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• Genetics of Lymphatic Anomalies from Center of Applied Genomics (CAG) at CHOP

  Lymphatic anomaly, a rare and devastating disease spectrum of mostly unknown etiologies, is characterized by diffuse or multicentric proliferation of dilated lymphatic vessels, and includes a variety of diagnoses: lymphangiectasia, central conducting lymphatic anomaly, generalized lymphatic anomaly, kaposiform lymphangiomatosis, and Gorham Stout disease. Currently, most treatments are considered palliative; lymphatic anomalies are often chronic debilitating conditions that require multiple yearly outpatient visits and hospital admissions for procedures that ameliorate symptoms, but do not correct the underlying cause. Identifying the causal genes will be hugely informative for our understanding of diseases. This will also allow for the development of affordable and successful diagnostic tests and therapies in keeping with "precision medicine" implementation.

  Study phs001802

• Epigenetic Analysis of Malnutrition

  The PROVIDE study (Dhaka, Bangladesh) is a randomized clinical trial platform which evaluated the efficacy of delayed-dose oral rotavirus vaccine as well as the benefit of an injectable polio vaccine replacing one dose of oral polio vaccine. This rigorous infrastructure supported the additional examination of hypotheses of vaccine underperformance. Primary and secondary efficacy and immunogenicity measures for rotavirus and polio vaccines were measured, as well as the impact of maternal and childhood malnutrition, environmental enteropathy, and additional exploratory variables. This study has been conducted to test the role of epigenetics in malnutrition, specifically the genome-wide role of histone modifications, which are known to provide a precise signature of metabolic state and immune system function.

  Study phs001073

• STAMPEED: Cardiovascular Health Study (CHS) GWAS to identify genetic variants associated with aging and CVD risk factors and events

  The primary aim of the study is to conduct a genome-wide association study to identify genetic variants associated with the incidence of myocardial infarction (MI), stroke, and heart failure (HF) among participants enrolled in the Cardiovascular Health Study (CHS) who were free of clinical cardiovascular disease at baseline. The secondary aim is to conduct genome-wide association study of other phenotypes in CHS. The study is an ancillary study to CHS. CHS is a population-based cohort study of risk factors for heart disease and stroke among older adults recruited at 4 US sites in 1989-1990. Subjects underwent an extensive baseline examination, and annual follow-up examinations through 1988-1999.

  Study phs000226

• Genomic landscape of Neutrophilic Leukemias of Ambiguous Diagnosis

  Chronic neutrophilic leukemia (CNL), atypical chronic myeloid leukemia (aCML), and unclassified myelodysplastic syndrome/myeloproliferative neoplasms (MDS/MPN-U) are a group of rare, heterogeneous myeloid disorders. There is strong morphologic resemblance amongst these distinct diagnostic entities as well as lack of specific molecular markers and limited understanding of disease pathogenesis, which has made their diagnosis challenging. Treatment has remained empirical, resulting in dismal outcomes. We, therefore, performed whole exome and RNA-sequencing on a cohort of over 100 cases of these rare hematologic malignancies and present the most complete survey of the genomic landscape of these diseases to date. [Abstract from manuscript currently under review so copyright not yet determined]

  Study phs001799

• Resilience and Susceptibility Patterns in the Viral Immune Response Using RNA-Seq (ReSP VIRUS Study)

  This is a cross sectional study to investigate the relationship between nasal mucosa gene expression and clinical outcomes in infants with critical Respiratory Syncytial Virus (RSV) infection. We collected nasal mucosa samples from infants admitted to the pediatric intensive care unit with polymerase chain reaction confirmed RSV bronchiolitis. Samples were obtained by mucosal scrape biopsy of the inferior turbinate using a sterile plastic curette and bulk RNA-sequencing of mRNA was performed. Clinical data was extracted from the electronic health record including: demographics, medical history, duration of symptoms, time from admission to sample collection, hospital and intensive care unit length of stay, and type and duration of respiratory support.

  Study phs003053

• Sequence Analysis of Mutations and Translocations Across Breast Cancer Subtypes

  This study combined whole exome (103 samples) and whole genome (22 samples) sequencing over a total of 108 breast tumors and matched normal DNA to identify novel mutations and translocations. Samples were subjected to paired-end Illumina sequencing with goal of 30x coverage of tumor/normal for whole genomes and 100x tumor/normal coverage for whole exomes. From these sequences, we used various computational techniques to identify somatic point mutations, insertion/deletions and structural rearrangements in these tumors. From these data, we identified new insights into the rates of background mutations in these cancers, novel recurrent mutated genes, and multiple gene rearrangements. One of these rearrangements appears to be a recurrent event in breast cancer.

  Study phs000369

• Temporal Dissection of Tumorigenesis in Primary Cancers

  The earliest genetic abnormalities in cancer represent a unique opportunity for timely clinical diagnosis. Classic deep sequencing of tumors identifies many aberrations acquired later in cancer progression. In this study, data regarding simple mutation and chromosomal aberration were integrated to trace the evolution of cutaneous squamous cell carcinomas and ovarian adenocarcinomas. Only after the second allele of TP53 was lost did the genome enter a window of extreme genomic vulnerability, in both cancer types, eventually acquiring more than 100,000 mutations in skin cancers. Inactivating Notch mutations were also identified as prevalent secondary changes. These results add context to the idea of TP53 mutation as dominant negative and occurring later in tumorigenesis.

  Study phs000418

• Epilepsy Genetics Initiative

  The Epilepsy Genetics Initiative (EGI) was created in 2014 with the goal of amassing a database of clinically-generated exome sequence data for patients with epilepsy who have had diagnostic whole exome sequencing. Most of the subjects enrolled in the study did not receive a secure genetic diagnosis from their initial sequencing. Following participant/family consent, EGI transfers raw data from the respective clinical lab to the Institute for Genomic Medicine at Columbia University Medical Center. The strategy of the initiative has been to carry out systematic reanalysis of data to identify new diagnoses that were not possible or missed at the time of initial sequencing and to aid in novel gene discovery in epilepsy.

  Study phs001551

• NHLBI TOPMed - NHGRI CCDG: UCSF Atrial Fibrillation Study

  The University of California San Francisco (UCSF) Cardiovascular Research Institute (CVRI) Resource in Arteriosclerosis and Metabolic Disease is an ongoing multi-ethnic study of adults ≥ 18 years of age which was started in 1989 and now includes 28,000 participants recruited from the UCSF medical system. Within the Resource lies data and biospecimens from nearly 1,000 patients presenting to the electrophysiology laboratory for electrophysiology procedures that were densely phenotyped for electrophysiologic characteristics with biospecimens collected from various intra and extra-cardiac chambers. Phenotyping of all participants was achieved via interview and review of medical records. A subset of 113 participants with early-onset atrial fibrillation underwent WGS as a part of the TOPMed Program.

  Study phs001933

• Center for Common Disease Genomics [CCDG] - Cardiovascular: The Bangladesh Risk of Acute Vascular Events (BRAVE) Study

  The Bangladesh Risk of Acute Vascular Events (BRAVE) study is a hospital-based case-control study in Bangladesh which was established by the Cardiovascular Epidemiology Unit of Cambridge University in the UK in partnership with the key local cardiology and research centres to examine environmental, genetic, lifestyle and biochemical determinants of myocardial infarction (MI) among this South Asian population. By the end of 2016, this study has recruited ~8000 clinically confirmed first-ever MI cases (with a significant proportion being early-onset MI), and ~8000 healthy controls frequency-matched by age and sex. This site hosts data from ~500 whole genomes and ~1500 whole exomes (50% cases and 50% controls)

  Study phs001398

• Genome-Wide Association Study of Lung Cancer Susceptibility in Never-Smoking Women in Asia

  To learn about the etiology of lung cancer among never-smoking women in Asia, we formed the Female Lung Cancer Consortium in Asia (FLCCA), which includes studies of lung cancer in Eastern Asia and conducted a GWAS. We analyzed a total of 5510 lung cancer cases and 4544 controls and identified 3 novel loci (Lan et al., 2012). Of these study subjects, 4922 lung cancer cases and 3959 controls are available for posting. Lan et al.., Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia. Nat Genet. 2012 Dec;44(12):1330-5. doi: 10.1038/ng.2456. Epub 2012 Nov 11. PubMed PMID: 23143601.

  Study phs000716

• Phylogenetic Analyses of Melanoma Reveal Complex Patterns of Metastatic Dissemination

  Subpopulations of cells in a primary melanoma can disseminate and establish metastases. Still, the precise ancestral relationship between primary tumors and their metastases is not well understood. Using whole-exome sequencing (for discovery) and targeted sequencing (for validation), we analyzed mutation patterns of primary melanomas and two or more metastases in each of 8 patients to determine their phylogenetic relationships, profiling a total of 31 total tumors. The resulting data show that in 6 of 8 cases, genetically unique cell populations in the primary metastasized in parallel to distinct anatomic sites, rather than sequentially. These data also indicate that individual metastases were sometimes founded by multiple cell populations of the primary that were genetically distinct.

  Study phs000941

• Malnutrition and Enteric Disease Network (Mal-ED) Birth Cohort in Brazil

  The Malnutrition and Enteric Disease Network (Mal-ED) Birth Cohort in Brazil enrolled 242 children between 2010 and 2014; an additional 101 infants recruited under the ICIDR (International Center for Infectious Disease Research) program and evaluated by the same procedures as Mal-ED were included in the cohort. The aim of the study was to evaluate the role of enteropathogens in causing intestinal inflammation and a failure of growth and development.This submission includes genetic and corresponding anthropometric data on a subset of 279 participants. More information on this project and its related projects can be found here: Studies of diarrheal susceptibility, growth, and development, in pediatric populations in Northeastern Brazil

  Study phs003172

• Multi-Ethnic Study of Atherosclerosis (Electrocardiogram Tracing Repository)

  The Multi-Ethnic Study of Atherosclerosis (MESA) is a study of the characteristics of subclinical cardiovascular disease (disease detected non-invasively before it has produced clinical signs and symptoms) and the risk factors that predict progression to clinically overt cardiovascular disease or progression of the subclinical disease. MESA researchers study a diverse, population-based sample of 6,814 asymptomatic men and women aged 45-84. Thirty-eight percent of the recruited participants are white, 28 percent African-American, 22 percent Hispanic, and 12 percent Asian, predominantly of Chinese descent. Electrocardiogram Tracing Repository includes ECG tracings performed during MESA Exam 1 conducted between 2000 and 2002 and during MESA Exam 5 conducted between 2010 and 2012.

  Study phs003703

• Pathologically Expanded Peripheral B Cell-Helper T Cells in Rheumatoid Arthritis

  PROSET-HD aims to identify and study immune cell populations altered in patients with autoimmune and inflammatory diseases. We have identified a population of PD-1hi CXCR5- 'peripheral helper' T (Tph) cells that are expanded in the joints and circulation of patients with seropositive rheumatoid arthritis. This T cell population uniquely combines potent B cell-helper function with a migratory program that directs homing to inflamed tissues. RNA sequencing was performed on sorted memory CD4+ T cell subpopulations to compare the global gene expression profiles of PD-1hi CXCR5- CD4+ T cells, PD-1hi CXCR5+ follicular helper T cells, and other T cell populations obtained from blood of rheumatoid arthritis patients.

  Study phs001262

• Comparison of WGBS, EPIC array, EM-seq, and Nanopore sequencing in assessing DNA methylation marks

  Bisulfite sequencing has long been the default method for analyzing methylation marks due to its single base resolution. However, the associated DNA degradation poses a concern for fragmented samples. Although several methods have been proposed to circumvent this issue, there has yet to be a clear consensus on which method is best suited for detecting methylation. We present an overview of the two mostly used and two alternative approaches: whole-genome bisulfite sequencing (WGBS), Illumina methylation microarray (EPIC), Enzymatic Methyl-sequencing (EM-seq) and third-generation sequencing by Oxford Nanopore Technologies (ONT). We evaluated DNA methylation levels in three human genomes derived from tissue, cell line, and whole blood.

  Study EGAS00001008014

• Comprehensive molecular and clinicopathological profiling of glioma

  Various molecular profiles are needed to classify malignant brain tumors, including gliomas, based on the latest classification criteria of the World Health Organization, and their poor prognosis necessitates new therapeutic targets. The Todai OncoPanel 2 RNA Panel (TOP2-RNA) is a custom-target RNA-sequencing (RNA-seq) using the junction capture method to maximize the sensitivity of detecting 455 fusion gene transcripts and analyze the expression profiles of 1,390 genes. This study aimed to classify gliomas and identify their molecular targets using TOP2-RNA. A total of 124 frozen samples of malignant gliomas were subjected to TOP2-RNA for classification based on their molecular profiles and the identification of molecular targets.

  Study JGAS000671

• The role of gut microbiota in metabolic diseases

  Diabetes is a major disease in the elderly and is responsible for increased risk of myocardial infarction and stroke. Recently, the relationship between microbiota and diabetes has been reported in animals and humans. In this study, blood, stool, and saliva samples were collected from examinees at the University of Tokyo Health Screening Center, and 16S rRNA and metagenomic analyses were performed to determine the variation of microbiota. Furthermore, metabolome analysis and transcriptome analysis (CAGE analysis) using blood were performed to reveal changes in host metabolites and gene expression. By comparing the host- and bacteria- derived information with the metabolic parameters, we analyzed whether microbiota can be a predictor of metabolic diseases.

  Study JGAS000569

• Ultra-deep Error-corrected Sequencing of Peripheral Blood for Clonal Hematopoiesis in Patients Undergoing AAA Surgery

  Patients undergoing elective abdominal aortic aneurysm (AAA) surgery were enrolled to investigate the prevalence and characteristics of clonal hematopoiesis. Peripheral blood was collected at the time of surgical admission using PAXgene DNA tubes. Genomic DNA was extracted and subjected to ultra-deep error-corrected targeted sequencing using a custom gene panel covering recurrent clonal hematopoiesis-associated genes. Sequencing libraries were prepared following established protocols and sequenced on an Illumina NovaSeq X system. The resulting dataset includes paired-end FASTQ files for each participant, enabling high-sensitivity detection of somatic variants down to low variant allele frequencies. This study provides a comprehensive sequencing resource for evaluating clonal hematopoiesis in AAA patients.

  Study JGAS000864

• Long-read whole genome sequencing of gastric cancer

  Gastric cancer (GC) remains a significant health challenge globally, with a particularly high incidence in Asia, including Singapore. Understanding the genomic landscape of normal gastric and the different GC subtypes along with its precursor lesions such as intestinal metaplasia (IM) as well as GC metastatic sites is crucial for advancing diagnostics, prognostics, and therapeutics. Long-read sequencing technologies offer an opportunity to delve deeper into the genomic and epigenetic alterations underlying these conditions and to complement existing short-read omics data. By integrating these data with previously generated in-house multi-omics data (such as RNA sequencing and whole exome sequencing), we hope to better elucidate the molecular mechanism underlying GC initiation and progression.

  Study EGAS50000001607

• Lebanon_HighCov_seq

  We propose to investigate the genomics of a Lebanese sample. we plan (1) genotyping (2.5M) of 120 Lebanese individuals, choosing this platform to allow comparison with the 1000 Genomes and African Genome Variation project populations, (2) 8x sequencing of 100 individuals to provide unbiased population-level sequence information including allele frequencies, and (3) 30x sequencing of four individuals to allow inferences such as from PSMC/MSMC to be obtained. The current form is for the high-coverage sequencing. 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 EGAS00001002085

• Genetic landscape of pediatric Medulloblastoma

  Medulloblastoma is a heterogenous disease made up of at least four distinct subtypes of disease which appear to exploit and disrupt naturally occurring developmental pathways of cellular growth and hindbrain development. To better understand the driver mutations of this disease, we performed whole genome sequencing of 37 medulloblastomas and the corresponding normal DNA of the 37 affected children treated at St. Jude Children's Research Hospital. We have found several novel mutations which appear subtype specific. These mutations were checked for frequency in a separate tumor cohort of 56 children with medulloblastoma, also treated on the St. Jude Medulloblastoma 2003 trial, and were tested in several animal models of medulloblastoma for proof of oncogenic potential.

  Study EGAS00001000347

• DNA_repair_in_BLM_deficient_hiPSCs

  We are aiming to investigate repair of a double strand break (DSB) within the genome in the presence and absence of the BLOOM protein. Zinc Finger Nucleases introduce DSBs at specified loci within the genome. Using sequencing we will assess the size of the deletion following repair. Protocol1. Transfect normal and BLOOM deficient human iPS cells with ZFNs, using AMXA2. Harvest cells after 5 days3. Perform column extraction of DNA4. PCR-amplify the ZFN region 5. Sequence and analyse repair of the DSBThis 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 EGAS00001000740

• HTAS of CD34+ HSPCs in relation to evaluating gene editing outcomes for CGD-causing variants in CYBA and CYBB

  High-throughput amplicon sequencing were performed on CD34+ hematopoietic stem and progenitor cells (HSPCs) derived from 4 healthy donors and one unaffected heterozygous carrier of a CYBB c.252G>A variant causing X-linked granulomatous disease. Targeted genome editing were performed in the HSPCs of CYBA and CYBB genes using CRISPR-Cas9 and recombinant AAV6. To assess gene editing outcomes in CD34+ HSPCs, the targeted loci were amplified from genomic DNA and sequenced with 150-bp paired-end reads on an Illumina iSeq 100 or MiniSeq. Editing rates were determined with CRISPResso2 in HDR mode using standard parameters. The dataaset here contains paired raw fastq files of each sample.

  Study EGAS50000001155

• Genomic and transcriptomic analysis of thymic epithelial tumors

  Thymic epithelial tumors (TETs), comprising various histologic types of thymomas and thymic carcinomas, originate from thymic epithelial cells. Each histologic type is typically associated with a distinct immune cell composition and clinical manifestation. A better understanding of the cellular origins and molecular pathways underlying this heterogeneity is needed to improve patient stratification and treatment. Here, we conducted an integrated genomic and transcriptomic analysis of 124 thymomas and 13 thymic carcinomas, including 20 newly sequenced cases combined with 117 cases from publicly available datasets. This approach stratified TETs into three subgroups with different possible origins: GTF2I-mutant (GTF2I-type) thymomas, copy number-altered (CN-type) thymomas, and thymic carcinomas.

  Study EGAS00001004227