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• Embryonal Rhabdomyosarcoma sequencing data

  This study shares DNA and RNA sequencing data from embryonal rhadbomyosarcoma patients

  Study EGAS00001005502

• Epithelioid sarcoma sequencing data

  This study shares DNA and RNA sequencing data from Epithelioid sarcoma patients

  Study EGAS00001005983

• Rhabdoid tumor sequencing data

  This study contains sequencing DNA and RNA sequencing data for rhabdoid tumors

  Study EGAS00001006351

• nNGM analysis of treatment-naive MIBC and NMIBC

  nNGM analysis of treatment-naive MIBC (N=49) and NMIBC (N=16).

  Dataset EGAD00001010899

• Clonal evolution study of Intrahepatic cholangiocarcinoma: 69 PDPCs and 6 tissues.

  Clonal evolution study of Intrahepatic cholangiocarcinoma: 69 PDPCs and 6 tissues.

  Dataset EGAD00001003574

• Whole genome and whole exome sequencing of ATCWGS42

  This dataset contains whole genome and whole exome sequencing data of ATCWGS42

  Dataset EGAD50000002147

• Longitudinal Study of Immune Mediated Disorders After Allogenic Hematopoietic Cell Transplantation (HCT)

  Allogeneic hematopoietic cell transplantation (HCT) is the only known curative option for many hematologic disorders. After transplantation, many patients develop immune mediated disorders that may be life-threatening. Post-HCT immune mediated disorders are rare relative to other diseases but the prototype of graft versus host disease (GVHD) develops in 30-70% of patients. The morbidity and mortality associated with these HCT-associated immune mediated disorders are major barriers to successful use of transplantation to cure rare hematologic malignancies such as leukemia, lymphoma, multiple myeloma, myelodysplastic/myeloproliferative syndromes amongst other diseases. The purpose of this study is to characterize and more completely define the onset and course of immune mediated disorders after allogeneic HCT, focusing on participants who develop cutaneous sclerosis, bronchiolitis obliterans syndrome (BOS), late acute graft-vs.-host disease (GVHD), and chronic GVHD. Of the participants undergoing allogeneic hematopoietic cell transplantation (HCT), can we, the researchers better identify who will develop immune-mediated disorders, what types of disorders participants will have, and whether these disorders will be severe or respond to currently available therapies? This is a longitudinal study of 1118 individuals (1081 adults and 100 children). Those participating in this study will be evaluated over a 3 year period at 9 study sites. Participants will be enrolled pre-transplant, or up to day 121 post transplantation. This wide enrollment window will allow sites to use recruitment methods that are most efficient at their institutions. At least 2 years of follow-up will ensure an adequate sample size, and sufficient time for observation of the full spectrum of immune mediated disorders. The data of 1023 individuals have been submitted to dbGaP.

  Study phs001331

• Exome Sequencing to Identify Medically Relevant Associations in Finnish Sub-Isolate Samples from the FINRISK Cohort

  We propose to undertake, at the McDonnell Genome Institute of Washington University, a collaborative exome sequencing project of ~10,000 samples from a large Finnish population cohort, FINRISK, a participating component of the Sequencing Initiative Suomi (SISu) consortium. Together these sequenced samples will provide a unique resource for identification of infrequent or rare variants with a large impact on cardiovascular and metabolic disorders as well as on a wide range of heritable, disease-related quantitative phenotypes. Our collaborative group has already shown, in exome sequencing studies of smaller Finnish samples, that numerous loss of function variants are dramatically more frequent in Finland compared to other European populations, and that such variants demonstrate strong associations to several disease-related traits. Finland is the largest population isolate in Europe and the enrichment of these variants reflects its rapid growth from a severe population bottleneck about 100 generations ago. Northern and Eastern parts of Finland experienced additional, more recent bottlenecks, and therefore the enrichment of particular high-impact variants in these regions is even more extreme (Stoll et al., 2013, PMID: 23912948). We therefore propose to focus exome sequencing efforts on about 10,000 members of FINRISK who are specifically drawn from these sub-isolate regions. As a very wide range of phenotypes are available from this cohort (including cardiovascular and metabolic disease outcomes obtained from national registries) we hypothesize that the proposed exome sequencing will identify numerous new disease-related associations. Within the National Biobanks of Finland (www.nationalbiobanks.fi) we have DNA and tissue samples from over 200,000 individuals of whom 50,000 have GWAS data; these samples provide an exceptional resource for both imputation from the sequencing studies proposed here, as well as for replication of associations.

  Study phs000756

• Genetic Analysis of Parkinson's Disease

  A portion of the sample includes multiplex PD families recruited as part of a previously funded study (R01NS037167; PI: Tatiana Foroud). Families were ascertained initially through a living affected sibling pair. Subsequently, ascertainment was loosened to include PD probands having a positive family history of PD in a first degree relative, who was not required to be part of the study. All individuals completed an in-person evaluation at one of the > 65 Parkinson Study Group sites participating in this study. Individuals completed a detailed evaluation that included the Unified Parkinson Disease Rating Scale (UPDRS), Mini-Mental State Examination (MMSE), Geriatric Depression Scale (GDS) and a diagnostic checklist that implemented the UK PD Brain Bank inclusion and exclusion criteria. An autopsy program was established in this study and brain tissue for confirmation of diagnosis and further experimental study are available from over 100 participants. Autopsy confirmation of the PD diagnosis was nearly 100% for those who met UK PD Brain Bank criteria. In addition, because this was a cross sectional study and family members were often seen very early in disease course, among those who did not meet UK PD Brain Bank criteria but had a subsequent autopsy, a significant subset (>1/3) had autopsy confirmation of PD. The second source of samples is from the NINDS Human Genetics DNA and Cell Line Repository located at the Coriell Institute. Currently DNA from 4,509 PD patients is available from the Coriell Institute. We restricted the selected sample to include only Caucasians and ensured there was no overlap with samples contributed by the PROGENI Study.

  Study phs001004

• Binding of Epstein Barr Virus EBNA2 Unifies Multiple Sclerosis Genetic Mechanisms

  This study is focused on multiple sclerosis (MS). MS is likely caused by a combination of genetic and environmental factors; however, the mechanisms contributing to these factors remain poorly understood. Epstein-Barr virus (EBV) in particular is a well-established environmental risk factor for MS. We have created a computational algorithm that systematically searches for common molecular mechanisms that might be impacted at multiple MS-associated loci. Using this algorithm, we have discovered that over 40% of MS-associated loci contain MS genetic variants that fall within regions of the human genome occupied by the EBV-encoded EBNA2 protein. The same MS-associated variants also impact gene expression levels of MS-associated genes in EBV-infected B cell lines. Our hypothesis is that allele-dependent binding of EBNA2 and its co-factors explains the allele-dependent risk at many MS genetic loci. Importantly, this hypothesis links the genetic associations of MS to the known molecular roles played by EBV and Notch signaling in disease processes.Subjects with and without MS were recruited into an Institutional Review Board (IRB)-approved protocol through the Cincinnati Autoimmune Registry and Repository. From each subject, DNA from peripheral blood was isolated for whole genome sequencing (WGS). These data will be used to identify genotype-dependent transcriptional regulation in cells assessed from patients and controls. This WGS data was deposited before the full integration of sequence data with other functional genomic data types.From each subject, 90 mL of blood is drawn for isolation of peripheral blood mononuclear cells from which primary B and T cells will be isolated. For each B cell isolation, an EBV-transformed B cell line will be derived.

  Study phs003240