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• Arcagen - NET / NEC G3

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here were are submitting the dataset that contains NGS files in .BAM format from 85 patients with extra-pulmonary neuroendocrine tumour or cancer grade 3 (NET / NEC G3).

  Dataset EGAD50000000913

• MultiOMICS study of a pair of infant monozygotic twins with concordant B-cell ALL (WGBS)

  B-cell acute lymphoblastic leukemia (B-cell ALL) is the most common cancer in childhood. Studying identical twins with B-cell ALL provides a unique and tractable model for deciphering the developmental timing of pre- and post-natal mutations contributing to clonal evolution. To date, this has mainly focused on major cytogenetic subgroups of childhood B-cell ALL, including MLL fusions, ETV6-RUNX1, hyperdiploidy, and BCR-ABL1. However, formal demonstration of the prenatal origin and “backtracking” the natural history of the leukemia remains understudied in “B-other”/Normal Karyotype (NK) B-cell ALL. To characterize the epigenetic landscape of this particular leukemia subtype, we performed DNA bisulfite-sequencing on a pair of 8-month-old monozygotic twins diagnosed with concordant “B-other”/NK B-cell ALL.

  Dataset EGAD00001005018

• MultiOMICS study of a pair of infant monozygotic twins with concordant B-cell ALL (WGS)

  B-cell acute lymphoblastic leukemia (B-cell ALL) is the most common cancer in childhood. Studying identical twins with B-cell ALL provides a unique and tractable model for deciphering the developmental timing of pre- and post-natal mutations contributing to clonal evolution. To date, this has mainly focused on major cytogenetic subgroups of childhood B-cell ALL, including MLL fusions, ETV6-RUNX1, hyperdiploidy, and BCR-ABL1. However, formal demonstration of the prenatal origin and “backtracking” the natural history of the leukemia remains understudied in “B-other”/Normal Karyotype (NK) B-cell ALL. To characterize the genetic landscape of this particular leukemia subtype, we performed whole genome DNA- and B-cell receptor (BCR)- on a pair of 8-month-old monozygotic twins diagnosed with concordant “B-other”/NK B-cell ALL.

  Dataset EGAD00001005017

• Full blood mRNA sequencing of myotonic dystrophy type 1 patients after cognitive behavioural therapy

  Myotonic dystrophy type 1 (DM1) is an incurable multisystem disease caused by a CTG-repeat expansion in the DM1 protein kinase (DMPK) gene. The OPTIMISTIC clinical trial demonstrated positive and heterogenous effects of cognitive behavioral therapy (CBT) on the capacity for activity and social participations in DM1 patients. Here, we performed mRNA sequencing of full blood for 27 patients of the OPTIMISTIC cohort before and after the CBT intervention. We identified 608 genes for which their expression was significantly associated with the disease causing CTG-repeat expansion, as well as with 1176 genes significantly associated with the average clinical response towards the intervention. Remarkably, all 97 genes significantly associated with both returned to more normal levels in patients who benefited most from CBT. This trend was consistent with the difference observed between DM1 patients and controls in an earlier study of blood mRNA expression levels, singling these genes out as candidate biomarkers for therapy response. Together these results highlight the ability to find disease relevant information in full blood of DM1 patients and open new avenues to monitor therapy effects.

  Study EGAS00001005830

• Integrated Genomic Analysis of Chronic Lymphocytic Leukaemia

  Chronic lymphocytic leukaemia (CLL) is a frequent and heterogeneous disease whose genetic alterations determining the clinicobiological behaviour are not fully understood. Here, we describe a comprehensive evaluation of the genomic landscape of 452 CLLs and 54 monoclonal B-lymphocytosis (MBL), a precursor disorder. This study provides an integrated portrait of the genomic landscape of CLL, identifies new recurrent mutations acting as drivers of the disease, and suggests clinical interventions which may improve the management of patients with this neoplasia. The data here included was described in the ICGC-CLL manuscript published by Puente et al (Nature 2015). Note that complementary RNA-seq data generated within the IGCG-CLL can be found in EGAS00001000374.

  Study EGAS00001001306

• The patterns and dynamics of genomic instability in metastatic pancreatic cancer

  Pancreatic cancer is an aggressive malignancy with a five-year mortality of 97–98%, usually due to widespread metastatic disease. Previous studies indicate that this disease has a complex genomic landscape, with frequent copy number changes and point mutations, but genomic rearrangements have not been characterized in detail. Despite the clinical importance of metastasis, there remain fundamental questions about the clonal structures of metastatic tumours, including phylogenetic relationships among metastases, the scale of ongoing parallel evolution in metastatic and primary sites, and how the tumour disseminates. Here we harness advances in DNA sequencing to annotate genomic rearrangements in 13 patients with pancreatic cancer and explore clonal relationships among metastases. We find that pancreatic cancer acquires rearrangements indicative of telomere dysfunction and abnormal cell-cycle control, namely dysregulated G1-to-S-phase transition with intact G2–M checkpoint. These initiate amplification of cancer genes and occur predominantly in early cancer development rather than the later stages of the disease. Genomic instability frequently persists after cancer dissemination, resulting in ongoing, parallel and even convergent evolution among different metastases. We find evidence that there is genetic heterogeneity among metastasis-initiating cells, that seeding metastasis may require driver mutations beyond those required for primary tumours, and that phylogenetic trees across metastases show organ-specific branches. These data attest to the richness of genetic variation in cancer, brought about by the tandem forces of genomic instability and evolutionary selection.

  Study EGAS00000000064

• Data upcycling, powered by EGA

  In 2012 a collaborative effort headed by the teams of Carlos Caldas in Cambridge, UK and Samuel Aparicio, Canada, produced a pivotal study aimed at defining the mutational landscape of breast cancer. They gathered a collection of over 2000 breast cancer samples (METABRIC) associated with long-term clinical follow-up. They delineated an array of inherited and somatically acquired genetic variants and associated them to gene expression. This led to the identification of putative cancer-driving events and improved stratification of breast cancer patients. The study elicited huge attention and was tackled as herculean effort by fellow researchers. Cristina Curtis and her colleagues deposited the data in the EGA archive (EGAS00000000083). What they probably could not foresee is that their data would be reused more than 100 times, becoming one of the most downloaded datasets at EGA. In 2015, Frederik S. Varn and colleagues accessed the above-mentioned data from the New Hampshire, USA, to correlate it to transcriptional programs of hematopoietic cells infiltrated in breast tumours and found that those can influence patients' prognosis. Their findings, published in Nature Communications, improved the understanding of the interplay between immune system and cancer. Again, in 2017 the dataset was downloaded by an Italian/Polish collaboration and used to corroborate their mechanistic study that demonstrate how a long non-coding RNA (lncRNA) is aberrantly localized into the chromatin, where it modulates oncogenic isoforms expression, thus contributing to breast cancer. To date, the METABRIC dataset has been reused to contribute to 147 publications. Its impact on breast cancer research is incalculable, and it even spread beyond that, with recent contributions to the understanding of pan-cancer mechanisms and features. Some of the publications are translating into improvements in diagnosis and treatment of different types of breast cancer. This is just an example of how data upcycling can amplify the potential of any dataset, well past the scope of its creation, the imagination of its owners and any geographical border. At EGA, we are proud to empower such fruitful worldwide cycles of knowledge, providing a platform that enables safe sharing of sensitive genetic data.

  Blog data-upcycling-powered-by-ega

• 33 patients with Monoclonal Gammopathy of Undetermined Significance (MGUS)

  Monoclonal gammopathy of undetermined significance (MGUS) is a premalignant precursor of multiple myeloma (MM) with a 1% risk of progression per year. Although targeted analyses have shown the presence of specific genetic abnormalities such as IGH translocations, RB1 deletion, 1q gain, hyperdiploidy or RAS genes mutations, little is known about molecular mechanism of malignant transformation. We have performed whole exome sequencing together with SNP array analysis in 33 flow-cytometry separated abnormal PC samples of MGUS patients to describe somatic gene mutations and chromosome changes at the genome-wide level. Non-synonymous mutations (NS-SNVs) and copy number alterations (CNAs) were present in 97.0% and in 63.6% of cases, respectively. Importantly, the number of somatic mutations was significantly lower in MGUS compared to MM (p<10-4) and we have identified 6 myeloma significantly mutated genes which are KRAS, NRAS, DIS3, HIST1H1E, EGR1 and LTB in the MGUS dataset. We also found a positive correlation with increasing chromosome changes and somatic mutations. IGH translocations were present in 27.3% of cases comprising t(4;14), t(11;14), t(14;16) or t(14;20) and were in a similar frequency to MM, which corresponded with primary lesion hypothesis. Data from this study showed MGUS is a genetically comprehensive disease, however overall genetic instability is significantly lower compared to MM.

  Dataset EGAD00001001901

• Transcriptomic classes of BCR-ABL1 lymphoblastic leukemia

  In BCR-ABL1 lymphoblastic leukemia, treatment heterogeneity to tyrosine kinase inhibitors (TKIs), especially in the absence of kinase domain mutations in BCR-ABL1, is poorly understood. Through deep molecular profiling, we uncovered three transcriptomic subtypes of BCR-ABL1 lymphoblastic leukemia, each representing a maturation arrest at a stage of B-cell progenitor differentiation. An earlier arrest was associated with lineage promiscuity, treatment refractoriness, and poor patient outcomes. A later arrest was associated with lineage fidelity, deep and durable leukemia remissions, and improved patient outcomes. Each maturation arrest was marked by specific genomic events that control different transition points in B-cell development. Interestingly, these events were absent in BCR-ABL1+ pre-leukemic stem cells isolated from patients regardless of subtype, which supports that transcriptomic phenotypes are determined downstream of the leukemia-initialing event. Overall, our data indicate that treatment response and TKI-efficacy is an unexpected outcome of the differentiation stage at which this leukemia transforms.

  Study EGAS00001007167

• DIME study: Safety, dose-response and efficacy of treatment with Anaerobutyricum soehgenii on glucose metabolism in human subjects with metabolic syndrome

  The intestinal microbiota has been implicated in insulin resistance, although evidence regarding causality in humans is scarce. We herefore performed a phase I/II dose-finding and safety study on the effect of oral intake of the anaerobic butyrogenic Anaerobutyricum soehgenii on glucose metabolism in subjects with metabolic syndrome. We found that treatment with A. soehgenii was safe and observed an overall significant and dose-dependent increase in insulin sensitivity after 4 weeks in all treated subjects. This was accompanied by an altered microbiota composition and a change in bile acid metabolism. Finally, we show that metabolic response upon administration of A. soehgenii (defined as improved insulin sensitivity 4 weeks after A. soehgenii intake) is dependent on microbiota composition at baseline. These data in humans are promising and additional studies are needed to study long-term effects as well as modes of delivery.

  Study EGAS00001003498

• Mid-frequency hearing loss is a characteristic clinical feature of OTOA-associated hearing loss

  In this study, we performed NGS analysis of a large Japanese hearing loss cohort, and identified 7 patients with OTOA-associated hearing loss. As novel clinical features identified in this study, the audiometric configurations of OTOA-associated hearing loss patients was found to be mid-frequency.

  Study JGAS000200

• Modulation of the peripheral blood immune cell transcriptome by vitamin D3 supplementation in people with a first demyelinating event: a randomized placebo-controlled trial

  Vitamin D deficiency is a risk factor for developing multiple sclerosis (MS). Both in vitro and animal studies suggest an immunomodulatory effect of vitamin D. The PrevANZ trial, a phase IIb randomized placebo-controlled trial of oral vitamin D3 supplementation in people with a first demyelinating event (FDE), was conducted to determine if supplementation can prevent recurrent disease activity in this cohort at high risk of developing definite MS. As a sub-study of this trial, we used whole blood transcriptomic analyses to investigate the effect of vitamin D3 supplementation on peripheral immune cells in people with an FDE, and to gain insight into potential mechanisms by which vitamin D3 may regulate MS risk and disease activity. The PrevANZ trial randomized participants to 1000 IU, 5000 IU or 10,000 IU daily of oral vitamin D3 or placebo. Peripheral blood was collected at baseline and 12 weeks in PAXgene Blood RNA tubes. Transcriptomic datasets were generated by RNA sequencing.

  Study EGAS00001007346

• Genome-wide Association Study of Adiposity in Samoans

  The research goal of this study is to identify genetic variation that increases susceptibility to obesity and cardiometabolic phenotypes among adult Samoans using genome-wide association (GWAS) methods. DNA from peripheral blood and phenotypic information were collected from 3,119 adult Samoans, 23 to 70 years of age. The participants reside throughout the independent nation of Samoa, which is experiencing economic development and the nutrition transition. Genotyping was performed with the Affymetrix Genome-Wide Human SNP 6.0 Array using a panel of approximately 900,000 SNPs. Anthropometric, fasting blood biomarkers and detailed dietary, physical activity, health and socio-demographic variables were collected. We are replicating the GWAS findings in an independent sample of 2,500 Samoans from earlier studies. After replication of genomic regions and informative SNPs in those regions, we will determine sequences of the important genes, and determine the specific genetic variants in the sequenced genes that are associated with adiposity and related cardiometabolic conditions. We will also identify gene by environment interactions, focusing on dietary intake patterns and nutrients.

  Study phs000914

• Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older

  The Cardiovascular Health Study (CHS) is a prospective study of risk factors for development and progression of CHD and stroke in people aged 65 years and older. The 5,888 study participants were recruited from four U.S. communities and have undergone extensive clinic examinations for evaluation of markers of subclinical cardiovascular disease. The original cohort, enrolled in 1989-90, totaled 5,201 participants. A supplemental cohort of 687 predominantly African-American participants was enrolled in 1992-93. Clinic examinations were performed at study baseline and at annual visits through 1998-1999, and again in 2005-2006. Examination components included medical and personal history, medication inventory, ECG, blood pressure, anthropometry, assessment of physical and cognitive function, and depression screening. Other components done less frequently included phlebotomy, spirometry, echocardiography, carotid ultrasound, cerebral magnetic resonance imaging, measurement of ankle-brachial index and retinal exam. Participants were contacted by telephone annually between exams to collect information about hospitalizations and potential cardiovascular events. Since 1999, participants have been contacted every six months by phone, primarily to identify cardiovascular events and to assess physical and cognitive health. Standard protocols for the identification and adjudication of events were implemented during follow-up. The adjudicated events are myocardial infarction, angina, heart failure (HF), stroke, transient ischemic attack (TIA), claudication and mortality. The Cardiovascular Health Study 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" section of this top-level study page phs000287 Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older. phs000226 STAMPEED: Cardiovascular Health Study (CHS) phs000301 PAGE: CaLiCo: Cardiovascular Health Study (CHS) phs000377 CARe: Candidate Gene Association Resource (CARe) phs000400 GO-ESP: Heart Cohorts Exome Sequencing Project (CHS) phs000667 CHARGE: Cardiovascular Health Study (CHS)

  Study phs000287

• DPY30 ChIP-seq

  H9 human embryonic stem cells (hESCs) were cultured in feeder-free chemically-defined conditions in medium containing 10ng/ml Activin A and 12ng/ml FGF2 (Vallier L. 2011, Methods in Molecular Biology, 690: 57-66). Chromatin immunoprecipitation was performed as described in Brown S. et al. 2011. Stem Cells 29: 1176-85 by using 5ug of anti-DPY30 antibody (Sigma, cat. number HPA043761). This protocol was performed in control hESCs (expressing a scrambled shRNA) and in hESCs stably expressing an shRNA against DPY30 (Sigma, clone n. TRCN0000131112).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/

  Dataset EGAD00001001268

• Metagenomic Analysis to Identify Novel Infectious Agents in Systemic Anaplastic Large Cell Lymphoma

  Anaplastic large cell lymphoma (ALCL) is a rare T-cell non-Hodgkin lymphoma (NHL). Risk of systemic ALCL is markedly increased among immunosuppressed people, such as those with human immunodeficiency virus (HIV) infection or solid organ transplant recipients. This increased risk in immunosuppressed populations suggests a viral etiology, given similar elevations for diffuse large B-cell lymphoma (DLBCL), Burkitt lymphoma, and Hodgkin lymphoma (caused by Epstein-Barr virus [EBV]) and other virus-related cancers in immunosuppressed individuals. EBV might be a plausible candidate, but most reported ALCL tumors are EBV-negative. Therefore, we conducted a metagenomic analysis of microbial associations with ALCL to determine whether a known or novel pathogen is associated with the tumor. We obtained archived formal fixed paraffin embedded (FFPE) ALCL tumor tissue from the Iowa cancer registry and an additional case from an immunosuppressed individual infected with human immunodeficiency virus. Controls included 3 diffuse large B-cell lymphomas (DLBCLs) in transplant recipients (shown to be related to Epstein-Barr virus [EBV] by in situ hybridization) and 3 breast cancers (no known viral etiology). RNA was extracted from FFPE specimens, and total RNA libraries were prepared using the KAPA RNA HyperPrep Kit (Roche). Five samples (IA01, IA53, IA57, IA07, and IA17) were sequenced on a NextSeq 500 (Illumina) and the remainder on a NovSeq 6000 (Illumina). Using novel computational approaches, we eliminated human reads and aligned residual non-human reads to known microbial references using GATK-PathSeq or conducted de novo assembly of unassigned reads using virID pipeline. Although EBV was detected in the 3 DLBCL controls, we did not detect EBV or any novel pathogen in ALCL tumors or in the breast cancers. Our study had a modest sample size and only one case arising in HIV-infected individual. Therefore, further studies are required to characterize the metagenome of systemic ALCLs, especially cases arising in immunosuppressed people.

  Study phs002064

• 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

• AVENIO Expanded ctDNA panel sequence alignments (BAMs) from plasma DNA of BC, CRC and NSCLC patients

  The AVENIO ctDNA Expanded Kit is a next-generation sequencing (NGS) liquid biopsy assay with a 77 gene panel (192 kb) containing genes in U.S. National Comprehensive Cancer Network (NCCN) Guidelines and emerging cancer biomarkers. This pan-cancer assay was applied to 48 plasma samples from patients with breast, colorectal and non-small cell lung cancer. After sequencing 150bp paired-end, reads were aligned to the hg38 genome with the AVENIO Oncology Analysis Software (version 2.0). These files are the deduplicated alignments generated by the analysis software used for subsequent variant, indel and CNV calling.

  Dataset EGAD00001006301

• Clinical and Genetic Analysis of Costa Rican Patients with Parkinson's Disease

  This study is a pilot study designed to describe the clinical and genetic landscape of Parkinson's disease in Costa Rica. While most genetic studies have been conducted on Europeans, few have examined Parkinson's disease in Costa Ricans. 118 patients and 97 controls were recruited at the Movement Disorders Unit of the Department of Neurology, Hospital San Juan de Dios, Caja Costarricense de Seguro Social, Costa Rica. Familial Parkinson's disease genes were sequenced using Next-Generation Sequencing. We also measured and obtained different sociodemographic and clinical information.

  Study phs002495

• Impact of Mutated CTCF DNA binding sites of Topologically associating domains on nearby Cancer Gene Regulation: A Multi-Omics Analysis

  Cutaneous squamous cell carcinoma (cSCC) is the most common lethal malignancy world-wide. Due in most part to the extremely high mutational burden (TMB) in cSCC, making sense of it’s non-coding and regulatory regional genomic variation has lagged that of other far less common cancers. This study presents the first investigation of mutations at CCCTC-binding factor binding sites (CTCFbs) of Topologically associating domains (TAD) across defined cSCC progression stages—primary non-metastatic (PNM), primary metastat-ic (PM), and lymph node metastasis (LNM).

  Study EGAS50000001686

• A single-cell atlas of human glioma

  Although tumor-propagating cells can be derived from glioblastomas (GBMs) of the proneural and mesenchymal subtypes, a glioma stem-like cell (GSC) of the classical subtype has not been identified. It is unclear if mesenchymal GSCs (mGSCs) and/or proneural GSCs (pGSCs) alone are sufficient to generate the spectrum of cellular heterogeneity observed in GBM. This study sheds light on a long-standing debate regarding lineage relationships among GSCs.

  Study EGAS00001003845

• Evaluation of Nuclear DNA from Rootless Hairs for Forensic Purposes

  The study aims to overcome current limitations in the recovery of DNA from small, difficult forensic samples. Particularly, our goal is to produce a robust laboratory protocol and the accompanying software to accelerate adoption, as well as to evaluate the reliability and robustness of both the laboratory and computational aspects of generating genotype files from minute and/or degraded DNA samples, such as single, rootless hairs.The data accompanying this study includes raw, paired-end reads from high-throughput sequencing of two panels of saliva, head hair, and pubic hair samples collected from anonymous volunteers at the University of California, Santa Cruz. The smaller set (Hair1.0) comprises 8 individuals, while the larger (Hair2.0) comprises 50 individuals, with 3 overlapping individuals between the two panels identified in post-collection analysis. We did not collect phenotype data or personally identifying information from the participants. For the Hair2.0 panel, only a subset of volunteers provided pubic hairs for DNA extraction and sequencing. Also included are saliva-derived genotype array data for all 8 individuals in the Hair1.0 panel and 44 of 50 individuals in the Hair2.0 panel.

  Study phs002979

• VESPA: Vanderbilt Electronic Systems for Pharmacogenomic Assessment

  The Vanderbilt Electronic Systems for Pharmacogenomic Assessment (VESPA) Project is a large electronic medical record (EMR)- and biobank-based initiative for translational pharmacogenomics discoveries. Key research resources utilized in this effort include the BioVU DNA databank and associated Synthetic Derivative database of clinical information, and software tools developed to identify drugs and clinical events using EHR-derived structured and unstructured ("free text") data. Cohorts include subjects with primarily drug-response phenotypes, and most cases and controls identified include three data types: ICD-9 codes, medication regimens, and medical test results. Advanced informatics methods, such as natural language processing, were also used for some phenotypes. Algorithms used event-sequence analyses to establish temporal relationships between drugs and phenotypes. Both cases and control algorithms excluded records that contained specific comorbidities and were refined to achieve positive predictive value (PPV) > 90%. For automated algorithms failing to meet this threshold, manual review was coupled with algorithms to validate that the included cases were true positives. A total of 11,639 subjects met phenotyping criteria for a least one of the 28 phenotypes investigated. Across all phenotypes cases and controls, 90% were reused as either a case or control for a least one other phenotype. Data are deposited for individual phenotypes in the VESPA substudies. Substudies: VESPA: Genome Wide Association Study of Serum Creatinine during Vancomycin Therapy and Vancomycin Pharmacokinetics - phs000894 VESPA: Genome Wide Study of Clinically Diagnosed Ace Inhibitor Cough - phs000992

  Study phs000991

• A Phase II Trial of High Dose Interleukin-2 and Multi-site Stereotactic Ablative Radiotherapy for Patients with Metastatic Renal Cell Carcinoma

  Immune-based therapies have improved outcomes for metastatic renal cell carcinoma (mRCC) but there is still a significant margin for improvement. Here, we report the results of a phase II trial combining high dose Interleukin-2 (HD-IL-2) with stereotactic ablative body radiotherapy (SAbR) for patients with metastatic renal cell carcinoma.

  Study EGAS00001003605

• The Nurses' Health Study (NHS) GWAS of Mammographic Density

  The Nurses' Health Study is an on-going prospective cohort study of women that was initiated in 1976. This specific study was part of a larger study to advance our knowledge of breast cancer etiology, expand the current knowledge of mammographic density, and clarify the relationship between mammographic density and breast cancer risk. We conducted a nested case control study of breast cancer among women who provided a blood sample. We then targeted our mammogram collection to participants that were selected as part of this nested case-control study (i.e. those who had provided a blood sample). The mammogram closest to the date of blood draw (~1989-1990) was used. We assessed mammographic breast density from digitized film images using a computer assisted thresholding method (Cumulus). The women in this study were genotyped using the Illumina Omni Express Platform.

  Study phs000975