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• Genetic architecture of disease in Greenland is shaped by demographic history, fine-structure, and selection - WGS data

  This data was generated as part of the project titled "Genetic architecture of disease in Greenland is shaped by demographic history, fine-structure, and selection." The study was carried out to investigate the genetic architecture of the Greenlandic population and the consequences it has for disease mapping, diagnosis and prediction.

  Study EGAS50000000657

• Genetic architecture of disease in Greenland is shaped by demographic history, fine-structure, and selection - MEGA chip data

  This data was generated as part of the project titled "Genetic architecture of disease in Greenland is shaped by demographic history, fine-structure, and selection." The study was carried out to investigate the genetic architecture of the Greenlandic population and the consequences it has for disease mapping, diagnosis and prediction.

  Study EGAS50000000658

• PRDM9 loss of function follow up from Born-in-Bradford Autozygosity sequencing

  In the autozygosity exome sequencing of Born-in-Bradford samples of Pakistani origin there is a mother who is homozygous for an apparent truncating stop codon in PRDM9, the gene responsible for localising recombination during meiosis. We plan to deep sequence mother and child with X10, and physically phase the mother with PacBio sequencing. We will use this data to identify recombination locations, and test whether these are consistent with the known fine scale recombination map. Data Access is controlled by the Wellcome Trust Sanger Institute DAC and the Born In Bradford Executive Group.

  Dataset EGAD00001001686

• Deletion of FUNDC2 and CMC4 on chromosome Xq28 is sufficient to cause hypergonadotropic hypogonadism in men

  Hypergonadotropic hypogonadism (HH) is characterized by low sex steroid levels and secondarily elevated gonadotropin levels with either congenital or acquired etiology. Genetic factors leading to HH have yet to be fully elucidated. We submit genome and transcriptome data analyses from a male patient with HH and history of growth delay who has an inherited deletion of chromosome Xq28. Expression analyses were done for this patient and his unaffected family members, and compared to normal controls to identify dysregulated genes due to this deletion. Our patient's Xq28 deletion is 44,806 bp and contains only two genes, FUNDC2 and CMC4. Expressions of both FUNDC2 and CMC4 are completely abolished in the patient. Gene ontology analyses of differentially expressed genes in the patient in comparison to controls show that significantly up-regulated genes in the patient are enriched in Sertoli cell barrier regulation, apoptosis, inflammatory response and gonadotropin-releasing regulation. Indeed, our patient has an elevated FSH level, which regulates Sertoli cell proliferation and spermatogenesis. In his mother and sister, who are heterozygous for this deletion, X-chromosome inactivation is skewed towards the deleted X, suggesting a mechanism to avoid FSH dysregulation. Compared to the previously reported men with variable sized Xq28 deletions, our study suggests that the loss of function of FUNDC2 and/or CMC4 results in dysregulation of apoptosis, inflammation and FSH, and is sufficient to cause Xq28-associated HH.

  Study phs002234

• NHLBI GO-ESP Family Studies: Pulmonary Arterial Hypertension

  The NHLBI "Grand Opportunity" Exome Sequencing Project (GO-ESP), a signature project of the NHLBI Recovery Act investment, was designed to identify genetic variants in coding regions (exons) of the human genome (the "exome") that are associated with heart, lung and blood diseases. These and related diseases that are of high impact to public health and individuals from diverse racial and ethnic groups will be studied. These data may help researchers understand the causes of disease, contributing to better ways to prevent, diagnose, and treat diseases, as well as determine whether to tailor prevention and treatments to specific populations. This could lead to more effective treatments and reduce the likelihood of side effects. GO-ESP is comprised of five collaborative components: 3 cohort consortia - HeartGO, LungGO, and WHISP - and 2 sequencing centers - BroadGO and SeattleGO. Pulmonary arterial hypertension (PAH) is a progressive disease characterized by widespread occlusion of the smallest arteries of the lungs. Pulmonary vascular obstruction leads to increased pulmonary vascular resistance, which subsequently causes heart failure with mean survival of 3 years. PAH occurs at all ages and affects women more than twice as frequently as men. Sporadic Idiopathic pulmonary arterial hypertension (IPAH), comprises 94% of what was formerly known as primary pulmonary hypertension, and is clinically and pathologically indistinguishable from familial PAH (FPAH). Most FPAH is due to mutation in BMPR2, including more than 120 families in the US. Our goal here is to find other genes that are a basis for FPAH, so we selected for exome sequencing 5 families among 40 who do not have mutation in BMPR2, or other known genes (ACVRL1, SMAD8, ENG) that rarely are the basis for FPAH.

  Study phs000354

• Gabriella Miller Kids First Pediatric Research Project in Microtia in Hispanic Populations

  The Gabriella Miller Kids First Pediatric Research Program (Kids First) is a trans-NIH effort initiated in response to the 2014 Gabriella Miller Kids First Research Act and supported by the NIH Common Fund. This program focuses on gene discovery in pediatric cancers and structural birth defects and the development of the Gabriella Miller Kids First Pediatric Data Resource (Kids First Data Resource). All of the WGS and phenotypic data from this study are accessible through dbGaP and kidsfirstdrc.org, where other Kids First datasets can also be accessed. Microtia is a rare congenital deformity of the external ear, the pinna. The severity of microtia is variable and ranges from subtle deformities in the pinna to absence of the external ear. Microtia is often associated with closure of the external auditory ear canal causing significant hearing loss. Microtia can be an isolated, unilateral or bilateral malformation, or occur solely with ear canal deformities, or with additional craniofacial or syndromic manifestations. Earlier studies of identical twins with microtia demonstrated a significant genetic contribution. The molecular pathogenesis for most microtia remains unknown. We propose to leverage our clinical acumen in diagnosis and treatment of microtia (R.E.), our relationship to the microtia community (M.T.) and our collected DNA samples from microtia patients to identify genetic variant(s) that contribute to this congenital malformation. Microtia prevalence is much higher among Native Americans and some Latin Americans (17 per 10000 Ecuadorian births) than among individuals of European-descent (0.6 -1.6 per 10,000 births). To capitalize on this epidemiologic data, we have recruited microtia cohorts from Latin America and the U.S, including clinical data and DNA samples.

  Study phs002172

• Gene-Environment Interactions (GxE) and Complex Traits

  Functional variants associated with complex traits tend to fall in non-coding regions and affect regulatory mechanisms that are not yet well characterized. Furthermore, it is generally difficult to determine in which tissues and conditions they may have a functional impact. This is because the effect of a genetic variant on a molecular pathway, and ultimately on the individual's phenotype, may be modulated by "environmental" factors. We denominate such variants "gene-expression environment-specific quantitative trait nucleotides" GxE-QTNs. Achieving a better understanding of the mechanisms underlying GxE is a critical step in understanding the link between genotype and complex phenotype. It is also crucial to develop computationally efficient and statistically sound methods capable to integrate tissue/condition-specific functional genomics data to predict and validate when a sequence variant is functional. In this study we developed novel experimental and computational approaches to screen, analyze and functionally characterize genetic variants for complex traits modulated by environmental exposures. To identify and characterize genes with GxE, we analyzed allele specific gene expression in a panel of five relevant tissues (e.g. the vascular endothelium for cardiovascular diseases) under 50 controlled environmental conditions (e.g. glucocorticoids treatment, as a proxy for stress exposure). These data should be useful to develop computational tools that integrate different sources of evidence including data collected by ENCODE, RoadMap Epigenome and GTEx projects to functionally annotate GWAS variants. The experimental and computational tools developed by this project have widespread applicability, for example, can be used to tackle the functional basis of complex traits in other environmental contexts (e.g. other types of stress and hormonal levels) and genetic backgrounds. This resource represents the first comprehensive catalog of genetic variants that interact with environmental exposure in determining human complex traits.

  Study phs001176

• 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

• Center for Common Disease Genomics [CCDG] - Neuropsychiatric: Epilepsy: Epi25 Consortium

  Epilepsy genetics research is at an exciting stage where it is now feasible, with the power of a large cohort, to understand the more complex genetic components of epilepsy. The driving principle behind the Epi25 Consortium is collaboration and synergy - it is only possible to achieve this type of research by working together. The Epi25 Consortium was formed by the unification of various consortia, including Epi4K, EPIGEN, EuroEPINOMICS, the Epilepsy Phenome/Genome Project, EpiPGX, SANAD, and EpiCURE, and individual epilepsy investigators. The consortium's sample collection is the best resource in the world for this disease, both in terms of numbers of patients and quality of phenotypic information. As part of the NHGRI Centers for Common Disease Genomics (2016-2020), we aggregated a global sample collection from the various repositories for whole genome genotyping and whole exome sequencing (WES) at the Broad Institute (Cambridge, MA), initiating the largest and most ethnically diverse genetic study of epilepsy to date. The primary epilepsy phenotypes for Epi25 are based on strict standards agreed upon by the epilepsy community. The epilepsy cases contributed by Epi25 sites can be broadly defined as genetic generalized epilepsy (GGE), non-acquired focal epilepsy (NAFE), epileptic encephalopathies (EE), and lesional focal epilepsies. More information about eligibility criteria and phenotyping forms for Epi25, as well as the contributing centers, can be found here: epi-25.org The genomic data will be analyzed iteratively to identify genes and variants that explain these types of epilepsy. Summary clinical data compiled in the Epi25 clinical database will allow retrospective phenotypic analyses of groups of subjects with common genomic variant(s).

  Study phs001489

• Integrative genomic profiling of hepatocellular adenomas reveals recurrent FRK activating mutations and mutational processes of malignant transformation

  Hepatocellular adenomas (HCA) are benign liver tumors predominantly developed in women using oral contraception. Here, exome sequencing identified novel recurrent somatic FRK mutations that induce constitutive kinase activity, STAT3 activation and cell proliferation sensitive to Src inhibitors. We also found new recurrent mutations activating JAK1, gp130 or ß-catenin. Chromosome copy-number and methylation profiling revealed patterns that correlated with specific gene mutations and tumor phenotypes. Finally, integrative analysis of HCA transformed to hepatocellular carcinoma revealed ß-catenin mutation as an early alteration and TERT promoter mutations as associated with the last step of the adenoma-carcinoma transition. In conclusion, we identified the genomic diversity in benign hepatocyte proliferation, new therapeutic targets and the key genomic determinants of the adenoma-carcinoma transformation sequence. Significance: Malignant transformation of benign adenoma into malignant carcinoma is frequently observed in several epithelial tumor types. Adenoma-carcinoma transition is crucial for the patient prognosis, however, little is known on the molecular mechanisms involved. Here, we performed an integrated genomic analysis of hepatocellular adenomas (HCA). Among several novel gene mutations, we identified recurrent somatic mutation activating FRK, a Src-like kinase. FRK activating mutations induce STAT3 activation and cell proliferation that can be targeted by Src inhibitors. Focusing on malignant transformation of HCA in hepatocellular carcinoma, we identified CTNNB1 and TERT promoter mutation as early and late genomic events involved in adenoma-carcinoma transition. In conclusion, we propose new therapeutic targets and an identification of adenomas with the highest risk of malignant transformation. Highlights: - FRK is activated by somatic recurrent mutations. - FRK mutants promote cell proliferation sensitive to src inhibitors. - CTNNB1 activation is an early event in HCA transformation. - TERT promoter mutations are associated with adenoma-carcinoma transition.

  Study EGAS00001000679