysis of the specific hypomethylated enhancers in these HBL subtypes suggests specific binding of ASCL2, the regulatory transcription factor for definitive endoderm and digestive systems. Transcriptome and histochemical analysis revealed that ASCL2 is upregulated not in HCC and TLCT but in child and infant HBL, suggesting their ?cell of origin? derived from the premature hepatoblast with high proliferative potential such as intestinal epithelial cells. Systematic molecular profiling of HBL will provide a fundamental understanding of hepatoblast carcinogenesis and clues for risk stratification.

  Study JGAS000236

• TARGET-seq+ single-cell transcriptome sequencing

  Single-cell whole transcriptome sequencing data for bone marrow samples from 9 cases with clonal hematopoiesis and 4 control samples. The TARGET-seq+ protocol was used to generate plate-based 3' transcriptome data. For details on cell sorting and the TARGET-seq+ protocol see the methods section of the manuscript. One FASTQ file is provided per cell. Cells are named with their plate and well IDs and the subject ID. Empty wells (no-cell controls) are named "blank". Corresponding genotyping files use the same naming without the "_transcriptome" suffix.

  Dataset EGAD00001011175

• Mitochondrial DNA mosaicism in human somatic cells

  Genomic alterations accumulate in the somatic cells throughout an individual’s lifetime. Recent sequencing studies have documented widespread mutations in the nuclear genome and the frequent clonal competition of normal cells carrying mutations. However, the landscape of mitochondrial DNA (mtDNA) heteroplasmy in normal human tissues is poorly understood. This study investigated the whole genome sequences (WGSs) of 2,096 clones established from non-neoplastic healthy single cells obtained from 31 donors. In addition, we analyzed 31 WGSs of neoplastic cells, including 12 clones established from adenomatous polyps from one individual with MUTYH-associated polyposis and 19 matched colorectal carcinomas from individuals who donated normal colorectal clones.

  Dataset EGAD50000000373

• Targeted and exome sequencing data from 24 prostate cancer patients with somatic hypermutation

  This dataset contains all available targeted and exome sequencing paired fastq files from our study, "Identification of hypermutation and defective mismatch repair in ctDNA from metastatic prostate cancer". Patient identifiers are denoted by the first three characters of the sample aliases (e.g. "P01"), and additional information is appended to reflect the panel used (targeted 73 gene panel: "PC", or whole-exome panel: "WXS"), and whether the sample represents cell-free DNA ("cfdna") or paired white-blood cell control ("wbc"). Several patients have multiple serial collections available, and these are denoted by the characters "C1, C2, C3," etc. All samples were sequenced using Illumina technology.

  Dataset EGAD00001005474

• WGS

  A genome-wide approach based on next generation sequencing (NGS) is performed on trios ( Patient+ Father + Mother) with SAID in order to identify known and new gene variants associated with certain forms of the disease. Whole-genome sequencing (WGS) was performed on frozen PBMCs. DNA was extracted using Chemagic Prime ( Perkin Elmer) and quantified with nanodrop. The raw sequencing data is generated on the Novaseq 6000 using an S4 flowcell, with a sequencing depth of ~30X

  Dataset EGAD50000002026

• Women's Health Study Accelerometry Dataset

  Background The Women's Health Study (WHS) was a randomized trial testing low-dose aspirin and vitamin E for preventing cancer and CVD among 39,876 women aged ≥45 years throughout the US from 1992-2004. When the trial ended as planned, women who were willing to participate continued in an observational follow-up study. Participants in Accelerometer Study From 2011-2015, an ancillary study collected data on physical activity and sedentary behavior using accelerometers. Women were mailed a triaxial accelerometer (ActiGraph GT3X+, ActiGraph Corp) with a wear log, and asked to wear this on their hip for seven consecutive days, removing it only during sleep and water-based activities. Further details have previously been published (PMID: 30666321). A total of 17,708 women wore and returned their devices, and data were downloaded from the devices of 17,466 women; no data were available from the other 242 (device failure). By convention, a "valid day" of wear has data on at least 10 hours (PMID: 22698174). Among these 17,466 women, 17,062 had at least one valid day of wear. The data are provided for all 17,062 women. Additionally, "compliant wear" is conventionally defined for participants wearing the device for at least 10 hours, on at least 4 days (PMID: 22698174). Of the 17,062 women, 16,741 had compliant wear (PMID: 29109088). Self-reported Physical Activity and Sedentary Behavior After we received the accelerometer from a WHS participant, she was sent a questionnaire asking her to report the time she spent in different physical activities during the week that the accelerometer was worn (see questionnaire below). A total of 15,514 women (91% of participants in the Accelerometer Study) returned their physical activity questionnaires. In addition, beginning in October 2012, we included questions on sedentary behavior; a total of 9,430 women returned questionnaires that included questions on both physical activity and sedentary behavior.

  Study phs001964

• Targeted sequencing data of cfDNA, archival tissue, and WBC from 208 patients with mUC

  Targeted tissue (n=81), cfDNA (n=319), and WBC (n=208) Illumina sequencing of metastatic urothelial carcinoma patients. All cfDNA is collected in the metastatic setting, while archival tissue is from across the disease course. White blood cell (WBC) samples are used as patient matched germline samples. All files are in paired-end fastq format.

  Dataset EGAD50000002089

• Targeted sequencing data of cfDNA, archival tissue, and WBC from 226 patients with mUC

  Targeted tissue (n=210), cfDNA (n=402), and WBC (n=245) Illumina sequencing of metastatic urothelial carcinoma patients. All cfDNA is collected in the metastatic setting, while archival tissue is from across the disease course. White blood cell (WBC) samples are used as patient matched germline samples. All files are in paired-end fastq format.

  Dataset EGAD50000001571