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• Metformin for Oral Cancer Prevention

  The M4OC-PREVENT clinical trial addressed whether metformin has utility in the prevention of oral cancer. It is a phase IIa clinical trial of metformin ER 2,000 mg per day given for 12-14 weeks to individuals with oral premalignant lesions, either oral leukoplakia or erythroplakia (which are precursors to oral cancer). The goal was to determine if metformin decreases the size of oral leukoplakia (clinical response). Additionally, effects on biomarkers of cancer risk and metformin effect were ascertained. The clinical trial was performed at the University of California San Diego Moores Cancer Center, the University of Minnesota, and the British Columbia Cancer Agency, with monitoring and oversight provided by the University of Arizona.

  Study phs002437

• Germline

  This study is part of the 'First 1,000 Days of Life and Beyond' study at the Inova Translational Medicine Institute. Whole-genome sequencing data from 1,291 parent-offspring trios was used to study the properties of clustered de novo mutations. The maternal clusters were found to be enriched in regions with accelerated maternal mutation rate and show distinct mutational signatures. For additional details, please refer to: "Germline de novo mutation clusters arise during oocyte aging in genomic regions with increased double-strand break incidence". Jakob M. Goldmann, Vladimir B. Seplyarskiy, Wendy S.W. Wong, Thierry Vilboux, Pieter B. Neerincx, Dale L. Bodian, Benjamin D. Solomon, Joris A. Veltman, John F. Deeken, Christian Gilissen, John E. Niederhuber. Nature Genetics.

  Study phs001522

• Selenium Chemoprevention: Benefits and Harms

  Selenium is a trace element that may have anti-carcinogenetic effect, but heterogenous treatment effects have been observed. This genome-wide association study investigates if genetic variation modifies the effect of selenium chemoprevention in the Selenium and Celecoxib Trial, a randomized, double-blind, placebo-controlled trial conducted at the University of Arizona Cancer Center. The objective of the clinical trial was to determine whether daily intake of 200 µg/d of selenium as a supplement could reduce the risk for developing metachronous colorectal adenomas. The study participants were recruited between 2001 and 2011. Genome-wide association study was performed for 1,323 study participants who provided blood sample at the time of study entry.

  Study phs002283

• National Cancer Institute (NCI) Head and Neck Cancer Study

  Head and neck cancers have well-documented associations with tobacco and alcohol exposure, but the disease develops in only a small fraction of users, which implies an important role for genetic susceptibility. Therefore, head and neck cancers are an excellent model for studying genetic susceptibility to environmental carcinogens. The primary goal of this study is to perform a comprehensive two-stage, high-density, genome-wide single-nucleotide polymorphism (SNP) analysis of head and neck cancer cases and corresponding frequency matched controls to identify novel genetic risk factors for head and neck cancer. In the study, we genotyped 2242 head and neck cancer cases and 1198 controls using Illumina HumanOmniExpress-12v1 BeadChip.

  Study phs001173

• Gene-Environment Interactions in COCCaINE Use Disorder: Collaborative Case-Control Initiative in Cocaine Addiction

  Drug addiction is a phenotype that has high heritability estimates. In recent years, association studies of candidate genes and some genome-wide association studies (GWAS) have identified a large number of SNPs associated with substance use, abuse or dependence, particularly in phenotypes related to alcohol and nicotine use. Regarding snorted or smoked cocaine dependency, only one GWAS has been conducted so far. In addition, genetic association studies that specifically evaluated smoked cocaine dependence (e.g. crack) are rare, because of characteristics related to the route of administration and duration of the effect of the drug. Thus, the main aim of this GWAS was to identify genetic variations that modulate the risk for the cocaine dependence.

  Study phs001810

• International Consortium for Blood Pressure (ICBP)

  The ICBP consortium is an international effort to investigate blood-pressure genetics. The consortium was formed by two parent consortia, the CHARGE-BP consortium (Cohorts for Heart and Aging Research in Genomic Epidemiology - blood pressure) and the GBPGEN consortium (Global Blood Pressure Genetics Consortium). In 2011 we performed genome-wide association analyses based on genome-wide SNPs imputed to HapMap for systolic and diastolic blood pressure (SBP and DBP) and mean arterial pressure and pulse pressure (MAP and PP). In 2016 we performed an analysis based on the Cardio-MetaboChip for SBP and DBP. All these datasets are available here, however, full association statistics including effect size directions, only under controlled access by dbGaP.

  Study phs000585

• The Genomic Analysis of 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 phs000409

• Mucosal Melanoma Targeted Exome Sequencing Study (UCSF)

  Mucosal melanoma is a deadly disease that carries the worst prognosis amongst subtypes of melanoma. Like all melanomas, mucosal melanomas are frequently driven by activating mutations in the MAPK and/or PI3K pathways; however, unlike melanomas that arise on sun-exposed skin, mucosal melanomas harbor few point mutations. Instead, most somatic alterations involve structural alterations, which appear early during tumor progression. Molecular studies in mucosal melanoma generally only profile point mutations without interrogating copy number alterations, and pathogenic mutations are only found in 30% of cases. We sequenced 38 mucosal melanomas, and in addition to profiling point mutations, we looked for copy number alterations that amplify oncogenes or delete tumor suppressors.

  Study phs001594

• Genomic Psychiatry Cohort (GPC) Whole Genome Sequencing and Genotyping Study

  The Center for Genomic Psychiatry at the University of Southern California (USC), SUNY Downstate and an extensive network of academic medical centers have created the Genomic Psychiatry Cohort (GPC). The GPC consists of a large clinical cohort of patients with schizophrenia, bipolar disorder, and healthy controls. The data generation of genotyping and whole genome sequencing of the GPC has been done in collaboration with the USC and the Broad Institute of MIT and Harvard. Genome-wide association studies are being performed with the samples to identify genetic risks for psychiatric disease. Genotyping is also being used to determine ancestry informative markers and replication of candidate genes. Whole genome sequencing identifies functional variants associated with disease risk.

  Study phs001020

• The Genomics of Pilocytic Astrocytoma Formation in Neurofibromatosis Type 1

  Neurofibromatosis type 1 (NF1) inherited cancer predisposition syndrome is one of the most common autosomal dominant tumor predisposition syndromes in which affected individuals develop brain tumors. These low-grade glial neoplasms (pilocytic astrocytomas) typically arise in children younger than 7 years of age and are hypothesized to result from a combination of germline and acquired somatic NF1 tumor suppressor gene mutations. In this study, whole genome sequence analysis was performed on three NF1-associated pilocytic astrocytoma tumors (NF1-PA) and matched normal blood samples to establish the genomic landscape of NF1-PA. These data support the existence of multiple distinct mechanisms (mutation, LOH, and methylation) underlying somatic NF1 inactivation in NF1-PA tumors.

  Study phs000563

• Children's Hospital of Philadelphia: GWAS of Left-Sided Cardiac Defects

  This is a family-based genome-wide association study of congenital left-sided cardiac lesions (LSLs). Cases with LSLs and their parents were recruited from the Cardiac Center at The Children's Hospital of Philadelphia between 1997 and 2010. The discovery dataset included 405 LSL case-parent triads. DNA was extracted from blood or saliva samples from these subjects and genotyping was conducted using the Illumina Infinium II HumanHap550K array (V3). This study was conducted with approval from the Institutional Review Board for the Protection of Human Subjects of The Children's Hospital of Philadelphia and all research subjects provided either written informed consent or, when appropriate, assent.

  Study phs000781

• Genome Wide Association Study of Serum Creatinine during Vancomycin Therapy and Vancomycin Pharmacokinetics

  The goal of this study was to identify genetic variants associated with risk for acute kidney injury (AKI) in patients being treated with vancomycin and genetic variants associated with variability in vancomycin pharmacokinetics. AKI is a common adverse drug event and known complication of vancomycin therapy. Known risk factors fail to accurately predict renal toxicity. Our hypothesis, that genetic variants modify the risk of AKI, was tested by performing genome-wide association and linear regression in 429 patients of European descent using the outcome of peak serum creatinine while on vancomycin. We also tested the hypothesis that genetic variants associate with vancomycin pharmacokinetics, using vancomycin trough levels and calculated renal elimination rate constant as outcomes.

  Study phs000894

• Clinical and genetic analysis of retinopathy of prematurity - GWAS

  This project aims to identify genetic variants that contribute to the development of retinopathy of prematurity (ROP). ROP is a leading cause of childhood blindness worldwide. We have performed a genome wide association study (GWAS) using Illumina Global Screening Array (GSA) BeadChip. For this GWAS design we assembled the largest group of ROP patients described to date: around 1000 ROP patients in total. Demographic and phenotypic information associated with each sample includes gestational age, gender, ethnicity, multiple birth status, presence of ROP, and birth weight. The results of this study will help advance our understanding of the genetic susceptibility to ROP and may result in novel treatment options to slow the progression of the disease.

  Study phs002020

• PGRN-Leducq: Identification of the KCNE1 D85N Polymorphism as a Possible Modulator of Drug-Induced Torsades de Pointes

  The goal of this study was to search for genetic variants that could be responsible for modifying the risk of drug-induced long QT syndrome (diLQTS). diLQTS is a relatively common adverse drug event and has been a leading cause for drug relabeling and withdrawal from the market. Our hypothesis, that variants in genes which regulate electrical properties in the heart modify the risk of diLQTS, was tested by genotyping patients of European descent at 1424 single nucleotide polymorphisms (SNPs) in 18 candidate genes. We found that the SNP KCNE1 D85N was highly predictive of diLQTS with an odds ratio of 9.0 (95% confidence interval: 3.5-22.9).

  Study phs000617

• NHLBI TOPMed: Rare Variants for Hypertension in Taiwan Chinese (THRV)

  The THRV-TOPMed study consists of three cohorts: The SAPPHIRe Family cohort (N=1,271), TSGH (Tri-Service General Hospital, a hospital-based cohort, N=160), and TCVGH (Taichung Veterans General Hospital, another hospital-based cohort, N=922), all based in Taiwan. 1,271 subjects were previously recruited as part of the NHLBI-sponsored SAPPHIRe Network (which is part of the Family Blood Pressure Program, FBPP). The SAPPHIRe families were recruited to have two or more hypertensive sibs, some families also with one normotensive/hypotensive sib. The two Hospital-based cohorts (TSGH and TCVGH) both recruited unrelated subjects with different recruitment criteria (matched with SAPPHIRe subjects for age, sex, and BMI category).

  Study phs001387

• Phenotyping and Therapeutic Approaches for Patients with Sellar/Suprasellar Disorders

  The goal of the study is to phenotype and genotype patients with rare hypothalamic and pituitary disorders and identify biomarkers of disease diagnosis, presentation, and progression. We are investigating genetic mechanisms of pituitary tumorigenesis as well as genomic/transcriptomic markers of disease presentation and severity. Patients with suspected or confirmed hypothalamic and/or pituitary disorders and their family members are recruited. Biospecimens including peripheral blood, urine, tumor tissue (as available), and/or stool are collected. Genetic analysis may include a variety of techniques including peripheral blood or tumor tissue targeted Sanger sequencing of one or few genes, peripheral blood or tumor tissue whole exome sequencing, and other as applicable.

  Study phs003245

• Neurogenetic Investigations of Obsessive-Compulsive Disorder

  Obsessive-compulsive disorder (OCD) is a disabling early-onset neuropsychiatric disorder with a clear genetic contribution to risk but unclear underlying pathophysiology, which has hindered the development of new treatments and interventions. This study uses high-throughput sequencing approaches to identify OCD risk genes, detect gene expression differences in OCD, and determine epigenetic signatures driving gene expression in OCD brain. These studies will improve our understanding of the underlying mechanisms of OCD and identify points of traction for mechanistic studies in model systems, ultimately leading to novel therapeutics, and reducing the significant morbidity and mortality associated with this disabling illness. Furthermore, insights gained in these studies can inform gene discovery approaches to other complex neuropsychiatric disorders.

  Study phs001929

• 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

• Type 1 Diabetes Genetics Consortium (T1DGC): Case-only RNA-Seq Study

  Peripheral blood mononuclear cells (PBMC) from 82 T1D cases from the T1DGC study were fractionated by positive selection on magnetic beads into CD4+ T cells, CD8+ T cells and CD19+ B cells. RNA purification, library preparation and sequencing to an average of 50 million reads per sample were performed by the HudsonAlpha Genome Services Laboratory. The resulting dataset includes 82 subjects with data from at least one cell type; sequence data from all 3 cell types is available from 79 subjects. The individuals in this study can be linked to the phs000911 T1DGC ImmunoChip study via subject ids to obtain both genotypic and phenotypic information, including genotypes used for expression quantitative trait locus analysis.

  Study phs001426

• 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

• Genomic Landscape of High-Grade Neuroendocrine Neoplasms

  This project is a multi-omics study of high grade (grade 3) neuroendocrine neoplasms across diverse organs. Genomic analysis using low-pass whole genome sequencing for copy number analysis, whole exome sequencing and whole transcriptomic sequencing using RNAseq were performed. As high grade neuroendocrine neoplasms are highly lethal with a median survival of approximately 7 months, new insights are urgently needed for better prognosis, diagnosis and management. This study focuses on gene and pathway discoveries in this cancer, and includes samples from a diverse set of organs, including the lungs, gastroenteropancreatic tract, breast, prostate, head and neck and bladder. This study was made possible by a generous donation from The Helen B. Rodde Fund.

  Study phs002070

• Longitudinal Study of the Porphyrias

  This is an observational, longitudinal study of approximately 800 individuals with various types of porphyria. Those participants will be evaluated annually for 5 years, or longer if they agree. Participation in this project will include: Participating in annual visits or contacts. Providing samples, including blood, buccal cells (cells from inside of the mouth), saliva, and urine. The type of samples and amounts may vary from person to person, depending on the type of porphyria. Giving permission for samples to be stored and used for porphyrias research. Granting permission to obtain your medical records. Providing information about your medical history and family history. Completing a questionnaire about your porphyria symptoms and quality of life.

  Study phs001278

• 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

• Paired Acute Myeloid Leukemia (AML) Epigenetics Study on Epialleles and Clonality

  We describe methclone, a novel method to identify epigenetic loci that harbor large changes in the clonality of their epialleles (epigenetic alleles). Methclone efficiently analyzes genome-wide DNA methylation sequencing data. We quantify the changes using a composition entropy difference calculation and also introduce a new measure of global clonality shift, loci with epiallele shift per million loci covered, which enables comparisons between different samples to gauge overall epiallelic dynamics. Finally, we demonstrate the utility of methclone in capturing functional epiallele shifts in leukemia patients from diagnosis to relapse. Methclone is open-source and freely available at https://code.google.com/p/methclone. Reprinted with permission from BMC Publishing (Genome Biology).

  Study phs000793

• 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