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• Circular RNA characterization in functionally distinct brain regions

  Circular RNAs (circRNAs) represent a class of endogenous, non-coding RNAs that are formed when exons back splice to each other and that are both highly conserved and pervasively expressed in the mammalian brain. The goal of this study was thus to systematically identify and characterize circRNA expression and as well as to evaluate the predicted impact on regulatory networks in five functionally distinct cortical regions of healthy aged human brain - cerebellum (BC), inferior parietal lobe (IPL), middle temporal gyrus (MTG), occipital cortex (OC) and superior frontal gyrus (SGF).

  Study EGAS00001003128

• HipSci expression microarray for embryonic stem cell control lines

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we use commercially available embryonic stem cell lines as control samples against which to compare HipSci's iPS cell lines. We performed expression analysis using the Illumina HumanHT -12 Expression BeadChip.

  Study EGAS00001001729

• Human periportal liver assembloids recapitulate periportal liver tissue in vitro

  In vitro expansion of human hepatocytes from fresh patient tissues has not yet been achieved, limiting the possibility of modelling liver composite structures in vitro. Here, we developed human hepatocyte organoids from patient-donors that sustain the long-term expansion of hepatocytes in vitro. We profiled them using RNAseq to determine their gene expression pattern and compared this with the original native fresh isolated liver cell. Then, we used them to generate periportal liver assembloids by combining them with portal mesenchyme and cholangiocyte organoids. By increasing the number of mesenchymal cells we obtained structures with a fibrotic ratio of portal mesenchyme and we performed scRNAseq analysis to determine their gene expression and cell-cell interactions.

  Study EGAS50000000994

• Comprehensive Analysis of Structural Variants in Breast Cancer Genomes Using Single Molecule Sequencing

  This study used the SKBR3 breast cell line and tumor/normal organoids derived from breast tissue to explore the utility of long read sequencing for detecting structural variants in complex samples. Three technologies were used to characterize the samples: Illumina/10X, Pacific Biosciences, and Oxford Nanopore. Methylation results were derived from the Oxford Nanopore data. It is hoped that this resource will better help researchers better understand the utility of long read sequencing in cancer samples.

  Study phs002210

• Pilot experiment on functional genomics in osteoarthritis_RNA

  The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of large joint (hip and knee) osteoarthritis which culminates in the need for total joint replacement (TJR). In this pilot we will assess the feasibility of the approach in the relevant tissue. We will obtain diseased and non-diseased tissue (cartilage and endochondral bone) following TJR, coupled with a blood sample, from 12 patients. We will characterise the 12 pairs of diseased and non-diseased tissue samples in terms of transcription (RNASeq) The pilot will help assess the feasibility of isolating sufficient levels of starting material for the different approaches, and will instigate the development of analytical approaches to synthesising the resulting data.

  Dataset EGAD00001001331

• Starr County Health Studies' Genetics of Diabetes Study

  An initial observation in the 1970s that Starr County, Texas, had the highest diabetes-specific mortality of any of the 254 Texas counties led to the establishment of a field office in Rio Grande City, Texas (the county seat of Starr County) and the initiation of a series of studies to understand the epidemiology and genetics of type 2 diabetes, its complications and related conditions in this predominantly (97%) Mexican American population. The field office opened in February 1981 and has operated continuously since then. During this time, three systematic surveys of the population have been conducted as well as family and longitudinal studies. Culturally sensitive diabetes education programs have been developed and implemented and also a weight loss intervention. In total, more than 23,000 Mexican American individuals have been examined with more than 200,000 aliquots of biological specimens stored. Collectively, these studies are known as the Starr County Health Studies. The present Genetics of Diabetes Study has the goal of identifying loci/alleles that underlie susceptibility to type 2 diabetes in this high risk population using genome wide markers and association testing. The study makes use of two primary resources that have been developed in order to identify 1,000 type 2 diabetes cases and 1,000 disease free controls. In the first instance we have identified a subset of unrelated cases from the total cases that we have identified. Where multiply affected sibships were available, the youngest onset case with detailed phenotyping (including assessment of diabetic retinopathy) was selected. Controls came from a recent survey to establish a representative sample of the Starr County population. Blocks were randomly selected, households on selected blocks enumerated and one individual randomly selected from each household for a detailed examination. The examination included an oral glucose tolerance test. Those included as controls are those with no prior diagnosis of diabetes and a negative oral glucose tolerance test. This collection of cases and controls provides the opportunity to identify susceptibility loci for type 2 diabetes and its complications, specifically diabetic retinopathy and albuminuria. The data set also allows the examination of impaired fasting glucose and impaired glucose tolerance. The samples are split between those born in the United States and those born in Mexico and this gives a natural contrast for examining genotype and environmental interactions. It is anticipated that the understanding that will come will lead to strategies for delaying and preventing the onset of diabetes and its complications.

  Study phs000143

• A New CA19-9 Cut-Off Value Identifies Lewis Antigen Status and Refines Prognostic Stratification in PDAC

  This study investigates the clinical utility of serum CA19-9 levels in pancreatic ductal adenocarcinoma (PDAC), with a focus on identifying patients with Lewis antigen–negative status due to germline FUT3 variants. Using data from multicenter prospective cohorts in Taiwan, we analyzed CA19-9 classification, FUT2/FUT3 genotypes, and clinicopathological annotations. The goal of this study is to refine prognostic stratification and reduce false-negative interpretation of CA19-9 in PDAC patients. All participants provided informed consent, and the study was approved by the relevant institutional review boards.

  Study EGAS50000001575

• Knoll et al Identification of drug candidates targeting monocyte reprogramming in people living with HIV

  Introduction People living with HIV (PLHIV) are characterized by functional reprogramming of innate immune cells even after long-term antiretroviral therapy (ART). In order to assess technical feasibility of omics technologies for application to larger cohorts, we compared multiple omics layers. Methods Bulk and single-cell transcriptomics, flow cytometry, proteomics, chromatin landscape analysis by ATAC-seq as well as ex vivo drug stimulation was performed in a small number of blood samples derived from PLHIV and healthy controls from the 200-HIV cohort study. Results Single-cell RNA-seq analysis revealed that most immune cells in peripheral blood of PLHIV are altered in their transcriptomes and that a specific functional monocyte state previously described in acute HIV infection is still existing in PLHIV while other monocyte cell states are only occurring acute infection. Moreover, a reverse transcriptome approach on a rather small number of PLHIV was sufficient to identify drug candidates for reversing the transcriptional phenotype of monocytes in PLHIV. Discussion These scientific findings and technological advancements for clinical application of single-cell transcriptomics form the basis for the larger 2000-HIV multicenter cohort study on PLHIV, for which a combination of bulk and single-cell transcriptomics will be included as the leading technology to determine disease endotypes in PLHIV and to predict disease trajectories and outcomes.

  Study EGAS00001007460

• HeLa Cell Genome Sequencing Studies

  HeLa is a human epithelial adenocarcinoma cell line that was derived from biopsy specimens of a 31-year old patient named Henrietta Lacks who was being treated for cervical cancer at The Johns Hopkins University Hospital in 1951. The specimens were obtained without her knowledge or consent just before her death in 1951. HeLa is the oldest and most widely used human cell line and has been an extraordinarily important resource for researchers throughout the world. HeLa cells have served as a standard for understanding many fundamental biological processes, such as testing the polio vaccine, establishing basic techniques for cloning and in vitro fertilization, identifying the cause of cervical cancer (HPV), and advancing the development of anti-cancer drugs.This study contains all authorized whole genome sequence data of the HeLa cell line from datasets currently in dbGaP. These data have been approved for health, medical, and/or biomedical research purposes. Access to these data can be granted for one year. Accessible data will include the studies listed on this page and any additional authorized datasets that become available during this one-year period. The HeLa Genome Data Access Working Group of the Advisory Committee to the Director (ACD) will review requests from the research community for access to these datasets and assess whether the requests align with the terms of use defined in the HeLa Genome Data Use Agreement. The Working Group's findings will be reported to the ACD, and the ACD will make recommendations to the NIH Director about whether a request should be approved or disapproved. The NIH Director will decide whether access to the data will be granted.

  Study phs000640

• Multi-omic analyses from a randomized phase II study of epigenetic priming followed by nivolumab in previously treated metastatic non-small cell lung cancer

  Emergence of resistance to immune checkpoint blockade (ICB) mandates the development of strategies for ICB sensitization. We aimed to understand the effects of epigenetic priming in re-shaping the tumor microenvironment, together with molecular drivers of therapeutic response of epigenetic therapy followed by ICB in non-small cell lung cancer (NSCLC; NCT01928576). This was done through a multi-omic approach encompassing both genomic and transcriptomic analyses. Findings suggest that epigenetic therapy may reshape the tumor microenvironment towards a more inflamed phenotype and prime responses to immunotherapy.

  Study EGAS50000000913

• NHLBI GO-ESP: Lung Cohorts Exome Sequencing Project (Lung Health Study of Chronic Obstructive Pulmonary Disease)

  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. The Lung Health Study I was a randomized multicenter clinical trial with 5887 participants carried out from October 1986 to April 1994, designed to test the effectiveness of smoking cessation and bronchodilator administration in smokers aged 35 to 60 with mild lung function impairment. Participants were randomly assigned to one of three groups: usual care, who received no intervention smoking intervention with the inhaled bronchodilator ipratroprium bromide smoking intervention with an inhaled placebo The effect of intervention was evaluated by the rate of decline of forced expiratory volume in one second (FEV1).

  Study phs000291

• HuBMAP: A Spatially Resolved Molecular Atlas of Human Endothelium

  The human circulatory system plays a vital role in the proper functioning of every organ in the human body. Because vascular related diseases, such as atherosclerosis, do not occur homogeneously throughout the vascular tree, differences in the endothelium of various organs must exist. There is even evidence of heterogeneity of adjacent endothelial cells. We are studying normal endothelium throughout the body and across individuals of different ages to characterize these differences. The first step will be to procure normal tissue samples from a wide range of organs. From disaggregated samples of these tissues, we will perform single cell combinatorial indexing (sci-) to generate chromatin accessibility (sci-ATAC-seq) and transcriptome (sci-RNA-seq) data from millions of single cells across hundreds of samples.  Molecular heterogeneity might correlate with multiple facets of the anatomical distribution of endothelium, including vascular vs. lymphatic, arteries vs. veins, capillaries vs. larger vessels, differences between organs, organ zonation, cell-to-cell differences, etc. Based on heterogeneous markers defined from deep profiling of disaggregated cells, we will employ seqFISH to spatially relate the distinct endothelial subpopulations arising from the single nuclei data to histologic preparations. For example, this will allow us to identify subpopulations with particular markers as arterial, capillary, venous, or lymphatic. The end product will include multiparameter images in which the complete gene expression and chromatin accessibility profile can be interactively visualized for every cell.

  Study phs002267

• Illumina HiSeqX and HiSeq 2000 whole genome sequence data on 3,001 ALS samples including 212 with known C9orf72 repeat expansions

  Whole genome sequence (WGS) data was generated on 3,001 samples previously quantified for the presence of the C9orf72 repeat expansion (212 expanded and 2,789 wild type), These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer. The repeat expansions were called using ExpansionHunter to demonstrate the ability to call large repeats from high throughput, WGS data. Provided here are all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion in addition to reads aligned in pre-determined off target locations where the aligners are known to mis-align reads.

  Study EGAS00001002598

• ProjectMinE :llumina HiSeqX and HiSeq 2000 whole genome sequence data on 3,001 ALS samples including 212 with known C9orf72 repeat expansions

  Whole genome sequence (WGS) data was generated on 3,001 samples previously quantified for the presence of the C9orf72 repeat expansion (212 expanded and 2,789 wild type), These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer. The repeat expansions were called using ExpansionHunter to demonstrate the ability to call large repeats from high throughput, WGS data. Provided here are all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion in addition to reads aligned in pre-determined off target locations where the aligners are known to mis-align reads.

  Study EGAS00001003383

• A personalised medicine approach for ponatinib-resistant chronic myeloid leukaemia

  Chronic myeloid leukaemia (CML) is characterised by the presence of a fusion driver oncogene, BCR-ABL1, which is a constitutive tyrosine kinase. Tyrosine kinase inhibitors (TKIs) are the central treatment strategy for CML patients and have significantly improved survival rates, but the T315I mutation in the kinase domain of BCR-ABL1 confers resistance to all clinically approved TKIs, except ponatinib. However, compound mutations can mediate resistance even to ponatinib and remain a clinical challenge in CML therapy. Here, we investigated a ponatinib-resistant CML patient through whole genome sequencing (WGS) to identify the cause of resistance and to find alternative therapeutic targets.

  Study EGAS00001001150

• Targeted_sequencing_of_blood_DNA_from_Human_twins_

  The goals of this study is to investigate the prevalence and heritability of age-related clonal haemopoeisis (ARCH) in healthy elderly individuals.We will use a bespoke bait set to pull down DNA regions of interest in whole blood samples combined with HiSeq at a deep level . By correlating findings from each individual to their respective twin we hope to elucidate whether heritable traits influence the development of ARCH. a. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002210

• Next Generation Mendelian Genetics: Neonatal Diabetes

  The NHGRI Next Generation Mendelian Genetics project uses exome resequencing to identify variants in unsolved Mendelian diseases. Neonatal diabetes mellitus (ND) is a rare form of monogenic diabetes (90,000-260,000 live births) that is diagnosed in the first 6 months of life. The disease has been classified as transient or permanent and although it can be inherited, more frequently is sporadic as a result of 'de novo' mutations. Defects in 12 genes have been found as responsible for the disease (defects in the paternally imprinted chromosomal region 6q24, IPF1, SLCA2A, INS, EIF2AK3, GCK, FOXP3, GLIS3, PTF1A, HNF1Beta, KCNJ11 and ABCC8). The two subunits of the ATP-sensitive K channel (ABCC8 and KCNJ11) and the insulin gene (INS), account for almost half of the cases and similar to CHI, the other half, remains genetically unexplained. We became part of this study when we submitted 4 DNA samples for exome sequencing, from patients with NDM of Caucasian ancestry, which had no mutations identified in ABCC8 or KCNJ1, with the goal to identify new mutations in known genes or new mutations or genetic variants in new genes.

  Study phs000542

• RNA-Sequencing of B-Lymphoblastic Leukemia with Glucocorticoids and PI3K Delta Inhibition

  Mononuclear cells were isolated from bone marrow or peripheral blood of 7 pediatric subjects with B-lymphoblastic leukemia at the time of diagnosis. To determine the effect of PI3K delta inhibition on glucocorticoid-induced gene regulation, B-lymphoblastic leukemia cells were treated with glucocorticoids +/- the PI3K delta inhibitor, idelalisib, for 24 hours prior to RNA extraction and sequencing. Biological replicates were performed for 4 of the 7 subjects; 2 of these subjects had specimens demonstrating an additive response to the combination of glucocorticoids and idelalisib in viability testing in vitro, and 2 subjects' specimens demonstrated a synergistic response. All 7 subjects were analyzed together and the 4 specimens with biological replicates were also evaluated in an additional analysis. An average of 40 million reads per specimen and treatment condition were obtained. We compared gene expression in each treatment condition to vehicle-treated cells and expression in glucocorticoid or idelalisib only treated cells to combination treated cells. Using a high dose of dexamethasone (25 or 50 nM) and an equivalent dose of prednisolone, we found that the addition of idelalisib (500 nM) enhanced prednisolone-induced gene regulation but not dexamethasone-induced gene regulation. Surprisingly, the specimens with additive response to combination therapy demonstrated enhancement of prednisolone-induced gene regulation with the addition of idelalisib, while the specimens with synergistic responses did not. Raw sequencing data (FASTQ) and count tables will be available through dbGaP.

  Study phs003085

• Uterine leiomyoma: DNA methylation, chromatin activity and gene expression

  In this study, we observed the effects of different uterine leiomyoma driver mutations to tumor DNA methylation, chromatin activity and gene expression, to form a comprehensive view on the epigenetic consequences of the mutations.

  Study EGAS00001004499

• PELICAN33 longitudinal clinical and autopsy phenomic assessment in lethal metastatic prostate cancer

  Objective: To identify novel phenotypes and features associated with metastatic prostate cancer (mPC) outcome, and to identify biomarker and data requirements to be tested in future precision oncology trials. Design, Setting, and Participants: We analyzed deep longitudinal clinical, neuroendocrine expression, and autopsy data of 33 men who died from mPC between 1995 and 2004 (PELICAN33), and related findings to mPC biomarkers reported in the literature. Intervention: 33 men prospectively consented to participate in an integrated clinical-molecular rapid autopsy study of mPC.

  Study EGAS00001005399

• Efficacy of Bitter Taste Blockers on Flavor Acceptance in a Human Population

  The goal of this project is to determine variation in human bitter perception and the effectiveness of bitter blockers in individuals of different genotypes. The project is based on the parent project titled "Efficacy of bitter taste blockers on flavor acceptance in pediatric population", which addresses how bitter taste perception affects medication compliance. As a part of the parent project, mothers and their children were recruited from the general population of metropolitan Philadelphia through print and internet media as well as from a database of past research participants. Adults (mothers) were evaluated in the laboratory for bitter taste perception for a variety of "Generally Recognized As Safe" (GRAS) bitter compounds using the general Labeled Magnitude Scale (gLMS) which allows subjects to rate sensory intensity. Mothers were also evaluated for perception of the liquid formulation of the drug KaletraTM, a recommended 1st line treatment for infants with HIV infection, whose taste is rejected by some children and accepted well by others. DNA samples from mothers were genotyped as a part of this study to identify (1) novel genes associated with human bitter perception and (2) the ability of compounds to block bitterness.

  Study phs000839

• A Phase I Study with a Personalized Neoantigen Cancer Vaccine in Melanoma

  Effective anti-tumor immunity in humans has been associated with presence of T cells targeting neoantigens that arise from non-silent tumor-specific mutations. Here we conducted whole-exome sequencing of tumor and normal cells from individual patients to identify mutations. We assessed the expression of mutated alleles by RNA-sequencing of tumor. We demonstrated the feasibility, safety and immunogenicity of a vaccine that targets up to 20 personal neoantigens predicted to be presented by the autologous patient tumor.Antigen-specific CD8+ T cells that can recognize and eliminate cancer cells play a crucial role in anti-tumor immune responses. Here we conducted single-cell sequencing of cells infiltrating melanoma specimens originating from 4 patients and determine the TCR clonality of the CD8+ tumor infiltrating cells. We investigated the relationship between T cell clonality and phenotypic cell states coupling single-cell transcriptome to single-cell TCR seq. The surface expression of a panel of protein was detected in parallel using CITE-Seq antibodies. Sorted tumor and peripheral blood specimens were processed in parallel.In order to discover cancer antigens derived from annotated and unannotated protein-coding regions of the genome, we carried out matched ribosome profiling (Ribo-seq), RNA-sequencing, and whole genome sequencing on one of the patients, as well as Ribo-seq on an additional patient. We used it to discover novel or unannotated open reading frames (nuORFs), their expression levels, as well as somatic mutations within them to predict potential neoantigens.

  Study phs001451

• EOSC4Cancer Synthetic Colorectal Cancer Genomic data

  In this study there are stored the synthetic datasets produced by partners involved in EOSC4Cancer. The study contains independent datasets available for the research community. The synthetic genomes have been created trying to mimic real cancer data.

  Study EGAS50000000190

• Most HCCs in Taiwan show the mutational signature of aristolochic acid

  Plants in the genus Aristolochia contain the mutagen aristolochic acid (AA) and have been widely used in traditional medicines and for weight loss. AA binds covalently to genomic DNA and induces a highly distinctive mutational signature. While AA involvement in urinary-tract cancers in Taiwan is known, the possible role of AA in hepatocellular carcinomas (HCCs) in Taiwan has not been examined. Here, we whole-exome sequenced 98 unselected HCCs from Taiwan and analyzed the mutational signatures for evidence of AA mutagenesis. Remarkably, more than 78% of HCCs showed strong evidence of AA mutagenesis, often associated with high mutation burdens. Non-synonymous mutations in genes known to be HCC driver genes were detected. Importantly, we elucidated the potential of immunotherapy in this cohort of liver cancer patients.

  Study EGAS00001002301

• A Genome-Wide Association Analysis in Angiotensin-Converting Enzyme (ACE) Inhibitor-Associated Angioedema and ACE Inhibitor-Exposed Controls; A Collaboration between the NIH Pharmacogenomics Research Network and the RIKEN Yokohama Center for Genomic Medicine

  The purpose of this study is to identify genetic predictors of ACE inhibitor-associated angioedema. In addition to preventing the formation of the pressor angiotensin II, ACE inhibitors prevent the carboxyl-terminal degradation of the vasoactive substances bradykinin and substance P. Angioedema is hypothesized to result from defective amino-terminal degradation of bradykinin or substance P in patients in whom ACE is inhibited. For example, activity of dipeptidyl peptidase IV (DPP-IV), the enzyme responsible for the inactivation of substance P when ACE is inhibited, is decreased in patients with angioedema. In preliminary studies, we have identified SNPs in the DPP4 gene that associate with DPP-IV activity and, in blacks, with risk of angioedema. This project will use genome-wide genotyping to compare 250 cases and 568 ACE inhibitor-exposed control subjects (131 cases and 288 controls ascertained at Vanderbilt and 70 cases and 280 controls ascertained at the Marshfield Clinic). We plan a 2-stage analysis of associations between SNPs and angioedema - first, we will study DPP4 SNPs for association with angioedema and, second, we will explore associations using the full GWAS data set. Depending on the platform, additional DPP4 SNPs will be used to fully tag common genetic variants in both African American and European American samples. Based on the HapMap data, there are 14 tagging SNPs in people of European descent and 34 in Yoruba (selection criteria MAF>0.05 and r2>0.8). Cases were defined as having ACE inhibitor-associated angioedema if they had had swelling of the lips, throat, tongue or face while taking an ACE inhibitor but had never had angioedema while not taking an ACE inhibitor. For simplicity, intestinal edema was excluded. Control subjects were treated for at least 6 months with an ACE inhibitor without angioedema. Because black Americans are known to be overrepresented among patients with ACE inhibitor-associated angioedema, control subjects were prespecified to be 50% black American, 50% white American, and 50% female. At Vanderbilt, the medical history, including the history of angioedema, was confirmed by a research nurse or physician using a detailed case report form. Characteristics of Vanderbilt cases appear in the Table. At Marshfield, medical history will be confirmed by chart review. The Marshfield cohort is 98% white American and 57% female with a mean age of 47.2 years.

  Study phs000438

• PEACE melanoma 14

  Understanding the evolutionary pathways to metastasis and resistance to immune checkpoint inhibitors (ICI) in melanoma is critical for improving outcomes. Here we present the most comprehensive intra-patient metastatic melanoma dataset assembled to date as part of the PEACE research autopsy programme, including exome, panel-sequenced, RNA-seq, and single-cell whole-genome sequencing samples from 14 ICI-treated patients. The main goals of the project are to decipher the evolutionary dynamics of melanoma metastases and to elucidate mechnisms of resistance to therapies.

  Study EGAS00001007081

• Mapping the breast cancer metastatic cascade onto circulating tumour DNA using genetic and epigenetic clonal tracking

  Circulating tumour DNA (ctDNA) allows tracking the evolution of human cancers at high resolution, overcoming many limitations of tissue biopsies. However, exploiting ctDNA to determine how a patient’s cancer is evolving in order to aid clinical decisions remains difficult. This is because ctDNA is a mix of fragmented alleles, and the contribution of different cancer cell subpopulations from distinct lesions to ctDNA remains largely unknown. Profiling of ctDNA almost invariably requires prior knowledge of what genomic alterations to track. Here we leverage on a rapid autopsy programme to demonstrate that unbiased genomic characterisation of several metastatic sites and concomitant ctDNA profiling at whole-genome resolution reveals the extent to which ctDNA is representative of widespread disease. We also present a ctDNA methylation profiling method that allows tracking evolutionary changes in the cancer cell population at single-molecule resolution without prior knowledge. These results have critical implications for the use of liquid biopsies to monitor cancer evolution in humans and potentially guide treatment.

  Study EGAS00001004014

• Systolic Blood Pressure Intervention Trial (SPRINT-BioLINCC)

  Available DataThe available data include all elements of the previously released SPRINT Primary Outcome Paper (SPRINT-POP) data, the full SPRINT clinical data including the MRI and MIND data, and select ancillary study data (Ambulatory Blood Pressure Monitoring, APOL1, Acute Kidney Injury, ASK, Heart, FAST, PWV, Renal Resistance, Biomarkers, Plasma AD).ObjectiveThe Systolic Blood Pressure Trial (SPRINT) was conducted to test the hypothesis that treating systolic blood pressure to a target of less than 120 mm Hg, as compared to a target of less than 140 mm Hg, would reduce the incidence of cardiovascular disease.BackgroundHypertension is a highly prevalent condition among adults and is a leading risk factor for myocardial infarction and stroke. Further, isolated systolic hypertension is the most common form of hypertension in adults over 50 years of age. Observational studies have shown a monotonic increase in cardiovascular risk with systolic blood pressures above 115 mm Hg; however, general population clinical trials have only documented the benefits of lowering systolic blood pressure to a target of 150 mm Hg. A 2007 expert panel sponsored by the National Heart, Lung, and Blood Institute designated the hypothesis that lowering the systolic blood pressure goal to a level SubjectsA total of 9361 participants were enrolled, with 4,678 randomized to the intensive-treatment group and 4,683 randomized to the standard-treatment group.DesignSPRINT was a randomized, single blinded (outcome adjudicators were blinded to treatment assignment) treatment trial with participants randomized to a systolic blood-pressure target of either less than 140 mm Hg (the standard-treatment group) or less than 120 mm Hg (the intensive-treatment group). Following randomization, baseline hypertensive regimens were adjusted in accordance with study treatment algorithms established for each group. The study formulary included all major classes of antihypertensive agents. Investigators could prescribe other antihypertensive medications, but the use of drug classes with the strongest evidence for reduction in cardiovascular outcomes was encouraged. This included thiazide-type diuretics as the first-line agent, loop diuretics for participants with advanced chronic kidney disease, and beta-adrenergic blockers for participants with coronary artery disease. Medications for participants in the intensive-treatment group were adjusted on a monthly basis to target a systolic blood pressure of less than 120 mm Hg. Medications for participants in the standard-treatment group were adjusted to target a systolic blood pressure of 135 to 139 mm Hg, and the dose was reduced if systolic blood pressure was less than 130 mm Hg on a single visit or less than 135 mm Hg on two consecutive visits. Lifestyle modification was encouraged as part of the management strategy.Participants were seen monthly for the first 3 months and every 3 months thereafter. Demographic data were collected at baseline. Clinical and laboratory data were obtained at baseline and every 3 months thereafter. A structured interview was used in both groups every 3 months to obtain self-reported cardiovascular disease outcomes. Medical records and electrocardiograms were obtained for documentation of events. Incidences of hypotension, syncope, injurious falls, electrolyte abnormalities, and bradycardia that were evaluated in an emergency department were included in adverse event reporting. Occurrences of acute kidney injury or acute renal failure requiring hospitalization were also monitored. The primary outcome was a composite outcome of myocardial infarction, other acute coronary syndromes, stroke, heart failure, or death from cardiovascular causes.ConclusionsThe blood pressure intervention was stopped in August of 2015 (median follow-up of 3.26 years) after the cardiovascular outcome results exceeded the boundary for efficacy at two consecutive time points. Compared with a systolic blood pressure target of less than 140 mm Hg, an intensive systolic blood pressure target of 120 mm Hg resulted in lower rates of fatal and nonfatal major cardiovascular events and death from any cause. Significantly higher rates of some adverse events were observed in the intensive-treatment group.

  Study phs003483

• NHLBI TOPMed: Pediatric Cardiac Genomics Consortium (PCGC)'s Congenital Heart Disease Biobank

  The Pediatric Cardiovascular Genetics Consortium (PCGC) proposes to define genetic causes for congenital heart defects (CHD) as part of the TOPMed Program are the most common form of heart disease in childhood and are also the most prevalent form of birth defects, occurring in 2-3% of live births. The PCGC has recruited and clinically characterized = 10,000 CHD probands and parents (CHD trios). From whole exome sequencing (WES) of >2800 CHD trios, we identified a substantial enrichment of damaging de novo mutations in genes important for cardiogenesis, particularly implicating histone modifier enzyme gene defects. Analysis of whole genome sequencing (WGS) of 350 probands with CHD unexplained by WES and their parents preliminarily implicated de novo mutations in enhancers of genes previously shown to cause CHD in mouse knock out models. Sequencing of RNA (RNAseq) from discarded cardiac tissues from CHD probands has revealed likely causal allele-specific expression (ASE) as well as biallelic loss of expression (LOE). We have also discovered de novo epimutations, differentially methylated regions (DMRs), some with underlying de novo DNA variation, that are detectable in peripheral blood leukocytes and appear to underlie 10% of CHD. Of note, these assorted 'omic' approaches have enabled one another, both for attributing causality and assessing functional impact. Based on these extensive preliminary data, we hypothesize that PCGC probands with uninformative exomic analyses (WES-negative) harbor de novo genetic and/or epigenetic mutations in critical regulatory elements that participate in developmental expression of cardiac genes. To identify these etiologies, we propose analyses of WGS in 1000 WES-negative CHD trios, prioritizing those with probands with banked CHD tissues (n=78), one damaging variant in a recessive CHD gene, and older fathers (age>45). We also request WGS for 230 probands, for whom we have cardiac tissues but not parental DNAs. We request RNAseq for 308 cardiac tissues. For DNA methylation, which TOPMed will offer through the Illumina 850k array platform, we are requesting analysis of DNAs from peripheral blood leukocytes for all probands for whom WGS will be performed (1000 from trios, 230 singletons) as well as DNAs from cardiac tissues (n=308) to pair with the WGS, RNAseq and blood DNA methylation data. We will use existing resources and capabilities of the PCGC to confirm relevant mutations and those of its companion consortium in the Bench to Bassinet Program, the Cardiovascular Development Consortium, to inform analyses of non-coding mutations as well as to perform confirmatory functional genomics studies using cell and animal models. We expect that the studies resulting from data generated through TOPMed will provide novel insights into the molecular basis for CHD and fundamental knowledge about genes and pathways involved in cardiac development. Aside from being relevant to CHD, we anticipate that our findings will inform the understanding of later-onset cardiovascular diseases, including some arising in adulthood.

  Study phs001735

• Lethal malformation syndrome

  Identification of the genetic basis of rare monogenic diseases can provide insights into disease mechanisms, biological pathways and potential therapeutic targets. Exome sequencing has proven to be a powerful, efficient strategy for the identification of the genes underlying rare Mendelian disorders. The genetic defect behind the lethal malformation syndrome under study is known in some cases and has proven useful in revealing the primary underlying defect. We have six typical unrelated families with no known mutation. The aim of this study is to identify the locus associated with this lethal malformation syndrome in these families using exome sequencing.

  Study EGAS00001000061

• Heart Failure Network - Renal Optimization Strategies Evaluation in Acute Heart Failure and Reliable Evaluation of Dyspnea (HFN ROSE-BioLINCC)

  ObjectivesTo test the two independent hypotheses that when compared to placebo, addition of: (1) low dose dopamine; or (2) low dose nesiritide to diuretic therapy will enhance decongestion and preserve renal function in patients with acute heart failure and renal dysfunction.Background A primary treatment goal in acute heart failure is to achieve adequate decongestion while avoiding renal dysfunction and other side effects. Patients with acute heart failure and moderate or severe renal dysfunction are at risk for inadequate decongestion and worsening renal function - both of which are associated with worse outcomes. Renal adjuvant therapies that enhance decongestion and preserve renal function during treatment of acute heart failure are needed. Dopamine is an endogenous catecholamine which, at low doses, may selectively activate dopamine receptors and promote renal vasodilatation. Previous studies have suggested that the addition of low dose dopamine to diuretic therapy enhances decongestion and preserves renal function during diuretic therapy in acute heart failure; however, these studies were small with variable study designs and dopamine doses. B-type natriuretic peptide (BNP) is a cardiac peptide with vasodilating, renin and aldosterone inhibiting, natriuretic and diuretic properties. Nesiritide is human recombinant BNP approved for management of acute heart failure. The recommended dose lowers blood pressure and atrial pressures and produces modest improvement in dyspnea, but does not favorably impact clinical outcomes or renal function, potentially due to its hypotensive effects. Small studies using low dose nesiritide in acute heart failure and cardiac surgery patients have demonstrated favorable effects on urine output and renal function. Therefore, the Renal Optimization Strategies Evaluation (ROSE) trial was initiated to determine the benefits and safety of intravenous administration of low dose nesiritide or low dose dopamine in patients with congestive heart failure and kidney dysfunction. ParticipantsA total of 360 participants were enrolled. Design Participants were enrolled within 24 hours of hospital admission and randomized in a 1:1 ratio to the nesiritide or dopamine strategies. Participants randomized to the dopamine strategy were randomized in a double-blind 2:1 ratio to low dose dopamine (2 µg/kg/min for 72 hours infused via local guideline stipulated vascular access) or placebo. Participants randomized to the nesiritide strategy were randomized in a double-blind 2:1 ratio to low dose nesiritide (0.005 μg/kg/min for 72 hours infused via peripheral intravenous access without initial bolus) or placebo. All participants received open-label, intravenous loop diuretic treatment with a recommended total daily dose equal to 2.5x the total daily oral outpatient furosemide (or equivalent) dose at 7 days prior to admission up to a maximum of 600 mg/day. Participants naive to outpatient loop diuretics received 80 mg/day of intravenous furosemide. One-half of the total daily diuretic dose was administered as a bolus twice daily for at least 24 hours. Use of other medications and diuretic dosing after 24 hours were at the discretion of the clinician. All participants were placed on a 2000 mg sodium diet and 2000 cc fluid restriction. After the primary endpoint assessment at 72 hours, study drug was discontinued and subsequent treatment was at the clinician's discretion. The two co-primary endpoints were the 72-hour cumulative urinary volume as an index of decongestion efficacy and the change in cystatin-C from randomization to 72 hours as a measure of renal function preservation. Conclusions In participants with acute heart failure and renal dysfunction, neither low-dose dopamine nor low-dose nesiritide enhanced decongestion or improved renal function when added to diuretic therapy.

  Study phs003589

• National Sleep Research Resource (NSRR): Hispanic Community Health Study/Study of Latinos

  The Hispanic Community Health Study / Study of Latinos (HCHS/SOL) is a multi-center epidemiologic study in Hispanic/Latino populations to determine the role of acculturation in the prevalence and development of disease, and to identify risk factors playing a protective or harmful role in Hispanics/Latinos. The study is sponsored by the National Heart, Lung, and Blood Institute (NHLBI) and six other institutes, centers, and offices of the National Institutes of Health (NIH) contributed to the first phase of the project. Raw polysomnography data are available from the HCHS/SOL Baseline visit and raw actigraphy data are available from the Sueño Ancillary visit. Primary HCHS/SOL data can be requested through dbGaP phs000810 Hispanic Community Health Study /Study of Latinos (HCHS/SOL).

  Study phs003543

• Foetal_phylogeny_8pcw___WGS_of_LCM_tissues

  This study relates to the overall project of constructing the phylogeny of foetal haematopoiesis. This is an additional project relating to pre-existing work in projects 2043, 2169, 2243 and 2244. This project is to perform WGS (to around 40X) of polyclonal LCM tissues from the 8pcw foetus that have previously undergone library prep and targeted sequencing only. This work is to address reviewers comments for the publication of this work.

  Study EGAS00001004674

• Gene Expression in an African American Schizophrenia Dataset

  Schizophrenia is a common and severe psychotic disorder. While some common SNPs and rare copy number variants have been identified as being significantly associated with disease risk, the biological mechanisms remain largely undefined. To identify gene expression abnormalities in schizophrenia, we generated whole-genome gene expression profiles using RNAseq on lymphoblastoid cell lines from schizophrenia cases and controls of African American ancestry. Genes related to immune processes were enriched in the genes differentially expressed in the schizophrenia cases. Approximately half of the differentially expressed genes in this African American dataset were also differentially expressed by affection status in our previously studied European ancestry dataset (PMID: 28418402).

  Study phs002842

• Combination therapies for personalized cancer medicine

  It is the ambition of the team formed by members of the Netherlands Cancer Institute (NKI) and the Cancer Genome Project at the Wellcome Trust Sanger Institute (WTSI) to unravel the genomic and phenotypic complexity of human cancers in order to identify optimal drug combinations for personalized cancer therapy. Our integrated approach will entail (i) deep sequencing of human tumours and cognate mouse tumours; (ii) drug screens in a 1000+ fully characterized tumour cell line panel; (iii) high-throughput in vitro and in vivo shRNA and cDNA drug resistance and enhancement screens; (iv) computational analysis of the acquired data, leading to significant response predictions; (v) rigorous validation of these predictions in genetically engineered mouse models and patient-derived xenografts. This integrated effort is expected to yield a number of combination therapies and companion-diagnostics biomarkers that will be further explored in our existing clinical trial networks.

  Dataset EGAD00001000869

• Single cell sequencing of endoscopic biopsies from Barrett's oesophagus and proximal tissue from the normal GI tract

  Barrett’s oesophagus is a precursor of oesophageal adenocarcinoma. In this common condition, squamous epithelium in the oesophagus is replaced by columnar epithelium in response to acid reflux. Barrett’s oesophagus is highly heterogeneous and its relationships to normal tissues are unclear. We investigated the cellular complexity of Barrett’s oesophagus and the upper gastrointestinal tract using RNA-sequencing of single cells from multiple biopsies from six patients with Barrett’s oesophagus and two patients without oesophageal pathology.

  Study EGAS00001003144

• eMERGE Genome-Wide Association Studies of Obesity (Metabochip)

  The Geisinger eMERGE Genome Wide Association Studies of Obesity (Metabochip) Project is a genetic study of a cohort of primarily Caucasian patients with extreme obesity who have undergone bariatric surgery. Roux-en-Y gastric bypass (RYGB) surgery, in which intestinal anatomy is altered, dramatically ameliorates and/or eliminates Type 2 diabetes mellitus (T2D) in 50-80% of patients within hours to days following surgery, well before significant weight loss, in contrast to other types of bariatric surgeries, such as gastric banding, that attenuate insulin resistance as a result of substantial weight loss that occurs over months to years. The molecular mechanism by which RYGB exerts this clinical phenomenon is not known. The goal of this project was to conduct a genome wide association study (GWAS) to identify genetic variants associated with amelioration in T2D defined by medication independence. Identifying genetic variants that influence the dramatic resolution of T2D from RYGB may identify novel targets for pharmacological T2D therapies and/or identify patients in whom RYGB may not be effective.

  Study phs000380

• eMERGE Genome-Wide Association Studies of Obesity

  The Geisinger eMERGE Genome-Wide Association Studies of Obesity Project is a genetic study of a cohort of primarily Caucasian patients with extreme obesity who have undergone bariatric surgery. Roux-en-Y gastric bypass (RYGB) surgery, in which intestinal anatomy is altered, dramatically ameliorates and/or eliminates Type 2 diabetes mellitus (T2D) in 50-80% of patients within hours to days following surgery, well before significant weight loss, in contrast to other types of bariatric surgeries, such as gastric banding, that attenuate insulin resistance as a result of substantial weight loss that occurs over months to years. The molecular mechanism by which RYGB exerts this clinical phenomenon occurs is not known. The goal of this project was to conduct a genome-wide association study (GWAS) to identify genetic variants associated with amelioration in T2D defined by medication independence. Identifying genetic variants that influence the dramatic resolution of T2D from RYGB may identify novel targets for pharmacological T2D therapies and/or identify patients in whom RYGB may not be effective.

  Study phs000408

• Understanding Self- Organising Capacity of Stem Cells during Implantation and Early Post-implantation Development in vitro and in vivo: Implications for Human Development (2020-04-20)

  The aim of this project is to differentiate human embryonic stem cells to an extra-embryonic fate, specifically the hypoblast. This is of uttermost importance given the current lack of human hypoblast stem cells. We hypothesized that the pluripotent characteristics of the starting human embryonic stem cell population may dictate the competency for extra-embryonic cell fate specification. Based on this hypothesis and using human embryonic stem cells maintained in different naïve-like culture regimes, we have now developed conditions that allow the differentiation of human embryonic stem cells to a stable GATA6+ SOX2- population. This suggests that these cells may be putative human hypoblast stem cells. To validate this finding here we propose to perform RNA sequencing experiments of the differentiated human embryonic stem cells. By comparing their RNA expression profile to the single cell sequencing data of the human embryo that we are currently generating, we will be able to determine the identity of our GATA6+ SOX2- cells, and establish whether they represent the in vivo human hypoblast. This dataset contains all the data available for this study on 2020-04-20.

  Dataset EGAD00001006056

• Ghana Breast Health Study

  The Ghana Breast Health Study (GBHS) was a multi-disciplinary, population-based case-control study conducted in Accra and Kumasi, Ghana that was designed to investigate breast cancer etiology in the West Africa region. The study enrolled 1,126 invasive breast cancer cases and 2,106 frequency matched population-based controls using census-based sampling. GHBS participants were between the ages of 18 to 74 years of age. Breast cancer cases were recruited at the time they presented with lesions suspicious of breast cancer at three hospitals: Korle Bu Teaching Hospital (Accra), Komfo Anoyke Teaching Hospital (Kumasi) and Peace and Love Hospital (Kumasi). These hospitals are the primary providers of treatment for breast cancer in Ghana, allowing for cases in our study to represent most breast cancers diagnosed in these areas during the study period. The following publications describe the GBHS in detail: 1) Brinton LA et al. Design considerations for identifying breast cancer risk factors in a population-based study in Africa. Int J Cancer 2017;140:2667-2677 (PMID:28295287). 2) Nyante SJ et al. Recruiting population controls for case-control studies in sub-Saharan Africa: The Ghana Breast Health Study. PloS one 2019;14:e0215347 (PMID:30990841)Among subjects with an available source of germline DNA genotyping was performed using the Infinium Global Screening Array-24 per the manufacturer’s guidelines using the Infinium automated protocol. We excluded probable duplicates and close relatives, and samples with a call rate < 95% or samples with extreme heterozygosity. Female sex was verified by Identifiler using X chromosome heterozygosity and the X chromosome inbreeding coefficient F statistics. The GLU genetics’ ld.tagzilla module was used to confirm African ancestry. To resolve more detailed population substructure, principal components analysis was conducted among all unrelated subjects using the EIGENSOFT v7.2.1. Imputation was performed using the Michigan imputation server Minimac3 with 1K genomes phase3 as reference panel.

  Study phs002387

• Beacon v2

  Beacon v2: a tool for data discovery Motivation In the era of data-driven health research and personalised medicine, human genomic data has become extremely valuable. These are also identifiable data, as they carry information pointing to a specific individual as well as their own family; and as such, they must be protected. This makes data discovery particularly challenging: this is where “Beacon” comes in. A “Beacon” is an API aiming to enable the search of genomic variants and associated information without jeopardising the privacy of the dataset. Here, we refer to its current version, namely version 2 (v2). Definition Beacon v2 is a term that can refer to different aspects. The EGA is playing a central role in the following aspects: The Beacon v2 protocol is a Global Alliance for Health and Genomics standard. The Beacon v2 Reference Implementation (B2RI) is an “out-of-the-box” Beacon instance developed with ELIXIR, which facilitates Beacon deployment. The EGA Beacon(s) are Beacons following the v2 standard and using the B2RI, deployed on top of data hosted at the EGA and allowing for their discovery. Resources Depending on whether you are visiting us a stakeholder (you need more general information about Beacon), a deployer /implementer (you want to have your own Beacon instance), or an EGA user (you want to query Beacon and start browsing data), you will be interested in the following resources: Your role Beacon aspect Documentation type Stakeholder Beacon v2 protocol Beacon website Beacon page on the GA4GH website Deployer/Implementer Beacon v2 protocol Read the docs: Beacon v2 standard technical description GitHub repository Beacon v2 standard Beacon v2 Reference Implementation Read the docs: B2RI technical description GitHub repository B2RI Guide to deploy Beacon using B2RI EGA user EGA Beacon(s) API in construction UI in construction

  Documentation about/projects-and-funders/beacon

• scRNAseq of colonic organoids derived from biopsies taken from healthy human individuals treated with IL22

  scRNAseq dataset of colonic organoids derived from epithelium from biopsies taken from three healthy human individuals. The organoids have either been grown in standard conditions (control) or treated with IL22 (treated). Includes 6 samples in total, one control from each individual (ctrl1, ctrl2, ctrl3) and one treated from each (treat1, treat2, treat3). The samples have been multiplexed using the antibody hashing technique. The 6 samples have been pooled into the one organoids sample. In order to analyse the raw files, they have to be demultiplexed first. Information necessary for demultiplexing, as well as which files belong to which sample, can be found in the map_file.csv, attached to each sample. Dataset includes raw Fastq files and processed csv count matrices. Fastq files are divided into HTO (hashtag) and RNA (transcriptome) files. HTO has one index (I1) and two read (R1, R2) files and RNA has two index (I1, I2) and two read (R1, R2) files. The fastq files are for the pooled (organoids) sample and need to be demultiplexed. Count matrices contain comma-separated values with cell barcodes as column names and gene names as row names. Since count matrices have been created after the demultiplexing step, there’s one matrix for each of the 6 individual samples. scRNA-seq data from human colon organoids was analysed in the same manner as for the Colitis dataset, apart from the following changes. Data was generated with the Cell Hashing technique, which uses oligo-tagged antibodies against surface proteins to barcode single cells. This allows for samples to be multiplexed together and run in a single experiment. The data was demultiplexed using the HTODemux() function from Seurat (Hao et al., 2021).

  Dataset EGAD00001010168

• Sex chromosome aneuploidies give rise to changes in the circular RNA profile

  Purpose The landscape of circular RNAs (circRNAs), an important class of non-coding RNAs that regulate gene expression, has never been described in human disorders of sex chromosome aneuploidies. We profiled circRNAs in Turner syndrome females (45,X;TS) and Klinefelter syndrome males (47,XXY; KS) to investigate how circRNAs respond to a missing or an extra X chromosome. Methods Samples of blood, muscle and fat were collected from individuals with TS (n = 33) and KS (n = 22) and from male (n = 16) and female (n = 44) controls. CircRNAs were identified using a combination of circRNA identification pipelines (CIRI2, CIRCexplorer2 and circRNA_finder). Results Differential expression of circRNAs was observed throughout the genome in TS and KS, in all tissues. The host-genes from which several of these circRNAs were derived, were associated with known phenotypic traits. Furthermore, several differentially expressed circRNAs had the potential to capture micro RNAs that targeted protein-coding genes with altered expression in TS and KS. Conclusion Sex chromosome aneuploidies introduce pervasive changes in the circRNA transcriptome, demonstrating that the genomic changes in these syndromes are more complex than hitherto thought. CircRNAs may help explain some of the genomic and phenotypic traits observed in these syndromes.

  Study EGAS00001006404

• Mutational landscape of eccrine porocarcinoma (sweat gland tumour)

  Eccrine porocarcinoma (EP) is the most common form of sweat gland malignancy. The aetiology of EP is largely unknown. The current lack of data on somatic mutation patterns in EP hampers the development of effective therapies. We performed whole-exome sequencing in a well-characterized sample of 14 matched EP tumour/healthy surrounding tissue samples. Mutational profiling revealed a high overall median mutation rate. This was attributed to signatures of mutational processes related to ultraviolet (UV) exposure, APOBEC enzyme dysregulation, and defective homologous double-strand break repair. All of these processes cause genomic instability and are implicated in carcinogenesis. The analyses revealed alterations in the cancer driver genes and in crucial oncogenic pathways.

  Study EGAS00001004632

• Overcoming Clinical Resistance to EZH2 Inhibition Using Rational Epigenetic Combination Therapy

  Essential epigenetic dependencies have become evident in many cancers. Based on functional antagonism between BAF/SWI/SNF and PRC2 in SMARCB1-deficient sarcomas, we and colleagues recently completed the clinical trial of the EZH2 inhibitor tazemetostat, leading to its FDA approval. However, the principles of tumor response to epigenetic therapy in general and tazemetostat in particular remain unknown. Using functional genomics of patient tumors and diverse experimental models, we defined molecular mechanisms of tazemetostat resistance. We found distinct classes of acquired mutations that converge on the RB1/E2F axis, decoupling EZH2-dependent differentiation and cell cycle control. This allows tumor cells to escape tazemetostat-induced G1 arrest despite EZH2 inhibition and suggests a general mechanism for effective EZH2 therapy. Using RNA-sequencing of patient tumor specimens, we identified specific genes as markers of a deficient RB1/E2F axis, which we propose as prospective biomarkers for therapy stratification. This offers a paradigm for rational epigenetic combination therapy suitable for immediate translation to clinical trials.This study was performed on archived tumor tissue collected as part of the above clinical trial at Memorial Sloan Kettering Cancer Center. Patient tumors were classified into "Response" or "Progression" groups based on RECIST 1.1 criteria. "Response" included tumors exhibiting a complete response, partial response, or stable disease. All other tumors were classified under the "Progression" group. Archived frozen tumor samples were weighed and up to 20-30mg were homogenized in RLT buffer, followed by extraction using the AllPrep DNA/RNA Mini Kit (QIAGEN catalog 80204) according to the manufacturer's instructions. RNA was eluted in 13 μL nuclease-free water. After RiboGreen quantification and quality control by Agilent BioAnalyzer, 1 μg of total RNA with DV200 percentages varying from 78% to 100% underwent ribosomal depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and sequenced using NovaSeq 6000 in a PE150 mode, with the NovaSeq 6000 S4 Reagent Kit (Illumina). On average, 84 million paired reads were generated per sample and 70% of the data mapped to mRNA. For analysis, read adaptors were trimmed and quality filtered using 'trim_galore' and mapped to GRCh38/hg19 reference genome using STAR v2.7.9 with default parameters.

  Study phs003188

• The Institute for Genomic Medicine at Nationwide Children's Hospital Pediatric Cancer and Blood Disorder Project

  The aim of this study is to enable the unification of the clinical and research arms of comprehensive genomic profiling in the setting of cancer and hematologic disease. Increasingly, studies of the genomic etiology of cancer and hematologic diseases are being utilized for patient management, including prognostication, informing diagnosis, and evaluating eligibility for targeted therapeutics and clinical trials. Clinically available testing can be limited in scope and follow-up, and thus assessment of the impact on patient outcomes is difficult to ascertain. N-of-1 studies have the ability to more broadly impact our understanding of the mechanisms of cancer and hematologic disease, and can have benefit for the individual as well as the larger population of patients with these diseases. Thus, we seek to study and characterize the genomic underpinnings of cancer and hematologic disease through genomic profiling studies bridging both clinical and research components. We will rigorously perform and vet research sequencing and genomic studies protocols for the purpose of transitioning these assays to clinically valid testing for use in clinical patient care. We have been enrolling patients onto this comprehensive genomic profiling study since January 2018. As part of the genomic workup for these patients, we have been performing tumor and normal whole genome sequencing, whole exome sequencing and RNA-Seq. The project is largely supported by the Nationwide Children's Foundation, and we anticipate adding another 50-70 cases per year. This protocol is significant in that it expands our understanding of the etiology of cancer and hematologic disease through a comprehensive analysis aimed at detecting a broad scope of genomic aberrations. Additionally, it improves our understanding of the clinical utility of genomic profiling and has the potential to ultimately improve patient management and surveillance at both level of an individual and general populations of patients affected by these diseases. Primary Objectives: Aim 1: Use diagnostic, relapse, and/or germline samples for augmented whole exome sequencing to characterize the spectrum of germline and somatic genomic alterations in pediatric malignancies and hematologic disease. Aim 2: Examine gene expression and fusion events using whole RNA-seq "transcriptome" analysis or targeted RNA-seq analysis such as the Archer FusionPlex technology. Aim 3: Compare the results of our enhanced molecular profiling vs. that which is detectable by traditional methods as related to cytogenetic, molecular, and minimal residual disease analyses performed as part of standard of care. Aim 4: Examine the utility of comprehensive genomic profiling by collection and evaluation of outcomes data as related to enhancement/alteration in diagnosis, prognosis, treatment management, and clinical benefit. Secondary Objective: Aim 1: Use and clinically validate expanded laboratory methodologies and bioinformatic approaches to more broadly assess genomic complexity (e.g. whole genome sequencing, transcriptome sequencing, in vitro analyses, minimal residual disease testing, clonality assays, proteomics) in the setting of hematologic and oncologic disease. In so doing, we aspire to make novel discoveries and associations, as related to disease phenotypes and subtypes, variant causality, therapeutic targeting, and cancer biology.

  Study phs001820

• Sudden Cardiac Death in Heart Failure Trial (SCD-HeFT-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. Objectives The Sudden Cardiac Death in Heart Failure Trial (SCD-HeFT) was designed to evaluate the hypothesis that amiodarone or a conservatively programmed shock-only, single-lead implantable cardioverter defibrillator (ICD) would decrease the risk of death from any cause in a broad population of patients with mild-to-moderate heart failure. Background Patients with congestive heart failure (CHF) can die suddenly and unpredictably from arrhythmia despite the use of proven medical therapies, such as beta-blockade. Two approaches have been developed to prevent sudden death among patients with CHF: therapy with amiodarone and therapy with an ICD. However, most of the mortality data on amiodarone and ICD therapy at the time of the study had been obtained in clinical trials performed after myocardial infarction in patients without CHF or those with ventricular arrhythmias. Thus, more data was needed to guide these therapies in patients who did not meet these criteria. Participants There were a total of 2521 participants. 847 were randomly assigned to placebo, 845 to amiodarone, and 829 to ICD therapy. Design Before randomization, participants underwent electrocardiography, a 6-minute walk test, 24-hour ambulatory electrocardiography, liver and thyroid function studies, and chest radiography. Participants were required, if clinically reasonable, to receive treatment with a beta-blocker and an angiotensin-converting-enzyme inhibitor, as well as an aldosterone antagonist, aspirin, and statins, when appropriate. Participants were randomly assigned in equal proportions to receive placebo, amiodarone, or a single-chamber ICD programmed to shock-only mode. Participants assigned to amiodarone or matching placebo began therapy as outpatients immediately after randomization. Placebo and amiodarone were administered as a loading dose of 800 mg/day for one week, 400 mg/day for three weeks, and then as a daily maintenance dosage according to weight and bradycardia status. Participants assigned to ICD therapy received their device a median of three days after randomization. The goal of ICD therapy was to treat only rapid, sustained ventricular tachycardia or ventricular fibrillation. Dual-chamber or biventricular devices, or antitachycardia or rate-response pacing therapies were not permitted. The ICD was uniformly programmed to have a detection rate of 187 beats per minute or more. Antibradycardia pacing was initiated only if the intrinsic rate decreased to less than 34 beats per minute. Median follow-up was 45.5 months. The primary end point was death from any cause. Secondary outcome measures included cardiac mortality, arrhythmic mortality, morbidity, quality of life, and incremental cost-effectiveness of the interventions. Each active treatment arm was compared to the placebo drug arm. Conclusions In participants with NYHA class II or III CHF and LVEF of 35% or less, amiodarone had no favorable effect on survival, whereas single-lead, shock-only ICD therapy reduced overall mortality by 23%.

  Study phs003654

• Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults

  This observational study was designed to determine the cellular tropism of Influenza A and B Viruses (IAV, IBV) from samples taken from the upper respiratory tract collected during routine nasal washes during the 2017-2018 season. Using single-cell RNA sequencing (scRNA-seq) we sought to determine which cell types could be infected, what the cellular response was to infection in both infected and bystander cells, and to compare the intra/inter-host variability of IAV and IBV during a single season at a single healthcare provider location.

  Study phs002039

• NHLBI TOPMed - NHGRI CCDG: AF Biobank LMU in the context of the MED Biobank LMU

  The Atrial Fibrillation Biobank Ludwig Maximilian University (AFLMU) Study contributes to the spectrum of disease by adding carefully characterized patients with atrial fibrillation. Atrial fibrillation, one of the most common human arrhythmias confers major morbidity, mortality and health care cost, and has been demonstrated to be caused and influenced by genetic and -omics factors. Particularly, AFLMU enrolled patients with an early onset of atrial fibrillation to increase the genetic burden on disease pathophysiology. All patients were recruited applying standardized protocols to maintain homogeneity in data and DNA quality.

  Study phs001543

• 1. Identidication of molecular biological mechanism associated with the development and prognosis of uterine cancer, uterine sarcoma, and endometrial hyperplasia / 2. Identification of molecular biological mechanism associated with the development of endometriosis and malignant transformation, ovarian cancer, fallopian tubal cancer, peritoneal cancer, and other malignant tumors in gynecological organs

  To clarify the biological difference between clear cell carcinoma and other histological subtypes in ovarian carcinomas by comparing copy number variants, and to identify molecular subtypes and carcinogenesis in clear cell ovarian carcinomas by whole-exome sequencing and RNA-sequencing. Then, characterize high-grade serous carcinomas by NGS-based, integrative genomic analyses, with focus on homologous recombination deficiency, molecular subtypes, prognostic factors and effectiveness of PARP inhibitor. Based on the results of whole-exome sequencing, an investigator-initiated, phase 2 clinical trial will be conducted to evaluate the efficacy and safety of the PARP inhibitor olaparib in HRD-positive cases.

  Study JGAS000789

• Follow_up_for_second_tier_signals_from_the_arcOGEN_GWAS

  The arcOGEN UK nationwide consortium has been funded by the arc to undertake a genome-wide association scan in osteoarthritis. GWA genotyping has been carried out at the Sanger on the illumina 610k array. This replication study was desinged to follow-up second-tier signals from the arcOGEN GWS in 25 SNPs (1Sequenom iPLEX) with p<5x10^-6 on 6000 additional UK OA and control samples.

  Study EGAS00001001017

• 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

• Sarcopenia related to Head and Neck squamous cell carcinomas: transcriptome modifications of muscle cells induced by distant malignant cells

  The biological mechanisms of sarcopenia are still very poorly understood, particularly in the case of Head and Neck Squamous Cell Carcinomas (HNSCC). However, there is good reason to believe that diffusible factors originating from tumor cells exert a distant deleterious effect on muscle cells. To test this hypothesis we implemented a dual approach based both on experiments carried out in vitro and on the study of muscle fragments from patients.

  Study EGAS50000000669

• Longitudinal ctDNA in Uveal Melanoma

  Assess the efficacy of using multi-modal ctDNA analysis to detect relapse in patients with uveal melanoma

  Study EGAS00001006373

• Discovery of new fusion transcripts in a cohort of pediatric solid cancers at relapse

  This study aims to dissect further the complexity of fusion landscape in recurrent pediatric cancers. A retrospective study on RNA-sequencing data of 48 pediatric patients at relapse with different malignancies was conducted in order to detect and validate several fusions and predict their probable oncogenic potential and targetability. We obtained a high validation rate of 90% of selected candidates which will serve both clinical and research needs to detect and prioritize experimental validation studies leading to the development of new therapeutic options.

  Study EGAS00001003236

• Examination of Engineered LINE-1 Integration Events in HeLa Cells

  Long Interspsesed Element-1 (LINE1 or L1) encodes two proteins (ORF1p and ORF2p) required for its mobilization (i.e. retrotransposition) in the human genome. Human ORF2p, a 150kDa protein, has endonuclease (EN) and reverse transcriptase (RT) activities. L1 EN is classified as apurinic/apyrimidin-like endonuclease (APE) and is responsible for initiating target-site primer reverse transcription (TPRT) during the L1 retrotransposition cycle. During canonical TPRT, the L1 EN activity makes a single-strand endonucleolytic nick at a double-strand DNA target sequence in genomic DNA. The endonucleolytic nick is typically made at an L1 EN degnerate consensus cleavage sequence (5'-TTTT/A-3') exposing a free 3' hydroxy group that can be used as a primer by the ORF2p L1 RT activity to reverse transcribe the associated L1 RNA. Here, we characterized over 21,000 de novo engineered L1 retrotransposition events in HeLa cells to determine if L1 exhibits overt integration preferences in the human genome. Bru-seq of HeLa cells to determine actively transcribed regions of the genome was also performed. This Bru-seq data was used to determine if engineered L1 integration events preferentially integrate into transcribed regions of the genome, and to determine which strand during transcription may present itself as preferential during L1 retrotransposition.

  Study phs001669

• Genomic profiling of Acute Lymphoblastic Leukemia in Ataxia Telangiectasia patients reveals tight link between ATM mutations and chromothripsis

  Recent developments in sequencing technologies led to the discovery of a novel form of genomic instability, termed chromothripsis. This catastrophic genomic event, involved in tumorigenesis, is characterized by tens to hundreds of simultaneously acquired locally clustered rearrangements on one chromosome. We hypothesized that leukemias developing in individuals with Ataxia Telangiectasia, who are born with two mutated copies of the ATM gene, an essential guardian of genome stability, would show a higher prevalence of chromothripsis due to the associated defect in DNA double-strand break repair. Using whole-genome sequencing, fluorescence in situ hybridization and RNA sequencing, we characterized the genomic landscape of Acute Lymphoblastic Leukemia (ALL) arising in patients with Ataxia Telangiectasia. We detected a high frequency of chromothriptic events in these tumors, specifically on acrocentric chromosomes, as compared to tumors from individuals with other types of DNA repair syndromes (27 cases total, 10 with Ataxia Telangiectasia). Our data suggest that the genomic landscape of Ataxia Telangiectasia ALL is clearly distinct from that of sporadic ALL. Mechanistically, short telomeres and compromised DNA damage response in cells of Ataxia Telangiectasia patients may be linked with frequent chromothripsis. Furthermore, we show that ATM loss is associated with increased chromothripsis prevalence in additional tumor entities.

  Study EGAS00001002270

• High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma

  We investigated the role of 3D genome architecture in instructing functional properties of glioblastoma stem cells (GSCs) by generating the highest-resolution 3D genome maps to-date for this cancer. Integration of DNA contact maps with chromatin and transcriptional profiles identified specific mechanisms of gene regulation, including individual physical interactions between regulatory regions and their target genes. Residing in structurally conserved regions in GSCs was CD276, a gene known to play a role in immuno-modulation. We show that, unexpectedly, CD276 is part of a stemness network in GSCs and can be targeted with an antibody-drug conjugate to curb self-renewal, a key stemness property. Our results demonstrate that integrated structural genomics datasets can be employed to rationally identify therapeutic vulnerabilities in self-renewing cells.

  Study EGAS00001003493

• Studying Glioblastoma in a Human Organoid Tumor Transplantation Model

  This study comprises two complementary investigations that leverage innovative human model systems and cutting-edge molecular profiling to dissect glioblastoma (GBM) heterogeneity and tumor-microenvironment interactions. The first study uses a novel Human Organoid Tumor Transplantation (HOTT) model, in which freshly dissociated GBM tumor cells from five patients were transplanted into human embryonic stem cell-derived cortical organoids. This system enables the interrogation of tumor and microenvironment interactions in a human-specific, developmentally relevant context. Using single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq), the authors profiled over 216,000 cells, analyzing tumor heterogeneity across multiple media conditions. Ligand-receptor analysis (CellChat), immunofluorescence, and RNAScope were used to validate findings. The study revealed that the HOTT model faithfully recapitulates primary GBM cell types and microenvironmental components, and uncovered a novel bidirectional signaling axis mediated by PTPRZ1 that influences both tumor migration and cell fate in a context-dependent manner. PTPRZ1 is identified to be important for intercellular communication between tumor and microenvironmental cells, while PDGFRB, NOTCH3, HOPX, FAM107A, CLDN5, RGS5, FOXC1, SOX18 are key markers of the neurovascular progenitor that we identify to be a multipotent, restricted progenitor in GBM. Related datasets include the inclusion of immune cells in the HOTT system, termed “iHOTT”. The second study focuses on identifying and characterizing a rare but functionally potent neurovascular progenitor (NVP) population within GBM tumors. By generating a meta-atlas from seven publicly available GBM scRNA-seq datasets, the authors identified a unique tumor-derived cell population co-expressing neural progenitor and vascular markers. This population was validated in situ and in vivo through immunostaining and lineage tracing via DNA barcoding in the HOTT system. Functional knockdown of NVPs in a murine GBM model resulted in reduced cycling cells, altered tumor composition, and increased survival. Clonal analysis showed NVPs have dual potency to give rise to both neuronal and vascular-like tumor cells, contributing significantly to tumor cell diversity. Molecular technologies used across the studies include: Single-cell and single-nucleus RNA sequencing DNA barcoding and clonal lineage tracing (CellTag) Population information: Tumor samples were obtained directly from multiple GBM patients (all IDH1 wild-type, adult), including core and peripheral tumor regions. Human cortical organoids derived from human embryonic stem cells (hESCs) served as the microenvironment in the HOTT model. Principal findings include: HOTT recapitulates the heterogeneity and cell type fidelity of GBM, while enabling the study of tumor–microenvironment signaling. PTPRZ1 has opposing roles in tumor and microenvironment, influencing GBM cell migration and fate via non-catalytic mechanisms. A novel GBM neurovascular progenitor population (NVP) was identified, validated, and shown to contribute clonally to distinct tumor cell types. Elimination of NVPs in vivo reduces tumor aggressiveness and improves survival. Data to be available through dbGaP: Raw and processed single-cell and single-nucleus RNA-seq data (HOTT model and NVP studies) CellTag barcode-labeled scRNA-seq clonal lineage data Associated metadata including patient of origin, experimental condition, and sample annotations.

  Study phs003936

• Women's Health Initiative Clinical Trial and Observational Study

  The Women's Health Initiative (WHI) is a long-term national health study that has focused on strategies for preventing heart disease, breast and colorectal cancer, and osteoporotic fractures in postmenopausal women. The original WHI study included 161,808 postmenopausal women enrolled between 1993 and 1998. The Fred Hutchinson Cancer Research Center in Seattle, WA serves as the WHI Clinical Coordinating Center for data collection, management, and analysis of the WHI. The WHI has two major parts: a partial factorial randomized Clinical Trial (CT) and an Observational Study (OS); both were conducted at 40 Clinical Centers nationwide. The CT enrolled 68,132 postmenopausal women between the ages of 50-79 into trials testing three prevention strategies. If eligible, women could choose to enroll in one, two, or all three of the trial components. The components are: Hormone Therapy Trials (HT): This double-blind component examined the effects of combined hormones or estrogen alone on the prevention of coronary heart disease and osteoporotic fractures, and associated risk for breast cancer. Women participating in this component with an intact uterus were randomized to estrogen plus progestin (conjugated equine estrogens [CEE], 0.625 mg/d plus medroxyprogesterone acetate [MPA] 2.5 mg/d] or a matching placebo. Women with prior hysterectomy were randomized to CEE or placebo. Both trials were stopped early, in July 2002 and March 2004, respectively, based on adverse effects. All HT participants continued to be followed without intervention until close-out. Dietary Modification Trial (DM): The Dietary Modification component evaluated the effect of a low-fat and high fruit, vegetable and grain diet on the prevention of breast and colorectal cancers and coronary heart disease. Study participants were randomized to either their usual eating pattern or a low-fat dietary pattern. Calcium/Vitamin D Trial (CaD): This double-blind component began 1 to 2 years after a woman joined one or both of the other clinical trial components. It evaluated the effect of calcium and vitamin D supplementation on the prevention of osteoporotic fractures and colorectal cancer. Women in this component were randomized to calcium (1000 mg/d) and vitamin D (400 IU/d) supplements or a matching placebo. The Observational Study (OS) examines the relationship between lifestyle, environmental, medical and molecular risk factors and specific measures of health or disease outcomes. This component involves tracking the medical history and health habits of 93,676 women not participating in the CT. Recruitment for the observational study was completed in 1998 and participants were followed annually for 8 to 12 years. Extension Studies: The original protocol allowed for follow-up until March 2005, after which participants were invited to enroll in the first WHI Extension Study for follow-up through 2010. Participants were invited again to participate in the second WHI Extension Study with continued follow up from 2010 to at least 2015. As of March 31, 2011 there were 93,122 women enrolled in the second extension. In Extension Study 2, the overall WHI study population was divided into two new subsamples, the Medical Records Cohort (MRC) and the Self-Report Cohort (SRC). The MRC consists of all former hormone trial participants and all African American and Hispanic participants from all study components. The SRC consists of the remaining participants. The extent of outcome information collected differs between the two cohorts, with more extensive outcomes information collection on the MRC. As part of Extension Study 2, selected older WHI participants were invited to participate in an In Person Visit (a.k.a., Long Life Study) at their homes during which additional blood samples were collected and various measurements were taken (such as blood pressure, height, weight, waist circumference, grip strength, etc.). In October 2015, Extension Study 2 was renewed with continued follow-up planned through October 2020, pending annual contract review and renewal. Additional Information: The WHI website, https://www.whi.org/about/SitePages/About%20WHI.aspx has much more information about the study. For WHI data collection forms used over the years, please see https://www.whi.org/researchers/studydoc/SitePages/Forms.aspx. For additional dataset documentation, see https://www.whi.org/researchers/data/Pages/Available%20Data.aspx. For data preparation and use, please refer to 'WHI dbGaP Cohort Data Release Data Preparation Guide May 2018' for additional details about the WHI data. The WHI Cohort is utilized in the following dbGaP substudies. To view genotypes, analysis, expression data, other molecular data, and derived variables collected in these substudies, please click on the following substudies below or in the "Substudies" box located on the right hand side of this top-level study page phs000200 WHI Cohort. phs000386 WHI SHARe phs000281 GO-ESP WHISP phs000315 WHI GARNET phs000503 WHISE phs000227 PAGE WHI phs000675 WHIMS+ phs000746 WHI Harmonized and Imputed GWAS phs001334 WHI Metabolomics of CHD phs001335 WHI BA23 phs001614 WHI LLS Phase III GWAS

  Study phs000200

• Genomic Analyses of Germline and Somatic Variation in High-Grade Serous Ovarian Cancer

  The goal of this study was to identify and characterize germline and somatic genetic variation in women with high grade serous ovarian cancers treated at a single cancer center and their associations with relapse-free and overall survival. We conducted paired tumor/normal targeted next-generation sequencing of 577 genes in pathways of DNA repair, response to DNA damage, cell-cycle regulation, programmed cell death, MAPK, and P13K/AKT/MTOR signaling in 114 tumors from 71 women. In addition, we investigated single copy number alterations (SCNAs) and loss of heterozygosity in a subset of 61 tumors. We validated our results with data from ovarian tumors in TCGA. Our results were similar to other studies of high-grade serous carcinomas. As an example, we found that approximately one third of the tumors harbored loss of function variants in homologous recombination genes and that >90% had TP53 somatic mutations. Through GISTIC analysis of the OncoScan data on tumor DNA from 61 cases, we identified several regions of high copy number alterations including including NOTCH3 and PIK3R2 that were significantly associated with an increase in cancer recurrence and a reduction in overall survival. We identified few changes in mutation profiles where we had multiple tissues, either from multiple surgeries or from the primary site to metastatic sites within the same surgery. However, we did not investigate copy number alterations in multiple tissues from the same individuals, and so it may be that copy number alterations are more important. Data available through dbGAP will be the BAM files and the phenotypic data on the tumor samples, the age, race, ethnicity of the participants and their outcomes, and the Oncoscan OSCHP files.

  Study phs003198

• Genomic profiling for metastatic uveal melanoma from a phase I study of the protein kinase C inhibitor AEB071

  Up to 50% of patients with uveal melanoma (UM) develop metastatic disease, for which there is no effective systemic treatment. This study aimed to evaluate the safety and efficacy of the orally available protein kinase C inhibitor, AEB071, in patients with metastatic UM, and to perform genomic profiling of metastatic tumor samples, with the aim to propose combination therapies. Metastatic UM patients (n=153) were treated with AEB071 in a Phase I, single-arm study. Patients received total daily doses of AEB071 ranging from 450 to 1400 mg. First-cycle dose-limiting toxicities (DLTs) were observed in 13 patients (13%). These were most commonly gastrointestinal system toxicities and were dose related, occurring at doses > 700 mg/day. Preliminary clinical activity was observed, with 3% of patients achieving a partial response and 50% with stable disease (median duration 15 weeks). High-depth, targeted next-generation DNA sequencing (NGS) was performed on 89 metastatic tumor biopsy samples. Mutations previously identified in UM were observed, including mutations in GNAQ, GNA11, BAP1, SF3B1, PLCB4, and amplification of chromosome arm 8q. GNAQ/GNA11 mutations were observed at a similar frequency (93%) as previously reported, confirming a therapeutic window for inhibition of the downstream effector PKC in metastatic UM. In conclusion, the protein kinase C inhibitor AEB071 was well tolerated and modest clinical activity was observed in metastatic UM. The genomic findings were consistent with previous reports in primary UM. Together, our data allow envisaging combination therapies of PKC inhibitors with other compounds in metastatic UM.

  Study phs001953

• How mitochondrial DNA research can benefit from data reuse through EGA?

  Mitochondria are the only cellular organelles harbouring their own DNA, which encodes for proteins essentials in its respiration process. Despite its discovery in 1960, Mitochondrial DNA is often overlooked compared to nuclear DNA. Indeed, not all sequencing technologies capture a good representation of mtDNA (mitochondrial DNA). Recently, Ed Reznik's team (The Ed Reznik Lab | Memorial Sloan Kettering Cancer Center) carried out a massive analysis and reanalysis of single cells WGS (whole genome sequencing) produced with an amplification-free protocol (Direct library prep, DLP). As they demonstrated in the paper Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes - PMC, DLP is more effective in catching mtDNA compared to classical single-cell sequencing. These data allowed the team to unravel mtDNA dynamics in tumoral and normal samples, highlighting how mtDNA and nuclear DNA are co-regulated and their ratio is critical for phenotype. Data reuse to achieve the greatest results For this project, Reznik's team re-used data from 3 studies stored at the European Genome-phenome Archive (EGAS00001006343, EGAS00001004448 and EGAS00001003190) that comprised a total of 602 datasets. All of them were initially produced by the teams of Sam Aparicio and Sohrab P. Shah at the Memorial Sloan Kettering Cancer Centre, where Ed Reznik is a promising group leader. This demonstrates, once again, that networking, collaboration and data sharing can achieve the greatest results when coupled with innovative and smart ideas. At the EGA we are proud to provide the scientific community with an infrastructure to enable all those very smart ideas out there to find the right data to be tested.

  Blog mitochondrial-dna-research

• CRISPR-screening identifies mechanisms of resistance to KRASG12C and SHP2 inhibitor combinations in non-small cell lung cancer

  Although KRASG12C inhibitors show clinical activity in patients with KRAS G12C mutated NSCLC and other solid tumor malignancies, response is limited by multiple mechanisms of resistance. The KRASG12C inhibitor JDQ443 shows enhanced preclinical antitumor activity combined with the SHP2 inhibitor TNO155, and the combination is currently under clinical evaluation. To identify rational combination strategies that could help overcome or prevent some types of resistance, we evaluated the duration of tumor responses to JDQ443 �� TNO155, alone or combined with the PI3K�� inhibitor alpelisib and/or the CDK4/6 inhibitor ribociclib, in xenograft models derived from a KRASG12C-mutant NSCLC line and investigated the genetic mechanisms associated with loss of response to combined KRASG12C/SHP2 inhibition.

  Study JGAS000643

• Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma

  Follicular lymphoma (FL) is an incurable B-cell malignancy characterized by the t(14;18) and mutations in one or more components of the epigenome. Whilst frequent gene mutations in signaling pathways, including JAK-STAT, NOTCH and NF-κB, have also been defined, the spectrum of these mutations typically overlap with the closely-related diffuse large B cell lymphoma (DLBCL). A combination of discovery exome and extended targeted sequencing revealed recurrent somatic mutations in RRAGC uniquely enriched in FL patients (17%). More than half of the mutations preferentially co-occurred with ATP6V1B2 and ATP6AP1 mutations, components of the vacuolar H+-adenosine triphosphate ATPase (v-ATPase) known to be necessary for amino acid-dependent mTORC1 activation. RagC mutants increased raptor binding whilst rendering mTORC1 signaling resistant to amino acid deprivation through nucleotide-independent mechanisms. Collectively, the activating nature of the RRAGC mutations, their existence within the dominant clone and stability during disease progression supports their potential as an excellent candidate to be therapeutically exploited.

  Study EGAS00001001190

• Optimizing Primary Stroke Prevention in Children with Sickle Cell Anemia (STOP II)

  The STOP II trial evaluated whether prophylactic transfusion in patients with sickle cell disease and high risk of stroke can be safely halted after 30 months of treatment during which patients became low risk for stroke.Stroke causes substantial morbidity in children with sickle cell disease. To prevent first strokes, the Stroke Prevention Trial in Sickle Cell Anemia (STOP) used prophylactic transfusions in children who were identified by transcranial Doppler (TCD) ultrasonography as being at high risk for stroke. This strategy reduced the incidence of stroke among such children from 10% per year to less than 1% per year, leading to recommendations for TCD screening and prophylactic transfusion for children with abnormal velocities on ultrasonography. Despite the reduced risk of stroke, long-term use of transfusions can cause adverse side effects, such as iron overload or alloimmunization. However, cessation of transfusions is associated with recurrence of stroke, and at the time of the STOP II trial, there were no clinical or laboratory indicators to guide the duration of prophylaxis. Therefore the STOP II trial was initiated to determine whether transfusions could be limited by monitoring patients with TCD examinations after transfusions were halted and resuming transfusions if the examination indicated a high risk of stroke.The trial was halted for safety concerns after 79 of a planned 100 children were randomized. Discontinuation of transfusion for the prevention of stroke in children with sickle cell disease resulted in a high rate of reversion to abnormal blood-flow velocities on Doppler studies and stroke incidence.Instructions for requesting individual-level data are available on BioData Catalyst at https://biodatacatalyst.nhlbi.nih.gov/resources/data/. Apply for data access in dbGaP. Upon approval, users may begin accessing requested data in BioData Catalyst. For questions about availability, you may contact the BioData Catalyst team at https://biodatacatalyst.nhlbi.nih.gov/contact.

  Study phs002386

• Somatic_Genetics_of_lesions_from_a_POT1_patient

  In this project we will use exome sequencing to identify somatic mutations in lesions from a patient with a germline mutation in the protection of telomeres 1 gene (POT1).

  Study EGAS00001001343

• Chromatin run-on and RNA sequencing of fibrolamellar carcinoma

  Fibrolamellar carcinoma (FLC) is a rare, therapeutically intractable liver cancer that disproportionately affects youth. Here we used chromatin run-on sequencing to characterize the enhancer landscape in FLC and RNA sequencing to identify dysregulated genes in FLC.

  Study EGAS00001004169

• Distinct evolutionary trajectories of primary high grade serous ovarian cancers revealed through spatial mutational profiling

  High-grade serous ovarian cancer (HGSC) is characterized by poor outcome, often attributed to emergence of treatment-resistant sub-clones. We sought to measure the degree of genomic diversity within primary, untreated HGSC to examine the natural state of tumor evolution prior to therapy. We performed exome sequencing, copy number analysis, targeted amplicon deep sequencing and gene expression profiling on thirty-one spatially and temporally separated HGSC tumor specimens (six patients) including ovarian masses, distant metastases, and fallopian tube lesions. We found widespread intra-tumoral variation in mutation, copy number, and gene expression profiles, with key driver alterations in genes present in only a subset of samples (e.g. PIK3CA, CTNNB1, NF1). On average, only 51.5% of mutations were present in every sample of a given case (range: 10.2% to 91.4%), with TP53 as the only somatic mutation consistently present in all samples. Complex segmental aneuploidies, such as whole genome doubling, were present in a subset of samples from the same individual, with divergent copy number changes segregating independently of point mutation acquisition. Reconstruction of evolutionary histories showed one patient with mixed HGSC and endometrioid histology with common etiologic origin in the fallopian tube and subsequent selection of different driver mutations in the histologically distinct samples. In this patient, we observed mixed cell populations in the early fallopian tube lesion, indicating diversity arises at early stages of tumorigenesis. Our results reveal that HGSC exhibit highly individual evolutionary trajectories and diverse genomic tapestries prior to therapy, exposing an essential biological characteristic to inform future design of personalized therapeutic solutions and investigation of drug resistance mechanisms.

  Dataset EGAD00001000974

• Cell-Type Specific Effects of Genetic Variation on Chromatin Accessibility During Human Neuronal Differentiation

  Common genetic risk for neuropsychiatric disorders is enriched in regulatory elements active during cortical neurogenesis. However, the mechanisms mediating the effects of genetic variants on gene regulation are poorly understood. To determine the functional impact of common genetic variation on the non-coding genome longitudinally during human cortical development, we performed a chromatin accessibility quantitative trait loci (caQTL) analysis in neural progenitor cells and their differentiated neuronal progeny from 92 donors. We identified significant genetic effects on 988/1,839 neuron/progenitor regulatory elements, with highly cell-type and temporally specific effects. A subset (~30%) of caQTLs were also associated with changes in gene expression. Motif-disrupting alleles of transcriptional activators generally led to decreases in chromatin accessibility, whereas motif-disrupting alleles of repressors led to increases in chromatin accessibility. By integrating cell-type specific caQTLs and brain-relevant genome-wide association data, we were able to fine-map and identify regulatory mechanisms underlying non-coding neuropsychiatric disorder risk loci.

  Study phs001958

• A microRNA-signature that correlates with cognition and is a target against cognitive decline

  While some individuals age without pathological memory impairments, others develop age-associated cognitive diseases. Since changes in cognitive function develop slowly over time in these patients, they are often diagnosed at an advanced stage of molecular pathology, a time point when causative treatments fail. Thus, there is great need for the identification of inexpensive and minimal invasive approaches that could be used for screening with the aim to to identify individuals at risk for cognitive decline that can then undergo further diagnostics and eventually stratified therapies. In this study we use an integrative approach combining the analysis of human data and mechanistic studies in model systems to identify a circulating 3-microRNA signature that reflect key processes linked to neural homeostasis and informs about cognitive status. We furthermore provide evidence that expression changes of this signature represent multiple mechanisms de-regulated in the aging and diseased brain and are a suitable target for RNA therapeutics.

  Study EGAS00001005627

• Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole genome sequencing with histopathological features

  We performed whole genome sequencing on 42 prostate cancer samples from the prostate, seminal vesicles and regional lymph nodes of five treatment-naive patients with locally advanced disease who underwent radical prostatectomy. Using cancer cell fractions computed from single nucleotide variants and copy number alterations, we reconstructed the tumour phylogenies, which in turn allowed us to infer key molecular steps in the progression of prostate cancer in these individuals. We mapped the clonal composition of cancer sampled across the prostate in each individual and inferred the routes of spread of cancer cells within the prostate and to seminal vesicles and lymph nodes.

  Study EGAS00001007438

• Development and Use of Network Infrastructure for High-Throughput GWA Studies

  The "Development and Use of Network Infrastructure for High-Throughput GWA Studies" project is collaboration between Group Health Cooperative (GH), the University of Washington (UW), and the Fred Hutchinson Cancer Research Center (FHCRC). It is one of 5 sites participating in The Electronic Medical Records and Genomics (eMERGE) Network funded by the National Human Genome Research Institute (NHGRI) with additional funding from the National Institute of General Medical Sciences (NIGMS). The overall eMERGE project is designed to assess whether linking biorepositories of patients in healthcare delivery systems with electronic medical records (EMRs) is an efficient strategy for high-throughput genome wide association (GWA) studies and whether information can be pooled across sites. The primary phenotype in the Group Health/UW Aging and Dementia eMERGE study project is dementia. Phenotyped participants originated from four population-based sources. Seattle-area members of GH (a large integrated health care system in Washington State) consented and enrolled in 1) the University of Washington Alzheimer's Disease Patient Registry (ADPR) and 2) the Adult Changes in Thought (ACT) study, 3) Marshfield Clinic Personalized Medicine Research Project (PMRP), a population-based DNA, plasma and serum biobank of 20,000 adults, 4) Vanderbilt's BioVU, a de-identified DNA biobank. The ADPR (PI: Eric B. Larson; NIH/NIA U01 AG 006781) is a population-based registry of incident dementia cases designed to identify all new dementia cases within GH from 1987 to 1996. Potential dementia cases were identified through referrals from primary care physicians, mental health services, and neurologists, as well as review of CT scans, neurology, emergency room, geriatrician, and mental health clinic logs, and hospital discharge diagnoses. Medical history, physical, laboratory testing, and neuropsychological testing were performed on all consenting potential cases. These data were reviewed by a consensus conference including a neuropsychologist, study physicians, and an epidemiologist. After discussion of the case, dementia status is assigned using DSM-III-R criteria. Alzheimer's disease status was assigned using the National Institute of Neurological and Communicative Disorders and Stroke-Alzheimer's Disease and Related Disorders Association (NINCDS-ADRDA) criteria. The study base of the ADPR population was stable with an attrition rate of less than 1%/year. The ACT study (PI: Eric B. Larson; NIH/NIA U01 AG 006781) is an ongoing community-based cohort study designed to determine the incidence of Alzheimer's Disease (AD), other types of dementia, and cognitive impairment and to determine risk factors for these conditions. The original cohort of 2,581 was enrolled in 1994-1996. An expansion cohort of 811 was enrolled in 2000-2002. Continuous enrollment to keep 2,000 persons enrolled and at-risk for dementia outcomes was begun in 2005. To date the study has accrued more than 4,000 participants. Dementia-free participants are enrolled in this cohort and evaluated every two years by study personnel with many evaluations including an assessment of cognitive functioning using the Cognitive Abilities Screening Instrument (CASI), which is an extended version of the Mini-Mental State Examination that has been widely used in epidemiological studies of the elderly. Persons with CASI scores lower than 86 or in whom interviewers suspect unusual cognitive decline are followed up with dementia diagnostic evaluations which include physical and neurological examinations and neuropsychological tests. Medical records are reviewed, and laboratory tests and neuroimaging are obtained if not available. The dementia diagnoses and dementia subtypes are determined during a consensus conference attended by the examining clinicians and other study physicians, a neuropsychologist, and research nurse. After discussion of the case, dementia status is assigned using DSM-IV criteria. Alzheimer's disease status was assigned using NINCDS-ADRDA criteria. Individuals diagnosed with dementia are seen again one year following diagnosis using the same procedures. Individuals not diagnosed with dementia are returned to the pool of at-risk individuals and are seen at their next routinely scheduled biennial visit. The ACT sub-sample is stable; for the original cohort, median enrollment in GH was 19 years prior to joining the ACT study, and 85% of the cohort has ≥ 10 years of GH enrollment. DNA for the ADPR participants were obtained through a companion study, Genetic Differences in Cases and Controls (PI: Walter Kukull; NIH/NIA R01 AG007584). DNA obtained through both studies were extracted from blood using Gentra Systems Puregene methods. DNA concentration is determined by UV optical density. All samples are checked for quality by OD 260/280 ratio. For long-term storage, samples are aliquoted and stored at -70°C. The Marshfield study, Personalized Medicine Research Project (PMRP), a population-based DNA, plasma and serum biobank of 20,000 adults. PMRP was started in 2002 as a 3 Phase project. Completed in April 2004, the objectives of Phase I were to build and develop a large population-based biobank with DNA, plasma and serum samples to facilitate genomics research. Phase 1 was also to educate, inform and consult with the Marshfield Epidemiologic Study Area population and communities concerning potential studies, create the DNA foundation of the personalized medicine database and build the bioinformatics tools to store securely and analyze genotypic and phenotypic data. Phase I tasks included operation of the ethics and security advisory board, scientific advisory board and community advisory group. More than 18,000 residents aged 18 and above from 19 different zip codes surrounding Marshfield, WI were invited to participate in Phase I. After providing written informed consent, participants completed brief questionnaires that included questions about demographics, some environmental exposures, family history of disease, and adverse drug reactions, as well as family members living in the area. Participants provided 50ml of blood from which DNA was extracted and plasma and serum samples were stored. The informed consent process allowed access to electronic medical records and included language about non-disclosure of personal research results. A tick-off box was included so that participants could either allow or decline subsequent recontact for future research studied. The objectives of Phase II are to create the phenotypic database, establish the scientific and administrative infrastructure to support genetic mapping of the DNA and the initial discovery projects and genotype a sufficient portion of the genetic material to support these discovery projects. The objectives of Phase III are to expand the discovery projects, complete the genotyping of the genetic database and expand physician/health care provider education and community consultation. The Vanderbilt BioVU model uses discarded blood leftover from clinical care and de-identified clinical information, both of which are tracked with a Research Unique Identifier that is permanently disconnected from the medical record number used to generate it. The Vanderbilt IRB determined that the project does not qualify as "human subject" research under §46.102(f)(1)(2). The program has been reviewed by OHRP twice (the latest immediately prior to launch), and the determination of the Vanderbilt IRB that the project is consistent with the 8/10/2004 guidance has been validated. The model includes a simple opt out mechanism developed for patients who do not wish to have their samples included. Planning (including community involvement, ethics and IRB discussions, focus groups, development of operating procedures and pilot studies to assess them) began in May 2004, and the resource commenced sample collection in February 2007 and as of May 2009 contains approximately 56,000 samples. The current resource will be available to all Vanderbilt investigators who sign a Data Use Agreement. The resource represents Vanderbilt's broad patient population and thus provides a potential resource for research in a range of common and rare diseases as well as drug response or medication safety. BioVU patient protection model: There has been extensive involvement by the ethics community and the IRB to put in place procedures to provide privacy protection. The overall protection plan is multifaceted and includes a combination of technology and policy: (1) creation of the SD described above; (2) return of only the specific clinical data items requested by investigators (rather than the complete de-identified chart); (3) submission of any specific proposed project to the IRB and to a separate protocol review committee, both of which must approve; (4) implementing a Data Use Agreement that permits only approved queries and data analyses, specifically prohibits attempts at re-identification (at the risk of institutional sanctions), and mandates redeposit of all genetic information generated in a research study back into a genomic database; and (5) tracking and auditing all use.

  Study phs000234

• Fragmentomic features of individuals with different cfDNA concentrations

  The goal of this study is to explore fragmentomic patterns that vary between individuals of different concentrations of total cell-free DNA in plasma. We have selected a large cohort of individuals (ethnically Chinese men with a median age of 54 years, IQR 49-57) who were part of a screening of a large-scale clinical study to screen for nasopharyngeal carcinoma. Differences in fragmentomic features provided insights into the modulation of cfDNA levels in blood circulation. Fragmentomic and machine learning systems adopted in this study have also been applied to assess the quantity of cfDNA species of clinical interest, including the fraction of circulating fetal and tumor DNA, from pregnancy cases and individuals with hepatocellular carcinoma, respectively.

  Study EGAS50000000692

• ctDNA quantification in Ewing sarcoma patients

  Background. Treatment stratification and response assessment in pediatric sarcomas has relied on imaging studies and surgical/histopathological evidence of vital tumor cells. Such studies and evidence collection processes often involve radiation and/or general anesthesia in children. Cell-free circulating tumor DNA (ctDNA) detection in blood plasma is one available method of so-called liquid biopsies that has been shown to correlate qualitatively and quantitatively to some extent with the existence of vital tumor cells in the body. Our clinical observational study focused on the utility and feasibility of ctDNA detection in pediatric Ewing sarcoma (EWS) as a marker of minimal residual disease (MRD). Patients and Methods. We performed whole genome sequencing to identify the exact breakpoints in tumors known to carry the EWS-FLI1 fusion gene. Patient-specific fusion breakpoints were tracked in peripheral blood plasma using digital droplet PCR (ddPCR) before, during, and after therapy in six consecutive children and young adults with EWS. Presence and levels of fusion breakpoints were correlated with clinical disease courses. The genetic changes in the tumors were defined, and inter- and intra-individual changes in the tumor DNA copy loads were observed over time. Results. We show that the detection of ctDNA in the peripheral blood of EWS patients i) is feasible in the clinical routine and ii) allows for the longitudinal real-time monitoring of MRD activity in children and young adults. Although changing ctDNA levels correlated well with clinical outcome within patients, between patients, a high variability was observed (inter-individually) for the six patients described here. Conclusions. ctDNA detection by ddPCR is a highly sensitive, specific, feasible, and highly accurate method that can be applied in EWS for follow-up assessments as an additional surrogate parameter for clinical MRD monitoring and, potentially, also for treatment stratification in the near future.

  Study EGAS00001006433

• Human Companion Data for 'A Transcriptomic Atlas of Mouse Cerebellar Cortex Reveals Novel Cell Types'

  In this study, we used single-nucleus RNA-seq to comprehensively define the cell specialization of the mouse cerebellar cortex and vermis. We focused in particular on two interneuron populations—the unipolar brush cells (UBCs) and the molecular layer interneurons (MLIs), identifying continuous variation within the former population, and a new discrete axis of variation in the latter. Human postmortem tissue was used to demonstrate that these specializations are evolutionarily conserved in primates. Together, these findings provide the first comprehensive cellular atlas of the cerebellar cortex, and outline a methodological and conceptual framework for the integration of molecular, morphological, and physiological ontologies for defining brain cell types.

  Study phs002414

• 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

• Atezolizumab monotherapy following dCRT indicated a promising cCR rate in patients with unresectable locally advanced esophageal squamous cell carcinoma (EPOC1802)

  The objective is to analyze tumor and normal cell exome sequencing of esophageal cancer patients participating in the Tenergy trial before treatment and RNA sequencing specimens of tumor biopsy specimens at three points before treatment, after radiation chemotherapy, and after atezolizumab administration, in order to search for biomarkers to predict treatment response. Exome sequencing of pretreatment tumor tissue (27 specimens) and normal tissue (27 specimens) from esophageal cancer patients participating in the Tenergy trial, and RNA sequencing of tumor biopsy specimens at three time points before treatment (28 specimens), after radiation chemotherapy (25 specimens) and after atezolizumab administration (25 specimens).

  Study JGAS000708

• Multi-modal spatial characterization of tumor-immune microenvironments in diffuse large B-cell lymphoma

  We have leveraged spatial transcriptomics together with proteomic and genomic analysis to investigate the spatial immunology and pathobiology of DLBCL. We define distinct cellular niches that differ in frequency across tumors, related to both Epstein-Barr virus (EBV) infection status and the anatomical site of the tumor, and show that residence within different cellular niches is associated with divergent functional states of T-cells and tumor B-cells due to different patterns of cell-cell communication. This provides a framework for understanding stereotyped patterns of spatial organization in DLBCL and immunological interactions associated with heterogeneity in immune cell infiltration and function across patients.

  Study EGAS50000001146

• LLDeep DAG2+: scRNA-seq in PBMCs

  Single cell transcriptomics of PBMCs of 47 donors from the Lifelines Deep cohort (general population, Northern part of the Netherlands). Cells of five or six different donors were pooled together in one sample pool, resulting in eight different sample pools. In total, 28.855 cells were captured and their transcriptomes were sequenced to an average depth of 74k. Genotype data was available for each donor, which allowed us to use the Demuxlet method that uses variable SNPs between the pooled individuals to determine which cell belongs to which individual. Since genotype information is lacking of 2 individuals, the transcriptome of only 45 individuals could be retrieved.

  Dataset EGAD00001003459

• Genomic and Genetic Analysis of Brain Tumors and Analysis of Their Clinicopathological Significance

  The treatment outcome of glioma patients remains disappointing, and more studies are needed to improve therapeutic strategies. In particular, it is crucial to understand the mechanisms underlying resistance to treatment and malignant transformation, as well as the intratumoral heterogeneity and interaction of tumor cells and host immunity. Recent advances in omics analysis techniques, such as next-generation sequencing (NGS), have enabled us to obtain omics data more easily and accelerated our ability to integrate this information and precisely characterize cases. In our project, we have already collected more than 100 pairs of human glioma/normal tissue samples, of which some are multiple specimens collected from initial and recurrent tumors, and some include multiple specimens collected from different regions within a single tumor. We used our in-house algorithms, composed of alignment and variant calling programs, to analyze omics data from multiple platforms, such as whole-exome sequencing (WES), RNA sequencing (RNA-seq), and methylation array, with our original cohort of glioma patients. Using several informatics tools, the information about genetic and epigenetic status and expression signatures were analyzed. Those data are expected to provide key information for investigating the mechanisms discussed above. Through this project, we hope to improve strategies for personalized therapy based on comprehensive omics data.

  Study JGAS000004

• Indonesian Single Cell Data Access Committee

  This Data Access Committee manage and oversee the Data Access Policy sets forth the terms, conditions, and limitations governing access to and use of the raw sequencing data of samples in the Indonesian Single Cell dataset by individuals who are not part of the Data Producer. The IndoSC dataset comprises 203 human whole blood and PBMC samples collected in 4 communities in both Bali and Papua Provinces in Indonesia, that was collected to study the immune cell atlas of ancestrally- and environmentally diversed populations in Indonesia.

  Dac EGAC50000000870

• UK10K NEURO ASD SKUSE

  In the UK10K project we propose a series of complementary genetic approaches to find new low frequency/rare variants contributing to disease phenotypes. These will be based on obtaining the genome wide sequence of 4000 samples from the TwinsUK and ALSPAC cohorts (at 6x sequence coverage), and the exome sequence (protein coding regions and related conserved sequence) of 6000 samples selected for extreme phenotypes. Our studies will focus primarily on cardiovascular-related quantitative traits, obesity and related metabolic traits, neurodevelopmental disorders and a limited number of extreme clinical phenotypes that will provide proof-of-concept for future familial trait sequencing. We will analyse directly quantitative traits in the cohorts and the selected traits in the extreme samples, and also use imputation down to 0.1% allele frequency to extend the analyses to further sample sets with genome wide genotype data. In each case we will investigate indels and larger structural variants as well as SNPs, and use statistical methods that combine rare variants in a locus or pathway as well as single-variant approaches. This sample set of UK origin consists of clinically identified subjects with Autism Spectrum Disorders, mostly without intellectual disability (ie. Verbal IQs >70). The subjects represent children and adults with Autism, Asperger syndrome or Atypical Autism, identified according to standardized research criteria (ADI-algorithm, ADOS). A minority has identified comorbid neurodevelopmental disorders (e.g. ADHD). Family histories are available, with measures of broader phenotype in first-degree relatives.For further information on this cohort please contact David Skuse (d.skuse@ucl.ac.uk).

  Study EGAS00001000114

• University of Miami Study on Genetics of Autism and Related Disorders (AutismDisorders)

  Autism spectrum disorders (ASD) are neurodevelopmental in origin and characterized by impairments in reciprocal social interaction and communication accompanied by restricted and repetitive patterns of interest or behavior. With improved surveillance and a broadening of the diagnostic criteria, the most recent prevalence studies suggest that ASD may affect as many as 1/166 children in the US. Treatments are limited resulting in little impact on the profound morbidity. Little is known about the etiology of ASD, but there is a strong genetic component. Genetic studies over the past decade have failed to identify definitive ASD genes, but have clearly shown that the underlying genetics are more complex than anticipated with the likelihood that multiple genes are acting independently and/or interactively. With this realization the field of ASD genetics is at a critical juncture. To move forward we must embrace new and creative paradigms to successfully dissect the genetic etiology of this disease. Specifically the current study will: Extend our ascertainment to the full range of ASD. We will increase our ASD dataset by collecting 600 families who meet clinical diagnostic criteria for the three most common ASDs: autism (AUT), Asperger disorder (ASP) and Pervasive Developmental Disorder-NOS (PDD-NOS). Phenotype assessment will be expanded to include the Social Responsiveness Scale (SRS) and detailed seizure data. Ascertainment will focus on parent-child trios. Further characterize the ASD-associated variations in the Gamma-Aminobutyric Acid (GABA) receptor (GABR) subunits. We will complete our GABR subunit variant analysis, including coding, UTR, regulatory, and conserved intronic sequence, concentrating on GABRA4 and GABRB1. We will also investigate the role of variation in other GABR subunits. All AUT specific findings will be examined in the entire ASD dataset. Identify the chromosome 19p ASD gene. Multiple genome-wide screens have provided significant evidence for linkage to Chromosome 19p and we have found evidence for significant association in the linked families within an ~3 Mb region. We will genotype 768 SNPs spaced at ~4 kb to refine the candidate region and delineate specific candidate genes for further testing. We will screen the strongest associated candidate genes for additional variants and evaluate evidence for association in the entire ASD dataset (SA5). Develop and apply the Phenotypic Homogeneity Distinction (PHD) algorithm for identification of the phenotypic signature of linkage and/or association signals. The PHD algorithm identifies phenotypic covariates that discriminate a target sample subset (e.g. the positively linked families or families carrying the associated risk allele) from its complement. The resulting PHD discriminators will define a homogeneous subset from our newly-ascertained ASD dataset to use, as a confirmatory dataset and for localization within genes under study in our other aims. Test for gene-gene interactions. To fully explain the spectrum of autism risk, we will test for interactions between genetic variations associated with ASD (such as those in GABR subunit genes). We will build upon our experience using the MDR method and extend our analyses across biological pathways using the entire ASD data set.

  Study phs000436

• Rare Genetic Steroid Disease Consortium (GSD) Apparent Mineralocorticoid Excess (AME) Syndrome Natural History Clinical Protocol

  The objective of this project is to observe the natural history of apparent mineralocorticoid excess (AME). AME is a rare monogenic hypertensive disease first described by the Principal Investigator, Dr. Maria I. New, in 1977 [1], for which the first mutation in the causative HSD11B2 gene was reported by her group in 1995. [2] Little is known about the progression of this rare hypertensive disorder, which is defined by the presence of hypertension in conjunction with low renin, low to absent levels of the mineralocorticoid aldosterone, elevated urinary cortisol/cortisone metabolite ratio 5β-tetrahydrocortisol (THF) + allo-THF/ tetrahydrocortisone (THE) (i.e., THF+αTHF/THE) and the presence of mutations in the HSD11B2 gene on both alleles. The range of symptoms reflecting progressive end-organ damage is wide in the small number of affected individuals studied to date. It is important to develop accurate information on the longitudinal pattern of progression (natural history) of AME not only because it may improve the care of affected individuals, but also because it may serve as a platform for understanding the role of mineralocorticoid excess in other forms of low-renin hypertension, which constitute 40% of all forms of hypertension. In this study, we will recruit as widely as possible through the Rare Diseases Clinical Research Network (RDCRN) to identify individuals with the triad of low renin, low aldosterone, and elevated urinary THF+αTHF/THE and confirm their disorder as AME by molecular genetic testing of the HSD11B2 gene. We will gather clinical and biochemical data yearly for the duration of the grant. We will describe phenotype and genotype at diagnosis and follow the progression or regression of symptoms over time under standard treatment, with rigorous review of end organs potentially damaged by chronic hypertension. Finally, we will study the natural history of the carriers of HSD11B2 mutations, i.e., the heterozygote relatives of the probands, in order to ascertain evidence of existing or developing hypertension and resulting end-organ damage. This will be the first rigorous study of AME heterozygotes. The participant accrual for AME-affected patients and the carriers of HSD11B2 mutations will be at least two years, but as long as seven years.

  Study phs000603

• Somatic_mutation_and_clonal_evolution_in_the_human_bladder_TGS

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The study includes targeted sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer.

  Study EGAS00001002659

• Dataset for 9 samples from the study EGAS00001007891

  This dataset links 9 samples from the study "Phosphoproteomics adds value to treatment recommendations in molecular tumor boards" (EGAS00001007891) to the study EGAS00001007934. Further information about the samples can be found in the respective studies.

  Dataset EGAD50000002316

• Ischemic Stroke Genetics Study (ISGS)

  The third leading cause of death in the United States, stroke is an acute neurological event leading to death of neural tissues. Although the majority of strokes are ischemic strokes, meaning there is oxygen deprivation to the brain, almost 20% of strokes are hemorrhagic, resulting from bleeding into the brain. Stroke is a complex disorder and likely multigenic in nature, resulting from a combination of genetic and environmental factors. These well characterized risk factors that contribute to the incidence of stroke include hypertension, cardiac disease, sickle cell disease, hyperhomocysteinemia, family history of stroke and smoking. ISGS aim is to perform a prospective genetic association study of ischemic stroke focusing on the hemostatic system. ISGS is a 5-center case-control study of first-ever ischemic stroke cases and concurrent controls individually matched for age, sex and recruitment site. This data includes that from subjects both banked in the NINDS repository with biologicals publicly available, and those whose samples are not banked/not available. Important links to apply for individual-level data Data Use Certification Requirements (DUC) Apply here for controlled access to individual level data Participant Protection Policy FAQ --> This study utilized the NINDS Repository Cerebrovascular/Stroke Study, and neurologically normal controls from the sample population which are banked in the National Institute of Neurological Disorders and Stroke (NINDS Repository) collection for a first stage whole genome analysis.

  Study phs000102

• Combined MEK and BCL-2/XL inhibition is effective in high-grade serous ovarian cancer patient-derived xenograft models and BIM levels are predictive of responsiveness

  Most patients with late stage high-grade serous ovarian cancer (HGSOC) initially respond to chemotherapy but inevitably relapse and develop resistance, highlighting the need for novel therapies to improve patient outcomes. The MEK/ERK pathway is activated in a large subset of HGSOC, thus making it an attractive therapeutic target. Here, we systematically evaluated the extent of MEK/ERK pathway activation and efficacy of pathway inhibition in a large panel of well-annotated HGSOC patient-derived xenograft (PDX) models. The vast majority of models were nonresponsive to the MEK inhibitor cobimetinib (GDC-0973) despite effective pathway inhibition. Proteomic analyses of adaptive responses to GDC-0973 revealed that GDC-0973 upregulated the pro-apoptotic protein BIM, thus priming the cells for apoptosis regulated by BCL2-family proteins. Indeed, combination of both MEK inhibitor and dual BCL-2/XL inhibitor (ABT-263) significantly reduced cell number, increased cell death and displayed synergy in vitro in most models. In vivo, the GDC-0973 and ABT-263 combination was well tolerated and resulted in greater tumor growth inhibition than single agents. Detailed proteomic and correlation analyses identified two subsets of responsive models – those with high BIM at baseline that was increased with MEK inhibition and those with low basal Bim and high pERK levels. Models with low BIM and low pERK were non-responsive. Our findings demonstrate that combined MEK and BCL-2/XL inhibition has therapeutic activity in HGSOC models and provide a mechanistic rationale for clinical evaluation of this drug combination as well as the assessment of the extent to which BIM and/or pERK levels predict drug combination effectiveness in chemoresistant HGSOC.

  Study EGAS00001003427

• Natural History, Pathogenesis and Outcome of Melorheostosis

  Melorheostosis is a rare osteosclerotic disease resulting in exuberant excessive bone growth with a characteristic radiographic appearance often described as "dripping candle wax". As a result of these bony formations, patients report mild to moderate pain that interferes with their routine activities. It is usually diagnosed on radiographs but bone biopsy may be performed to exclude other osteosclerotic diseases and/or osteosarcoma. Deformities, limb-length discrepancy, muscle atrophy, neurological deficit have been reported as complications. A subset of patients have somatic mutations in MAP2K1. The cause of this disease is not known in all patients, the natural history poorly described and there is no clearly-defined systemic therapy. We propose a prospective observational study to investigate the natural history and pathogenesis of the disease. Subjects will undergo standardized initial evaluation and medically indicated testing. Skin biopsies may be performed to test for known mutations related to melorheostosis, and if negative affected bone and/or skin may be sent for genetic testing for acquired somatic mutations in genes that control bone homeostasis. Enrolled subjects will be followed every two to three years for assessment of disease progression and receive clinically indicated testing and treatment. The study of this rare bone disease offers the potential to generate new insights, provide answers as well as generate new questions into the biology of the skeletal and mineral metabolism.

  Study phs001976

• Genome-Wide Association Study of Preterm Birth

  Preterm birth (PTB, born before 37 weeks of gestation) is a leading cause of neonatal mortality and post-natal morbidity. PTB affects one in nine all live births in the U.S. Notably, the highest rate of PTB occurs among African Americans (one in six). PTB is a complex trait, likely determined by multiple environmental and genetic factors and their interactions. We demonstrated strong familial aggregation of preterm and low birthweight in the US Blacks and Whites (Wang et al, NEJM, 1995) and conducted the largest candidate gene study of preterm birth at that time (Hao et al, HMG, 2004). We showed that a subset of mothers with certain metabolic gene variants are particularly vulnerable to the adverse effects of cigarette smoking on low birthweight and preterm births (Wang et al, JAMA, 2002). We also published a number of papers that examined the effect of maternal pre-pregnancy BMI, micronutrient status, stress and environmental toxins on the risk of preterm birth and related conditions. This project, supported by a grant from the NICHD (2R01HD41702, PI, Xiaobin Wang), aimed to conduct a genome-wide association study (GWAS) and apply advanced statistical methods to identify susceptibility loci of PTB in a predominantly urban low-income African American sample, a subset of the Boston Birth Cohort. PUBLIC HEALTH REVELANCE: We anticipate that this study will lead to the identification of novel genetic loci of PTB and gene-environment interactions. Such findings not only will provide important insights into mechanisms leading to PTB, but also may help identify women at high-risk of PTB, which in turn, may lead to the development of early and targeted interventions that can prevent PTB or mitigate the severity and consequences of PTB.

  Study phs000332

• Single Cell RNASeq for ARMS tumors

  6 samples from 3 mice related to Alveolar Rhabdomysarcoma. In this study, we employ scRNA-seq to analyze ARMS tumors from a conditional mouse model of ARMS. The conditional knock-in mouse model of ARMS, in which the Pax3-Foxo1 allele is activated in the skeletal muscle cell lineage via Myf6Cre (Myf6CrePax3P3Fm/P3FmTrp53F2-10/F2-10; referred to hereafter as GEMM-ARMS) has been described previously23,24. These mice also carry Cre-activated reporters, eYFP to label Pax3::Foxo1-expressing cells and dsRED2 to labels Myh2-expressing cells. Some tumors are derived from GEMM-ARMS mice, and some are allografts of GEMM-ARMS tumors into immunodeficient mice

  Dataset EGAD50000002241

• Genome-wide expression profiles to compare array-based, RNAseq and NanoString technologies in patients with resected pancreatic ductal carcinoma.

  Using formalin-fixed paraffin embedded (FFPE) tissues collected prospectively in patients with resected pancreatic ductal carcinoma (PDC) we generated genome-wide expression profiles to compare array-based, RNAseq and NanoString technologies. Samples included in the study were collected 17 patients. After careful selection by the pathologist of 17 malignant cells-enriched, 7 stroma-enriched, and 6 normal (normal pancreas in 4 cases and normal duodenum in 2 cases) regions, sections were macrodissected, and total RNA extracted. Two additional FFPE-frozen matched-paired PDAC from our local Biobank were included. Our study represents the most extensive work comparing three technologies to generate gene expression profiles from FFPE samples, and provides technical guidance for future biomarker studies in samples collected prospectively in the context of clinical trials.

  Study EGAS00001002501

• T cell responses of ALS patients

  In this project, we aimed to understand how T cell responses contribute to the disease progression of amyotrophic lateral sclerosis (ALS). The present data is on single-cell sequencing isolated from human cerebrospinal fluid (CSF) cells from both ALS patients (n=5) and controls (n=4). This analysis was conducted as part of a bigger project which is summarized in the section below. We used flow cytometry to define T cell subsets and phenotypes in blood and CSF samples collected at the time of diagnosis on a cohort of 89 newly diagnosed ALS patients in Stockholm, Sweden. High frequency of CD4+FOXP3- effector T cells in blood and CSF was associated with poor survival whereas high frequency of activated regulatory T (Treg) cells and high ratio between activated and resting Treg cells in blood was associated with better survival. T cell profiles also predicted disease progression rate. On an independent cohort of cases and controls, we used single cell transcriptomics data to demonstrate that ALS patients had altered T cell gene expression patterns and clonally expanded CD4+ and CD8+ T cells in CSF. In summary, T cell responses contribute to disease progression of ALS, supporting modulation of adaptive immunity as a viable therapeutic option.

  Study EGAS00001006675

• Assessment of genomic copy number alterations in breast cancer

  The aim of this study was to assess genomic copy number alterations in a panel of breast cancer cell lines. These data were used to identify common aberrations associated with breast cancer, and also to identify aberrations associated with response to therapeutic compounds.

  Study EGAS00000000059

• Assessment of genomic copy number alterations in breast cancer

  The aim of this study was to assess genomic copy number alterations in a panel of breast cancer cell lines. These data were used to identify common aberrations associated with breast cancer, and also to identify aberrations associated with response to therapeutic compounds.

  Study EGAS00001000585

• National Cancer Institute Clinical and Laboratory Analysis of Familial Cancer

  The purpose of this study is to continue the analysis begun on 09C0079 which was focused on identification of the genetic mutation associated with a new gastric polyposis syndrome, Gastric Adenocarcinoma and Proximal Polyposis of the Stomach (GAPPS). GAPPS, first described in 2012, is an autosomal dominant gastric polyposis syndrome that confers a substantial risk for gastric adenocarcinoma. The GAPPS phenotype consists of a carpeting of greater than 100 fundic gland polyps (FGPs) in the oxyntic mucosa of the gastric body and fundus, with antral sparing with some FGPs displaying high-grade dysplasia. This is in contrast to sporadic FGPs that are benign, most often are not associated with high-grade dysplasia though low-grade dysplasia has been reported, and are fewer in number. Gastric FGPs have been found to be associated with Familial Adenomatous Polyposis (FAP) and attenuated FAP, which is an autosomal dominant condition associated with germ line mutations in APC which confers a phenotype consisting of multiple (>100) adenomatous polyps in the colon and rectum developing after the first decade of life. FGPs are reported to occur in 12-84% of patients with FAP, whereas sporadic FGPs are identified in ~5% of patients undergoing upper gastrointestinal endoscopy. Gastric adenocarcinoma arising from FGPs in individuals with FAP have been reported. Other manifestations of FAP and AFAP include polyps in the upper gastrointestinal tract, congenital hypertrophy of retinal pigment epithelium, osteomas and epidermoid cysts, supernumerary teeth, desmoid formation, and other malignancies such as thyroid, small bowel cancer, hepatoblastoma, and medulloblastoma. Thus far there are no reports in GAPPS of polyposis arising in the esophagus, gastric antrum, pylorus, small intestine, or colon.

  Study phs001935

• Pulmonary Fibrosis and Telomerase Dysfunction

  This study was used to perform an exome-limited analysis of whole genome sequencing data of patients with idiopathic pulmonary fibrosis (IPF) or familial pulmonary fibrosis. Case cohorts were derived from local centers at University of Southwestern or Columbia University, and subjects were from the IPFnet cohort of clinical trial. Rare damaging mutations in the coding regions of cases were compared to healthy controls, and gene burden analysis was performed to identify enrichment of novel risk genes in the development of pulmonary fibrosis. 

  Study phs002692

• Kids First: Whole Genome Sequencing Studies of Multiplex Nonsyndromic Cleft Lip/Palate Families

  Nonsyndromic cleft lip with or without cleft palate (NSCLP) is a common birth defect that affects approximately 135,000 newborns worldwide, and imposes significant medical, psychosocial and financial burdens to affected individuals and their families. Genetic variation in numerous genes has been associated with NSCLP, however the exact mechanisms by which they contribute to the condition remain largely unknown. Here, we will use whole genome sequencing and robust analytical approaches to systematically evaluate the causes of NSCLP in 923 individuals from large multigenerational families.

  Study phs002626

• Genetic Causes of Growth Disorders

  Description of the disorder: A very common disorder presenting to pediatricians/pediatric endocrinologists is childhood growth failure. Sometimes the cause is evident, for example, growth hormone deficiency. In other children, the etiology remains unknown despite extensive evaluation, resulting in the unhelpful diagnosis of severe idiopathic short stature (SISS). These conditions are quite heterogeneous, including children with isolated growth failure and others who also have other abnormalities such as developmental delay or a constellation of congenital anomalies (syndromic short stature). Sometimes, the disorder appears to primarily affect the growth plate, which drives skeletal growth and thereby determines overall body proportions, whereas in other children, the disorder affects skeletal and non-skeletal tissues equally. Some cases of SISS have a polygenic inheritance while others appear to follow a Mendelian inheritance model, recessive, dominant or X-linked. Very recently, genome-wide analysis for copy number variants (CNVs) and whole-exome sequencing have begun to identify some of the molecular etiologies of these disorders.1 Identifying the molecular etiology of growth disorders has clinical and scientific value. Clinically, identifying a molecular cause prevents extensive further testing and may direct anticipatory care for associated medical problems. For example, we recently studied aggrecan (ACAN) gene mutations in families with autosomal dominant short stature and accelerated skeletal maturation. These mutations affect both growth plate cartilage, causing linear growth failure, and also articular cartilage, causing osteochondritis dissecans and early-onset osteoarthritis.1 Etiological classification of idiopathic growth failure allows more precise characterization of prognosis and response to treatment, which are currently highly imprecise because of the locus heterogeneity. In some cases, finding the genetic etiology points to a novel treatment approach that targets the specific molecular pathway involved. The proposed project is central to the main focus of our group, the Section on Growth and Development, NICHD. Our primary goal is to investigate cellular and molecular mechanisms governing childhood growth and to gain insight into the many human genetic disorders causing childhood growth failure. The proposed project is well suited for the intramural program because it takes advantage of Clinical Center expertise to phenotype subjects with SISS. Study subjects: We will study subjects with SISS and nuclear family members. SISS will be defined by height SDS < -2.5 for age without evident cause after routine evaluation including: growth hormone axis evaluation; thyroid function testing; celiac disease screening; urinalysis; CBC; chemistry; karyotype (girls, for Turner syndrome); and testing for single gene defects based on the clinical evaluation (for example, SHOX or Noonan-associated genes). Candidate families will include isolated growth disorders and growth disorders that are accompanied by congenital anomalies, developmental delay, or other syndromic short stature. Strong preference will be given to subjects with a severe phenotype and a pedigree that indicates a Mendelian inheritance. Multiple independent families with the same phenotype will have priority. The pool of applicants for recruitment is large, and we receive many inquiries by emails and phone consultations from pediatric endocrinologists for advice regarding diagnosis and management of unusual growth disorders, including familial disease. Often these families are seeking further evaluation and are willing to participate in a research study. From this pool, we will be selecting pedigrees with very favorable Mendelian characteristics, for example de novo dominant occurrences where two normal parents have a child with SISS, and the child grows up to be an adult who passes this phenotype on to multiple grandchildren in the next generation. Subjects and family members will be brought to the NIH Clinical Center (NIHCC) for outpatient evaluation. Participants will be evaluated by pediatric endocrinology fellows (as part of our training program) and by senior staff to establish the clinical findings and construct a pedigree. Subjects will receive additional biochemical and imaging studies at the Clinical Center to complete the phenotyping and assign affected status. The growth abnormality will be evaluated by assessing body proportions, relative organ size, and skeletal imaging as indicated. Associated clinical abnormalities beyond altered growth will be characterized with the help of other Clinical Center subspecialists. Subjects and family members will be evaluated by SNP microarray and whole-exome sequencing. We anticipate 4-5 persons for each of 16-20 families, for a total of 72-90 whole-exome sequences. Half of the families will be recruited and studied within the first year and half in the second year. We will use freshly collected peripheral blood as the DNA source for SNP array and NextGen Sequencing. Analytic approach: The candidate genes will be chosen based on 1) inheritance state consistency, 2) population frequency in the ESP and UDP databases, and 3) predictions of deleteriousness. We will use VarSifter and the B road Institute Integrated Genome Viewer to filter and visualize these data. The genetic model will be dependent on the family's pedigree. For a simple trio, we will explore variants using genetic models including autosomal recessive, de novo (dominant), compound heterozygous, deletion/point mutation recessive, and X-linked (male only). The candidate variants will be identified using Boolean logic sets in VarSifter following intramural NHGRI/UDP methods. We will also use SNP microarray data to identify copy number variations, complete/single copy deletions, duplications, non-paternity, consanguinity for homozygosity mapping, uniparental isodisomy, mosaicism, and segregation patterns (bed file generation for use in VarSifter filter work). After a list of candidate sequence variants has been generated, annotation will include using the Exome Variant Server, Polyphen-2, MutationTaster, Sift, and CADD predictions of deleteriousness. Biological laboratory data will be included to prioritize candidate variants. Our group has expertise in the molecular mechanisms regulating both skeletal growth2,3 and growth of other tissues4,5, which may be helpful in this phase of the analysis. The most promising candidate mutations will be confirmed by Sanger sequencing and studied functionally, in vitro and/or in vivo. For mutations that affect skeletal growth, we will use experimental systems related to growth plate cartilage. For in vitro studies, we have experience transfecting chondrocyte cell lines, such as ATDC5, and primary chondrocytes. We will determine whether the mutation alters protein and/or cell function. In vivo studies can be used to explore pathophysiology. We have recently successfully used a new approach, the CAS9/CRISPR system to knockout multiple loci in mice (unpublished), which can be used again in the future to create mouse models efficiently. 1J Clin Endocrinol Metab, 2014 (PMID: 24762113) 2J Mol Endocrinol, 2014 (PMID: 24740736) 3Hum Mol Genet, 2012 (PMID: 22914739) 4Proc Natl Acad Sci U S A, 2013 (PMID: 23530192) 5Endocr Rev, 2011 (PMID: 21441345)

  Study phs001617