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• Honolulu Heart Program (HHP-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions. Access to Biospecimens is through the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC). Biospecimens from HHP include DNA, plasma, serum, and whole blood. Please note that use of biospecimens in genetic research is subject to a tiered consent. Objectives: The initial objectives of the Honolulu Heart Program were to: 1) estimate morbidity and mortality from coronary heart disease and stroke among Japanese men in Honolulu; 2) compare morbidity and mortality from coronary heart disease and stroke among Japanese men in Japan, Honolulu, and San Francisco; 3) investigate relationships among risk factors, coronary heart disease, and stroke in Japanese men in Honolulu; 4) compare distributions of risk factors among men in Japan, Honolulu, and San Francisco, and relate similarities and differences in risk factors to the occurrence of disease in these areas and in other populations, including Framingham and Puerto Rico; 5) conduct an autopsy study, and to relate pathological findings to morbidity and mortality data; and 6) investigate relationships between risk factors and pathological evidence of atherosclerosis and its complications.Background: The Honolulu Heart Program was initiated in 1965 by the NHLBI as a prospective study of environmental and biological causes of cardiovascular disease among Japanese Americans living in Hawaii. This population was known to have low incidence of coronary heart disease and higher incidence of stroke. The study provided opportunities to investigate relationships among disease frequencies, pathologic findings, and disease predictors in the cohort and to compare the findings in this population with those in other populations, especially cohorts of Japanese men resident in Japan or the U.S.Participants: There were 8006 participants.Design: The study began in 1965 with the first examination of a cohort of 8,006 Japanese-American men residing on the island of Oahu, Hawaii who were born during the period 1900-1919. The first examination was completed in 1968 and was followed by the initiation of a second examination that same year. Three subsequent sub-examinations (Lipoprotein Exams I, II and III) were conducted between 1970 and 1982 to collect lipid measurements on a subset of those who participated in Exam II. The fourth examination of surviving members of the original cohort was conducted during 1991-93 and collected data on 3,741 men. Morbidity and mortality follow-up continues through grant and contract-supported efforts, and the current HHP dataset includes events through 1998.

  Study phs003907

• Mapping Disease Pathways for Biliary Atresia

  Biliary atresia (BA) is a poorly understood rare disease that causes jaundice and liver failure at birth due to underdeveloped bile ducts. Associated defects include poor development of the portal vein and involvement of non-hepatic organs. After initial surgical drainage in all patients, the majority need liver transplantation because of progressive cirrhosis. In addition to the risks of lifelong immunosuppression after liver transplantation, the post-transplant biliary atresia patient can experience surgical complications like portal vein thrombosis along with the consequences of extrahepatic involvement often found in affected patients. To determine the genetic basis of this disease, a genome-wide association study of 811 BA cases, all of whom received liver transplantation, and 4654 controls was performed with a 2.5 million SNP array. The study found that BA associates with polygenic risk conferred by over 6000 common variants, minor allele frequencies >1%, in 102 ciliogenesis and planar polarity effector genes (CPLANE). Whole genome sequencing of 100 of 811 cases revealed that most cases harbored rare variants, allele frequencies Whole genome genotyping, gene expression and whole genome sequencing data is being made available.

  Study phs003458

• Whole Genome Sequencing for Metastatic Mutational Burden in Extraskeletal Myxoid Chondrosarcoma

  Extraskeletal myxoid chondrosarcoma (EMC) is an ultra-rare cancer. Though it has a favorable prognosis and an indolent course, it has high rates of local recurrence and metastasis to the lungs. EMC is most often characterized by a translocation involving the NR4A3 gene most often fusing with EWSR1, leading to constitutive expression of NR4A3, the biological significance of which is unknown. Our study presents a case of EMC with case-matched lung and advanced pelvic metastases. We conducted Whole Genome Sequencing to examine differences in the mutational landscape at two different stages of metastasis. This is the first study to our knowledge to analyze mega-base scale structural variants (SVs) in EMC. Our data validates copy number variants (CNVs) found in previous studies. While the primary tumor and lung metastasis had similar somatic variations and CNVs, the pelvic metastasis had more SVs with especially increased mutational burden of SVs in chromosome 2. This suggests that different molecular drivers appear in more advanced, relapsing EMC compared with the primary tumor and early lung metastasis. The sequencing data is available through dbGaP.

  Study phs003305

• NHLBI TOPMed: Trans-Omics Analysis for Congestive Heart Failure (TOPCHeF)

  Heart failure (HF) is a serious, common, morbid condition that has a huge public health impact. In 2012 alone, there were >1M hospital discharges and >1.7M outpatient visits where HF was the principal diagnosis. HF is the most common hospital discharge diagnosis of the elderly and led to costs in excess of $30B in 2012. Unfortunately, HF therapies have not impacted the 50% 5-year mortality over the past two decades. Our laboratory focuses on cardiomyopathies (CMs) and HF. Dilated cardiomyopathy (DCM) has been a main focus of our laboratory and is the first and third most frequent cause of heart transplantation and HF, respectively. Attention is shifting from the mere identification and cataloging of CM/HF genes and mutations to understanding the molecular and functional cellular processes that drive HF. In this study, we will utilize whole genome sequencing (WGS) and transcriptome analysis of left ventricle samples from adult and pediatric samples from heart banks at the University of Colorado Anschutz Medical Campus and the Children's Hospital Colorado to develop a complete understanding of left ventricular biology and a partial understanding of HF inferred through the lens of a single-chamber perspective.

  Study phs002038

• Development of a diagnostic gene panel for Gorlin syndrome and its application to liquid biopsy

  Gorlin syndrome is an autosomal dominant, rare disease caused by mutations in PTCH1, PTCH2, and SUFU with various symptoms in multiple organs making early diagnosis challenging. In this study, we generated a Gorlin syndrome gene panel that could help to overcome the difficulties in diagnosing Gorlin syndrome using a single test. This gene panel is time- and cost-efficient and highly reliable with a high-quality score of 30, on-target ratio, and coverage depth, and could detect more mutations than whole-exome sequencing of the same patient. Although the current in silico prediction tools have a limited genetic database of gene mutations in rare hereditary diseases, five prediction tools were used to identify pathological mutations. Pathogenic gene mutations were detected not only in PTCH1 but also in PTCH2 in five out of 12 patients with Gorlin syndrome diagnosed based on clinical symptoms. Using this gene panel, we showed the same gene mutation in the patients and their asymptomatic relatives; hence, it has enabled a highly reliable genetic diagnosis of Gorlin syndrome at a low cost requiring only blood sample.

  Study JGAS000308

• UK10K_COHORT_ALSPAC REL-2011-12-01

  For information about this sample set, please contact the sample custodian Nic Timpson: N.J.Timpson@bristol.ac.uk

  Dataset EGAD00001000195

• Tumor transcriptome profiling from the OAK and POPLAR randomized clinical trials of atezolizumab in 2L NSCLC

  This dataset includes full tumor transcriptomes from 891 advanced NSCLC tumors. These data originate from pre-treatment samples from two large randomized clinical trials for second-line non-small cell lung cancer (POPLAR and OAK). The patients in these trials were treated with either the PD-L1 inhibitor atezolizumab or chemotherapy.

  Dataset EGAD00001007703

• Targeted and Whole Exome Sequencing for Validation of PGDx elio tissue complete

  This dataset consists of 116 tumor and normal samples analyzed with whole exome sequencing on the HiSeq2500 instruments with 100bp paired-end reads as well as 760 tumor and normal samples analyzed with the PGDx elio tissue complete assay. The PGDx elio tissue complete assay is a hybrid capture approach targeting 500+ genes with sequencing on the NextSeq instruments with 150bp paired-end reads. The bam files provided have been adapter masked and contain duplicate reads.

  Dataset EGAD00001008099

• RNA-Seq of 584 DLBCL Cases of Non-China Cohort from Phoenix Clinical Trial

  Standard RNA-Seq datasets. Check the associated paper for more details.

  Dataset EGAD00001008131

• Dataset for neuroendocrine_adrenal_tumor-RNA

  Rare cancer sequencing data of 145 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008862