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dbGaP phs000021 Genome-Wide Association Study of Schizophrenia - Eligibility

- 2025-01-29 - 9 Formulär, 1 Item-grupp, 10 Dataelement, 1 Språk
Item-grupp: IG.elig
Principal Investigator: Pablo V. Gejman, MD, NorthShore University HealthSystem (NUH), Evanston, IL, USA MeSH: Schizophrenia https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000021 The goal of the study is to find susceptibility genes for schizophrenia. *Dataset versioning* - Version 1: European-American (EA) ancestry only - Version 2: Version 1 plus African-American (AA) ancestry *Consent groups and participant set* - General research use (GRU): 4591 cases and controls (1217 EA cases, 1442 EA controls, 953 AA cases, 979 AA controls) This consent group includes a subset of schizophrenia cases and all controls (which overlap with Bipolar study controls in Bipolar: GRU dataset). - Schizophrenia and related disorders (SARC): 475 cases (187 EA cases, 288 AA cases) This consent group includes a subset of schizophrenia cases.

pht000067.v2.p2

1 Item-grupp 119 Dataelement

pht000068.v1.p2

1 Item-grupp 38 Dataelement

pht000069.v1.p2

1 Item-grupp 253 Dataelement

pht000287.v1.p2

1 Item-grupp 253 Dataelement

pht002001.v1.p2

1 Item-grupp 2 Dataelement

pht002002.v1.p2

1 Item-grupp 2 Dataelement

dbGaP phs000048 Mayo-Perlegen LEAPS (Linked Efforts to Accelerate Parkinson's Solutions) Collaboration - Eligibility

- 2025-01-29 - 3 Formulär, 1 Item-grupp, 2 Dataelement, 1 Språk
Item-grupp: IG.elig
Principal Investigator: Demetrius M. Maraganore, Mayo Clinic, Rochester, MN, USA MeSH: Parkinson Disease https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000048 We performed a two-tiered, whole-genome association study of Parkinson disease (PD). For tier 1, we individually genotyped 198,345 uniformly spaced and informative single-nucleotide polymorphisms (SNPs) in 443 sibling pairs discordant for PD. For tier 2a, we individually genotyped 1,793 PD-associated SNPs (P.01 in tier 1) and 300 genomic control SNPs in 332 matched case-unrelated control pairs. We identified 11 SNPs that were associated with PD (P.01) in both tier 1 and tier 2 samples and had the same direction of effect. For these SNPs, we combined data from the case-unaffected sibling pair (tier 1) and case-unrelated control pair (tier 2) samples and employed a liberalization of the sibling transmission/disequilibrium test to calculate odds ratios, 95% confidence intervals, and P values. A SNP within the semaphorin 5A gene (SEMA5A) had the lowest combined P value (P=7.62E-6). The protein encoded by this gene plays an important role in neurogenesis and in neuronal apoptosis, which is consistent with existing hypotheses regarding PD pathogenesis. A second SNP tagged the PARK11 late-onset PD susceptibility locus (P=1.70E-5). In tier 2b, we also selected for genotyping additional SNPs that were borderline significant (P.05) in tier 1 but that tested a priori biological and genetic hypotheses regarding susceptibility to PD (n=941 SNPs). In analysis of the combined tier 1 and tier 2b data, the two SNPs with the lowest P values (P=9.07E-6; P=2.96E-5) tagged the PARK10 late-onset PD susceptibility locus. Independent replication across populations will clarify the role of the genomic loci tagged by these SNPs in conferring PD susceptibility. Note: The following instruments were used: 1)clinical assessments form and manual; 2) sibling screening form and manual; 3) unrelated control screening and manual; and 4) risk factors questionnaire and manual. All cases underwent #1, as did sibling controls screening positive (see below). Unrelated controls were not examined. All siblings underwent #2. All unrelated controls underwent #3. All subjects (cases, sibling controls, and unrelated controls) underwent #4. Any publications using the data are to cite the original American Journal of Human Genetics article (Maraganore et al., 2005). Investigators using the data collection instruments are to acknowledge Drs. Maraganore and Rocca, and cite grants ES-10751 and NS-33978.

pht000184.v1.p1

1 Item-grupp 6 Dataelement

pht000071.v1.p1

1 Item-grupp 6 Dataelement

dbGaP phs001657 Functional Genomic Landscape of Acute Myeloid Leukemia - phs001657

- 2025-01-29 - 1 Formulär, 3 Item-grupper, 9 Dataelement, 1 Språk
Item-grupper: pht009391, pht009392, pht009393
The implementation of targeted therapies for acute myeloid leukemia has been challenged by complex mutational patterns within and across patients as well as a dearth of pharmacologic agents for most mutational events. Here, we report initial findings from the Beat AML program on a cohort of 672 tumor specimens collected from 562 patients. We assessed these specimens using whole exome sequencing, RNA-sequencing, and ex vivo drug sensitivity analyses. Our data reveal novel mutational events not previously detected in AML. We show association of drug response with mutational status, including instances of drug sensitivity that are specific to combinatorial mutational events. Integration with RNA-sequencing also revealed gene expression signatures, which predict a role of specific gene networks in drug response. Collectively, this report offers a dataset, accessible by the Beat AML data viewer, that can be leveraged to address clinical, genomic, transcriptomic, and functional inquiries into the biology of AML. NCT 01728402 https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001657

dbGaP phs000018 Search for Susceptibility Genes for Diabetic Nephropathy in Type 1 Diabetes (GoKinD study participants), GAIN - Eligibility

- 2025-01-22 - 6 Formulär, 1 Item-grupp, 32 Dataelement, 1 Språk
Item-grupp: IG.elig
Principal Investigator: J.H. Warram, Joslin Diabetes Center, Boston, MA, USA MeSH: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000018 Genetics of Kidneys in Diabetes (GoKinD) study is an initiative aimed at identifying susceptibility genes for diabetic nephropathy in type 1 diabetes. A large number of individuals with type 1 diabetes were screened to identify two subsets, one with clear-cut kidney disease and another with normal renal status despite long-term diabetes. Those who met additional entry criteria and consented to participate were enrolled. When possible, both parents were also enrolled to form family trios. Altogether, GoKinD includes 3043 participants comprising 931 cases, 944 singletons, 268 pairs of parents of cases, and 316 pairs of parents of control. Accessible as a GAIN database are 905 of the cases, 890 of the controls, 10 pairs of parents of cases and 10 pairs of parents of controls. The other parents and the remaining cases and controls are available by a separate application process through NIDDK (dbGaP phs000088 *Search for Susceptibility Genes for Diabetic Nephropathy in Type 1 Diabetes (GoKinD study participants and parents), NIDDK*). Interested investigators may request the DNA collection and corresponding clinical data for GoKinD participants using the instructions and application form available at Juvenile Diabetes Research Foundation. *Consent groups and participant set* - Diabetic complications only (DCO): 1825 (904 cases, 881 controls, 40 others)

pht004354.v1.p1

1 Item-grupp 2 Dataelement

pht004355.v1.p1

1 Item-grupp 6 Dataelement

pht004356.v1.p1

1 Item-grupp 4 Dataelement

pht000062.v1.p1

1 Item-grupp 54 Dataelement

pht004357.v1.p1

1 Item-grupp 2 Dataelement

dbGaP phs001833 Genetic Model of MS Severity Predicts Future Accumulation of Disability - F.4

- 2023-06-26 - 4 Formulär, 1 Item-grupp, 5 Dataelement, 1 Språk
Item-grupp: pht009153
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001833 NCT00794352 The goal of "Comprehensive Multimodal Analysis of Neuroimmunological Diseases of the CNS" is to define the pathophysiological mechanisms underlying the development of disability in immune-mediated disorders of the central nervous system (CNS) and to distinguish these from physiological (and often beneficial) responses of the human immune system to CNS injury. The long-term objective of the trial is to acquire knowledge that would allow us to therapeutically inhibit the pathogenic mechanisms and enhance repair mechanisms in immune-mediated CNS diseases, thereby minimizing the extent of CNS tissue damage and promoting recovery. To date, 460 patients with a confirmed diagnosis of multiple sclerosis (MS) have been enrolled into the natural history clinical trial. In addition to standardized clinical, functional, neuroimaging and molecular/immunological data, blood samples were also collected for genetic research. However, only 299 study participants with confirmed MS currently have whole genome sequencing data available. In addition to the genome-wide data available for the 299 MS patients, this dbGaP submission provides demographic and phenotypic information for each subject collected at various points throughout the trial. We include race and family history of MS collected at the baseline visit as well as age and measures of disease severity collected at the most recent visit. As these data were randomized into discovery and validation cohorts, we also indicate the assigned group in the phenotypic data. It is hoped that these data may be applied to the development of clinically-useful tools such as diagnostic tests and new, sensitive scales of neurological disability, disease severity and CNS tissue destruction. Principal Investigator: Bibiana Bielekova, PhD. National Institutes of Health, Bethesda, MD, USA Funding Sources: Intramural Research Program of the National Institute of Allergy and Infectious Diseases. National Institutes of Health, Bethesda, MD, USA Acknowledgement Statement: Please cite/reference the use of dbGaP data by including the dbGaP accession phs001833.v1.p1.

F.1

1 Item-grupp 2 Dataelement

F.2

1 Item-grupp 2 Dataelement

F.3

1 Item-grupp 7 Dataelement

dbGaP phs001297 PROP Functional and Lymphocytic Markers of Respiratory Morbidity in Hyperoxic Preemies - Dataset pht006199

- 2023-06-26 - 4 Formulär, 1 Item-grupp, 4 Dataelement, 1 Språk
Item-grupp: pht006199
dbGaP Study Accession: phs001297.v1.p1 NCT01607216 Approximately 550,000 babies born prematurely each year in the United States suffer from birth at a time in development when the respiratory tract and immune system would normally be protected and maintained in a naïve state. This project is a component of the NIH Prematurity and Respiratory Outcomes Program (PROP) whose goals are the identification of disease mechanisms and biomarkers to stratify premature infants, at the time of discharge, for their risk of subsequent pulmonary morbidity. This Clinical Research Center (CRC) project will investigate prematurity-dependent alterations in cellular innate and adaptive immune systems resulting in increased susceptibility to respiratory infections and environmental irritants, and leading to respiratory morbidity in the first year of life. Prior studies have established developmental (maturity) and disease-related changes in circulating and pulmonary lymphocyte populations, but a comprehensive assessment of their relationship to disease risk/outcome has not been undertaken. We hypothesize that cellular and molecular immuno-maturity is altered due to intrinsic and extrinsic factors presented by premature birth in such a way as to reduce resistance to viral infections and to promote cytotoxic damage to the lung. We will evaluate immunologic maturity by comprehensively phenotyping lymphocyte populations in peripheral blood sampled at premature delivery, at the time of discharge from the hospital and at twelve months corrected age. The lymphocytic phenotype will be analyzed particularly in the context of gestational age and maternal-fetal stressors capable of modulating oxidative stress (oxygen exposure, infection and environmental tobacco smoke exposure). Additionally, we will assess changes in the molecular phenotype of isolated CD8 lymphocytes, a cell type preferentially recruited to the lungs of premature infants and capable of contributing to disease pathogenesis, by genome-wide expression profiling, in order to uncover novel disease pathways and define a gene expression signature associated with disease risk. We propose to build a statistical model, using cellular and molecular phenotypes and additional clinical variables, for stratifying risk of lung morbidity within the first year of life. Finally, we will assess the development of the gut microbiome in the preterm subjects to correlate with the observation of development of the adaptive immune system. Study Design: Prospective Longitudinal Cohort Study Type: Observational Longitudinal Prospective Cohort Total number of consented subjects: 277 Acknowledgement Statement: Please cite/reference the use of dbGaP data by including the dbGaP accession phs001297.v1.p1. Additionally, use the following statement to acknowledge the submitter(s) of this study: The datasets used for the analyses described in this manuscript were obtained from dbGaP ( https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001297.v1.p1 ) through dbGaP study accession numbers phs001297.v1.p1 . The data for the study Functional and Lymphocytic Markers of Respiratory Morbidity in Hyperoxic Preemies were provided by Drs. Gloria Pryhuber, Tom Mariani, Steven Gill, Rita Ryan, and Anne Marie Reynolds, University of Rochester and University at Buffalo Center for the Prematurity and Respiratory Outcomes Program (PROP). This study was supported by the U.S. National Institutes of Health (NIH), National Heart, Lung, and Blood Institute (NHLBI) grants U01 HL101813 and U01 HL101794, NHLBI and National Institute of Child Health and Human Development (NICHD) supplement grant R01 HL101794-01S1, National Institute of Allergy and Infectious Diseases (NIAID) contract HHSN272201200005C, and National Center for Advancing Translational Sciences (NCATS) grant UL1 TR000042. Dr. Pryhuber and her collaborators request that publications resulting from these data cite their original publications: Misra RS, Bhattacharya S, Huyck HL, Wang J-C E, Slaunwhite CG, Slaunwhite SL, Wightman TR, Secor- Soch S, Misra SK, Bushnell TP, Reynolds A-M, Ryan RM, Quataert SA, Pryhuber GS, Mariani TJ. Flow-Based Sorting of Neonatal Lymphocyte Populations for Transcriptomics Analysis. J Immunol Methods 2016; 437: 13-20. PMID: 27438473. PMCID in process. (And original microbiome publication to follow, after submission).

Dataset pht006201

1 Item-grupp 10 Dataelement

Dataset pht006202

1 Item-grupp 27 Dataelement

Dataset pht006200

1 Item-grupp 5 Dataelement

44967_dbGaP phs000019 Collaborative Association Study of Psoriasis - pht000063.v1.p1

- 2022-10-12 - 5 Formulär, 1 Item-grupp, 18 Dataelement, 1 Språk
Item-grupp: pht000063
Principal Investigator: Gonçalo R. Abecasis, University of Michigan School of Public Health, Ann Arbor, MI, USA MeSH: Psoriasis,Psoriatic Arthritis https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000019 The goal of this collaborative study is to combine the resources and expertise of three groups with long-standing studies of psoriasis genetics in order to identify new genetic susceptibility factors for psoriasis, a common inflammatory skin disease that affects over 4 million Americans. *Consent groups and participant set* - General research use (GRU): 1677 (950 cases, 692 controls, 35 others) - Autoimmune disease (AD): 1198 (449 cases, 734 controls, 15 others)

pht000064.v1.p1

1 Item-grupp 4 Dataelement

pht000179.v1.p1

1 Item-grupp 3 Dataelement

pht000180.v1.p1

1 Item-grupp 7 Dataelement

pht000181.v1.p1

1 Item-grupp 3 Dataelement

dbGaP phs000020 Major Depression: Stage 1 Genomewide Association in Population-Based Samples - pht000668.v1.p1

- 2022-10-12 - 4 Formulär, 1 Item-grupp, 2 Dataelement, 1 Språk
Item-grupp: pht000668
Principal Investigator: MeSH: Major Depressive Disorder https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000020 Identification of genomic regions that confer susceptibility to or protection from major depressive disorder (MDD) via genomewide association. *Consent groups and participant set* - Psychiatric and Related Somatic Conditions (PRSC): 3741 (1821 cases, 1822 controls, 98 others)

pht000070.v1.p1

1 Item-grupp 228 Dataelement

Eligibility

1 Item-grupp 2 Dataelement

pht000667.v1.p1

1 Item-grupp 2 Dataelement

dbGaP phs000741 Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) Lipidomics Study - F.1

- 2022-06-13 - 1 Formulär, 1 Item-grupp, 104 Dataelement, 1 Språk
Item-grupp: pht003918.v2
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000741.v2.p1 NCT00083369 The GOLDN study was initiated to assess how genetic factors interact with environmental (diet and drug) interventions to influence blood levels of triglycerides and other atherogenic lipid species and inflammation markers (registered at clinicaltrails.gov, number NCT00083369). The study recruited Caucasian participants primarily from three-generational pedigrees from two NHLBI Family Heart Study (FHS) field centers (Minneapolis, MN and Salt Lake City, UT). Only families with at least two siblings were recruited and only participants who did not take lipid-lowering agents (pharmaceuticals or nutraceuticals) for at least 4 weeks prior to the initial visit were included. A total of 1048 GOLDN participants were included in the diet intervention. The diet intervention followed the protocol of Patsch et al. (1992). The whipping cream (83% fat) meal had 700 Calories/m2 body surface area (2.93 MJ/m2 body surface area): 3% of calories were derived from protein (instant nonfat dry milk) and 14% from carbohydrate (sugar). The ratio of polyunsaturated to saturated fat was 0.06 and the cholesterol content of the average meal was 240 mg. The mixture was blended with ice and flavorings. Blood samples were drawn immediately before (fasting) and at 3.5 and 6 hours after consuming the high-fat meal. For the GOLDN lipidomics study, sterols and fatty acids were measured from stored plasma (-80 degrees Celsius) collected at fasting and 3.5 hours after the diet intervention using TrueMass Panels from Lipomics (West Sacramento, CA). A total of 11 sterols were quantified in nmols/gram of sample including total cholesterol, 7-dehydrocholesterol, desmosterol, lanosterol, lathasterol, cholestanol, coprostanol, beta-sitosterol, campesterol, stigmasterol, and 7alpha-hydroxycholesterol. A total of 35 fatty acids were quantified in nmols/gram of sample inlcuding myristic acid (14:0); pentadecanoic acid (15:0); palmitic acid (16:0); stearic acid (18:0); arachidic acid (20:0); behenic acid (22:0); lignoceric acid (24:0); myristoleic acid (14:1n5); palmitoleic acid (16:1n7); palmitelaidic acid (t16:1n7); oleic acid (18:1n9); elaidic acid (t18:1n9); vaccenic acid (18:1n7); linoleic acid (18:2n6); gamma-linolenic acid (18:3n6); alpha-linolenic acid (18:3n3); stearidonic acid (18:4n3); eicosenoic acid (20:1n9); eicosadienoic acid (20:2n6); mead acid (20:3n9); di-homo-gamma-linolenic acid (20:3n6); arachidonic acid (20:4n6); eicsoatetraenoic acid (20:4n3); eicosapentaenoic acid (20:5n3); erucic acid (22:1n9); docosadienoic acid (22:2n6); adrenic acid (22:4n6); docosapentaenoic acid (22:5n6); docosapentaenoic acid (22:5n3); docosahexaenoic acid (22:6n3); nervonic acid (24:1n9); and plasmalogen derivatives of 16:0, 18:0, 18:1n9, and 18:1n7.

dbGaP phs000016 International Multi-Center ADHD Genetics Project - Eligibility

- 2022-05-20 - 10 Formulär, 1 Item-grupp, 9 Dataelement, 1 Språk
Item-grupp: IG.elig
Principal Investigator: S. Faraone, SUNY Upstate Medical University, Syracuse, NY, USA MeSH: Attention Deficit Disorder with Hyperactivity https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000016 The goal of the project is to complete a 600,000 tag SNP genome-wide association scan of 958 parent-child trios from the International Multisite ADHD Genetics (IMAGE) project, in order to assess the association of SNP markers with ADHD, analyze quantitative ADHD phenotypes, complete copy number analyses, assess parent of origin effects and season of birth effects, and test for epistasis among apparently uncorrelated genes. *Acquiring DNA Samples* All consent forms stipulate that the samples can only be used by researchers who have been approved by the National Institute of Mental Health (NIMH), National Institutes of Health. All consent forms, except those used at the Zürich site (N=141 subjects), explicitly indicate that the samples may be used by researchers from commercial enterprises seeking to benefit financially from the analysis of the samples. The Zürich consent does not prohibit such use. The Zürich consent form also included an "opt out" that allowed the subjects to indicate that they did not want their samples stored at the NIMH repository or used by researchers external to the project. No subjects enrolled in the project opted out. *Consent groups and participant set* - ADHD (ADHD): 2758 (924 trios)

pht000051.v2.p2

1 Item-grupp 60 Dataelement

pht000052.v2.p2

1 Item-grupp 200 Dataelement

pht000053.v2.p2

1 Item-grupp 34 Dataelement

pht000049.v2.p2

1 Item-grupp 25 Dataelement

pht000050.v2.p2

1 Item-grupp 81 Dataelement

pht001038.v1.p2

1 Item-grupp 2 Dataelement

dbGaP phs000021 Genome-Wide Association Study of Schizophrenia - pht000067.v2.p2

- 2022-05-12 - 8 Formulär, 1 Item-grupp, 119 Dataelement, 1 Språk
Item-grupp: pht000067.v2.p2
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000021.v3.p2 The goal of the study is to find susceptibility genes for schizophrenia. *Dataset versioning* - Version 1: European-American (EA) ancestry only - Version 2: Version 1 plus African-American (AA) ancestry *Consent groups and participant set* - General research use (GRU): 4591 cases and controls (1217 EA cases, 1442 EA controls, 953 AA cases, 979 AA controls) This consent group includes a subset of schizophrenia cases and all controls (which overlap with Bipolar study controls in Bipolar: GRU dataset). - Schizophrenia and related disorders (SARC): 475 cases (187 EA cases, 288 AA cases) This consent group includes a subset of schizophrenia cases.

pht000068.v1.p2

1 Item-grupp 38 Dataelement

pht000069.v1.p2

1 Item-grupp 253 Dataelement

pht000287.v1.p2

1 Item-grupp 253 Dataelement

pht000288.v1.p2

1 Item-grupp 38 Dataelement

pht002001.v1.p2

1 Item-grupp 2 Dataelement

pht002002.v1.p2

1 Item-grupp 2 Dataelement

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