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dbGaP phs001048 The FUSION Tissue Biopsy Study - Eligibility

- 09-07-23 - 5 Formulieren, 1 Itemgroep, 2 Data-elementen, 1 Taal
Itemgroep: IG.elig
Principal Investigator: Michael Boehnke, University of Michigan, Ann Arbor, MI, USA MeSH: Diabetes Mellitus, Type 2 https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001048 The Finland-United States Investigation of NIDDM Genetics (FUSION) study is a long-term effort to identify genetic variants that predispose to type 2 diabetes (T2D) or that impact the variability of T2D-related quantitative traits (QTs). Skeletal muscle and adipose are major insulin target tissues and play key roles in insulin resistance. We hypothesize that a subset of T2D and related QT variants alter gene expression in skeletal muscle and adipose tissue. For this FUSION Tissue Biopsy Study, we have obtained and are analyzing RNA-Seq, microRNA (miRNA)-Seq, and DNA methylation (methyl)-Seq data on biopsy samples from 331 individuals from across the range of glucose tolerance: 124 normal glucose tolerance (NGT), 77 impaired glucose tolerance (IGT), 44 impaired fasting glucose (IFG), and 86 newly-diagnosed T2Ds. Participants completed two study visits, two weeks apart. First visits comprised most of the clinical phenotyping, including four-point OGTT (fasting, and 30, 60, and 120 minute post-load); BMI, WHR; lipids; blood pressure; and many other variables. Participants also completed FUSION health history, medication, and lifestyle questionnaires. At second visit, we obtained ~250mg *vastus lateralis* skeletal muscle, ~750mg abdominal subcutaneous adipose, and a ~5x15mm section of abdominal skin. Visits were completed in March 2013. RNA isolation is ongoing in the Collins laboratory at the NIH, RNA and miRNA sequencing at the NIH Intramural Sequencing Center (NISC), and genotyping at the Center for Inherited Disease Research (CIDR). Individual-level data is available here for the 306 individuals who consented to data deposit. To focus on evaluation of gene expression and its regulation in skeletal muscle, we analyzed mRNA extracted from *vastus lateralis* skeletal muscle obtained from 271 of the 331 individual subjects from Finland, along with genome-wide genotypes. Individual-level data is available here for the 250 subjects who reconsented to the use of their data. Release phs001048.v2.p1 adds muscle data for an additional 42 subjects and data from adipose tissue for 276 subjects. Total RNA was isolated using Trizol extraction in the Collins laboratory at the NIH. The mRNA was poly-A selected, 24-plex libraries were generated using the Illumina TruSeq directional mRNA-seq library protocol and RNA sequencing was performed on HiSeq2000 sequencers using 101bp paired-end reads at NISC. miRNA libraries were prepared from total RNA from 296 muscle and 270 adipose samples, pooled and sequenced 50bp single-end reads on Illumina HiSeq2500. Data for 272 muscle and 251 adipose samples are available here for individuals with consent for data deposit. DNA was extracted from blood in the Collins laboratory, and genotyping on the Illumina Omni2.5M array was performed at CIDR. Genotypes were imputed using the HRC 2016 reference panel. In order to assess regions of open chromatin in skeletal muscle, we obtained muscle tissue from a commercial provider to perform ATAC-seq; these samples were sequenced at the University of Michigan DNA Sequencing Core. Greater than 90% of the approximately 80 loci associated with T2D and the 100s of loci associated with T2D-related traits (glucose and insulin, anthropometrics, lipids) through genome-wide association studies occur in non-coding regions, suggesting a strong regulatory component to disease susceptibility. Regulatory element activity is often tissue-specific, which further complicates discovery of the causal/functional variation. Therefore, there is a critical need to understand the full spectrum of genetic variation and regulatory element usage in T2D-relevant tissues. To that end, this study contains whole genome sequence and whole genome bisulfite sequence, and/or Illumina MethylationEPIC Array data, of two tissues relevant to T2D: skeletal muscle and adipose tissue from individuals with glucose tolerance categories ranging from normal to T2D, providing a comprehensive survey of both individual genetic variation as well as DNA methylation across different tissues from multiple individuals.

pht005658.v2.p1

1 Itemgroep 6 Data-elementen

pht005659.v2.p1

1 Itemgroep 2 Data-elementen

pht005660.v2.p1

1 Itemgroep 13 Data-elementen

pht008898.v1.p1

1 Itemgroep 13 Data-elementen

dbGaP phs001166 Type 2 Diabetes Starr County GWAS and Exome Sequencing - pht000644.v2.p1

- 29-06-23 - 6 Formulieren, 1 Itemgroep, 24 Data-elementen, 1 Taal
Itemgroep: pht000644
Principal Investigator: Craig L. Hanis, PhD, The University of Texas Health Science Center at Houston, Houston, TX, USA, USA MeSH: Diabetes Mellitus, Type 2 https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001166 *The T2D Seq GWAS Starr County Cohort is utilized in the following dbGaP sub-studies.* To view genotypes, other molecular data, and derived variables collected in these sub-studies, please click on the following sub-studies below or in the "Sub-studies" section of this top-level study page phs001166 T2D Seq GWAS Starr County Cohort.- phs000143 CIDR T2D Hanis - phs001099 T2D GENES Starr County

pht005631.v1.p1

1 Itemgroep 5 Data-elementen

pht005632.v1.p1

1 Itemgroep 6 Data-elementen

pht005633.v1.p1

1 Itemgroep 23 Data-elementen

pht005634.v1.p1

1 Itemgroep 6 Data-elementen

pht005635.v1.p1

1 Itemgroep 4 Data-elementen

dbGaP phs001093 T2D-GENES Multi-Ethnic Exome Sequencing Study: UK South Asian - Eligibility

- 21-06-23 - 5 Formulieren, 1 Itemgroep, 7 Data-elementen, 1 Taal
Itemgroep: IG.elig
Principal Investigator: David Altshuler, Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA MeSH: Diabetes Mellitus, Type 2 https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001093 T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Multi-Ethnic Samples) is a NIDDK-funded international research consortium which seeks to identify genetic variants for type 2 diabetes (T2D) through multiethnic sequencing studies. T2D-GENES Project 1 is a multi-ethnic sequencing study designed to assess whether less common variants play a role in T2D risk and to assess similarities and differences in the distribution of T2D risk variants across ancestry groups. The individuals were obtained from 14 cohorts that are listed in Table 1. The strategy was to perform deep exome sequencing of 12,940 individuals, 6,504 with T2D and 6,436 controls, divided among five ancestry groups: Europeans, East Asians, South Asians, American Hispanics, and African Americans. Sequencing was performed at the Broad Institute using the Agilent v2 capture reagent on Illumina HiSeq machines. Please note that while we summarize the full sample list in publications and below, the Kooperative Gesundheitsforschung in der Region Augsburg (KORA) study does not have a sub study, as it is not consented to be deposited in dbGAP. *Table 1.* T2D-GENES Whole Exome Sequencing Studies table border="1" tr th*Ancestry*/th th*Study*/th th*Countries of Origin*/th th*# Cases*/th th*# Controls*/th /tr tr tdAfrican American/td tdJackson Heart Study/td tdUS/td td502/td td527/td /tr tr tdAfrican American/td tdWake Forest School of Medicine Study/td tdUS/td td518/td td532/td /tr tr tdEast Asian/td tdKorea Association Research Project/td tdKorea/td td526/td td561/td /tr tr tdEast Asian/td tdSingapore Diabetes Cohort Study; Singapore Prospective Study Program/td tdSingapore (Chinese)/td td486/td td592/td /tr tr tdEuropean/td tdAshkenazi/td tdUS, Israel/td td506/td td352/td /tr tr tdEuropean/td tdMetabolic Syndrome in Men Study (METSIM)/td tdFinland/td td484/td td498/td /tr tr tdEuropean/td tdFinland-United States Investigation of NIDDM Genetics (FUSION) Study/td tdFinland/td td472/td td476/td /tr tr tdEuropean/td tdKooperative Gesundheitsforschung in der Region Augsburg (KORA)/td tdGermany/td td97/td td90/td /tr tr tdEuropean/td tdUK Type 2 Diabetes Genetics Consortium (UKT2D)/td tdUK/td td322/td td320/td /tr tr tdEuropean/td tdMalmö-Botnia Study/td tdFinland, Sweden/td td478/td td443/td /tr tr tdHispanic/td tdSan Antonio Family Heart Study, San Antonio Family Diabetes/ Gallbladder Study, Veterans Administration Genetic Epidemiology Study, and the Investigation of Nephropathy and Diabetes Study Family Component/td tdUS/td td272/td td219/td /tr tr tdHispanic/td tdStarr County, Texas/td tdUS/td td749/td td704/td /tr tr tdSouth Asian/td tdLondon Life Sciences Population Study (LOLIPOP)/td tdUK (Indian Asian)/td td530/td td538/td /tr tdSouth Asian/td tdSingapore Indian Eye Study/td tdSingapore (Indian Asian)/td td563/td td585/td /table The London Life Sciences Population Study (LOLIPOP) contributed 530 cases and 538 controls to T2D-GENES Project 1.

pht005610.v1.p1

1 Itemgroep 4 Data-elementen

pht005612.v1.p1

1 Itemgroep 24 Data-elementen

pht005613.v1.p1

1 Itemgroep 5 Data-elementen

pht005611.v1.p1

1 Itemgroep 3 Data-elementen

dbGaP phs001095 T2D-GENES Multi-Ethnic Exome Sequencing Study: Ashkenazi - pht005621.v1.p1

- 21-06-23 - 5 Formulieren, 1 Itemgroep, 5 Data-elementen, 1 Taal
Itemgroep: pht005621
Principal Investigator: David Altshuler, Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA MeSH: Diabetes Mellitus, Type 2 https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001095 T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Multi-Ethnic Samples) is a NIDDK-funded international research consortium which seeks to identify genetic variants for type 2 diabetes (T2D) through multiethnic sequencing studies. T2D-GENES Project 1 is a multi-ethnic sequencing study designed to assess whether less common variants play a role in T2D risk and to assess similarities and differences in the distribution of T2D risk variants across ancestry groups. The individuals were obtained from 14 cohorts that are listed in Table 1. The strategy was to perform deep exome sequencing of 12,940 individuals, 6,504 with T2D and 6,436 controls, divided among five ancestry groups: Europeans, East Asians, South Asians, American Hispanics, and African Americans. Sequencing was performed at the Broad Institute using the Agilent v2 capture reagent on Illumina HiSeq machines. Please note that while we summarize the full sample list in publications and below, the Kooperative Gesundheitsforschung in der Region Augsburg (KORA) study does not have a sub study, as it is not consented to be deposited in dbGAP. *Table 1.* T2D-GENES Whole Exome Sequencing Studies table border="1" tr th*Ancestry*/th th*Study*/th th*Countries of Origin*/th th*# Cases*/th th*# Controls*/th /tr tr tdAfrican American/td tdJackson Heart Study/td tdUS/td td502/td td527/td /tr tr tdAfrican American/td tdWake Forest School of Medicine Study/td tdUS/td td518/td td532/td /tr tr tdEast Asian/td tdKorea Association Research Project/td tdKorea/td td526/td td561/td /tr tr tdEast Asian/td tdSingapore Diabetes Cohort Study; Singapore Prospective Study Program/td tdSingapore (Chinese)/td td486/td td592/td /tr tr tdEuropean/td tdAshkenazi/td tdUS, Israel/td td506/td td352/td /tr tr tdEuropean/td tdMetabolic Syndrome in Men Study (METSIM)/td tdFinland/td td484/td td498/td /tr tr tdEuropean/td tdFinland-United States Investigation of NIDDM Genetics (FUSION) Study/td tdFinland/td td472/td td476/td /tr tr tdEuropean/td tdKooperative Gesundheitsforschung in der Region Augsburg (KORA)/td tdGermany/td td97/td td90/td /tr tr tdEuropean/td tdUK Type 2 Diabetes Genetics Consortium (UKT2D)/td tdUK/td td322/td td320/td /tr tr tdEuropean/td tdMalmö-Botnia Study/td tdFinland, Sweden/td td478/td td443/td /tr tr tdHispanic/td tdSan Antonio Family Heart Study, San Antonio Family Diabetes/ Gallbladder Study, Veterans Administration Genetic Epidemiology Study, and the Investigation of Nephropathy and Diabetes Study Family Component/td tdUS/td td272/td td219/td /tr tr tdHispanic/td tdStarr County, Texas/td tdUS/td td749/td td704/td /tr tr tdSouth Asian/td tdLondon Life Sciences Population Study (LOLIPOP)/td tdUK (Indian Asian)/td td530/td td538/td /tr tr tdSouth Asian/td tdSingapore Indian Eye Study/td tdSingapore (Indian Asian)/td td563/td td585/td /tr /table The Ashkenazi study contributed 506 cases and 352 controls to T2D-GENES Project 1.

Eligibility

1 Itemgroep 11 Data-elementen

pht005618.v1.p1

1 Itemgroep 4 Data-elementen

pht005619.v1.p1

1 Itemgroep 3 Data-elementen

pht005620.v1.p1

1 Itemgroep 27 Data-elementen

dbGaP phs001096 T2D-GENES Multi-Ethnic Exome Sequencing Study: KARE - pht005606.v1.p1

- 20-06-23 - 5 Formulieren, 1 Itemgroep, 4 Data-elementen, 1 Taal
Itemgroep: pht005606
Principal Investigator: David Altshuler, Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA MeSH: Diabetes Mellitus, Type 2 https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001096 T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Multi-Ethnic Samples) is a NIDDK-funded international research consortium which seeks to identify genetic variants for type 2 diabetes (T2D) through multiethnic sequencing studies. T2D-GENES Project 1 is a multi-ethnic sequencing study designed to assess whether less common variants play a role in T2D risk and to assess similarities and differences in the distribution of T2D risk variants across ancestry groups. The individuals were obtained from 14 cohorts that are listed in Table 1. The strategy was to perform deep exome sequencing of 12,940 individuals, 6,504 with T2D and 6,436 controls, divided among five ancestry groups: Europeans, East Asians, South Asians, American Hispanics, and African Americans. Sequencing was performed at the Broad Institute using the Agilent v2 capture reagent on Illumina HiSeq machines. Please note that while we summarize the full sample list in publications and below, the Kooperative Gesundheitsforschung in der Region Augsburg (KORA) study does not have a sub study, as it is not consented to be deposited in dbGAP. *Table 1.* T2D-GENES Whole Exome Sequencing Studies table border="1" tr th*Ancestry*/th th*Study*/th th*Countries of Origin*/th th*# Cases*/th th*# Controls*/th /tr tr tdAfrican American/td tdJackson Heart Study/td tdUS/td td502/td td527/td /tr tr tdAfrican American/td tdWake Forest School of Medicine Study/td tdUS/td td518/td td532/td /tr tr tdEast Asian/td tdKorea Association Research Project/td tdKorea/td td526/td td561/td /tr tr tdEast Asian/td tdSingapore Diabetes Cohort Study; Singapore Prospective Study Program/td tdSingapore (Chinese)/td td486/td td592/td /tr tr tdEuropean/td tdAshkenazi/td tdUS, Israel/td td506/td td352/td /tr tr tdEuropean/td tdMetabolic Syndrome in Men Study (METSIM)/td tdFinland/td td484/td td498/td /tr tr tdEuropean/td tdFinland-United States Investigation of NIDDM Genetics (FUSION) Study/td tdFinland/td td472/td td476/td /tr tr tdEuropean/td tdKooperative Gesundheitsforschung in der Region Augsburg (KORA)/td tdGermany/td td97/td td90/td /tr tr tdEuropean/td tdUK Type 2 Diabetes Genetics Consortium (UKT2D)/td tdUK/td td322/td td320/td /tr tr tdEuropean/td tdMalmö-Botnia Study/td tdFinland, Sweden/td td478/td td443/td /tr tr tdHispanic/td tdSan Antonio Family Heart Study, San Antonio Family Diabetes/ Gallbladder Study, Veterans Administration Genetic Epidemiology Study, and the Investigation of Nephropathy and Diabetes Study Family Component/td tdUS/td td272/td td219/td /tr tr tdHispanic/td tdStarr County, Texas/td tdUS/td td749/td td704/td /tr tr tdSouth Asian/td tdLondon Life Sciences Population Study (LOLIPOP)/td tdUK (Indian Asian)/td td530/td td538/td /tr tr tdSouth Asian/td tdSingapore Indian Eye Study/td tdSingapore (Indian Asian)/td td563/td td585/td /tr /table The Korea Association Research Project (KARE) studies contributed 526 cases and 561 controls to T2D-GENES Project 1.

pht005607.v1.p1

1 Itemgroep 3 Data-elementen

pht005609.v1.p1

1 Itemgroep 5 Data-elementen

Eligibility

1 Itemgroep 11 Data-elementen

pht005608.v1.p1

1 Itemgroep 26 Data-elementen

dbGaP phs001097 T2D-GENES Multi-Ethnic Exome Sequencing Study: Singapore - Eligibility

- 20-06-23 - 5 Formulieren, 1 Itemgroep, 7 Data-elementen, 1 Taal
Itemgroep: IG.elig
Principal Investigator: David Altshuler, Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA MeSH: Diabetes Mellitus, Type 2 https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001097 T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Multi-Ethnic Samples) is a NIDDK-funded international research consortium which seeks to identify genetic variants for type 2 diabetes (T2D) through multiethnic sequencing studies. T2D-GENES Project 1 is a multi-ethnic sequencing study designed to assess whether less common variants play a role in T2D risk and to assess similarities and differences in the distribution of T2D risk variants across ancestry groups. The individuals were obtained from 14 cohorts that are listed in Table 1. The strategy was to perform deep exome sequencing of 12,940 individuals, 6,504 with T2D and 6,436 controls, divided among five ancestry groups: Europeans, East Asians, South Asians, American Hispanics, and African Americans. Sequencing was performed at the Broad Institute using the Agilent v2 capture reagent on Illumina HiSeq machines. Please note that while we summarize the full sample list in publications and below, the Kooperative Gesundheitsforschung in der Region Augsburg (KORA) study does not have a sub study, as it is not consented to be deposited in dbGAP. *Table 1.* T2D-GENES Whole Exome Sequencing Studies table border="1" tr th*Ancestry*/th th*Study*/th th*Countries of Origin*/th th*# Cases*/th th*# Controls*/th /tr tr tdAfrican American/td tdJackson Heart Study/td tdUS/td td502/td td527/td /tr tr tdAfrican American/td tdWake Forest School of Medicine Study/td tdUS/td td518/td td532/td /tr tr tdEast Asian/td tdKorea Association Research Project/td tdKorea/td td526/td td561/td /tr tr tdEast Asian/td tdSingapore Diabetes Cohort Study; Singapore Prospective Study Program/td tdSingapore (Chinese)/td td486/td td592/td /tr tr tdEuropean/td tdAshkenazi/td tdUS, Israel/td td506/td td352/td /tr tr tdEuropean/td tdMetabolic Syndrome in Men Study (METSIM)/td tdFinland/td td484/td td498/td /tr tr tdEuropean/td tdFinland-United States Investigation of NIDDM Genetics (FUSION) Study/td tdFinland/td td472/td td476/td /tr tr tdEuropean/td tdKooperative Gesundheitsforschung in der Region Augsburg (KORA)/td tdGermany/td td97/td td90/td /tr tr tdEuropean/td tdUK Type 2 Diabetes Genetics Consortium (UKT2D)/td tdUK/td td322/td td320/td /tr tr tdEuropean/td tdMalmö-Botnia Study/td tdFinland, Sweden/td td478/td td443/td /tr tr tdHispanic/td tdSan Antonio Family Heart Study, San Antonio Family Diabetes/ Gallbladder Study, Veterans Administration Genetic Epidemiology Study, and the Investigation of Nephropathy and Diabetes Study Family Component/td tdUS/td td272/td td219/td /tr tr tdHispanic/td tdStarr County, Texas/td tdUS/td td749/td td704/td /tr tr tdSouth Asian/td tdLondon Life Sciences Population Study (LOLIPOP)/td tdUK (Indian Asian)/td td530/td td538/td /tr tr tdSouth Asian/td tdSingapore Indian Eye Study/td tdSingapore (Indian Asian)/td td563/td td585/td /tr /table The Singapore studies contributed 1049 cases and 1177 controls to T2D-GENES Project 1.

pht005614.v1.p1

1 Itemgroep 4 Data-elementen

pht005615.v1.p1

1 Itemgroep 3 Data-elementen

pht005616.v1.p1

1 Itemgroep 27 Data-elementen

pht005617.v1.p1

1 Itemgroep 5 Data-elementen

dbGaP phs001130 NIDDM-Atherosclerosis Study (NIDDM-Athero) - pht008417.v1.p1

- 16-06-23 - 6 Formulieren, 1 Itemgroep, 4 Data-elementen, 1 Taal
Itemgroep: pht008417
Principal Investigator: Jerry L. Nadler, Eastern Virginia Medical School, Norfolk, VA, USA MeSH: Diabetes Mellitus, Type 2,Diabetes Complications https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001130 The NIDDM-Atherosclerosis Study, funded by NHLBI, was designed as a family study to examine the genetic basis of subclinical atherosclerosis and diabetes in Hispanic families. Family members of probands with T2D were recruited in the Los Angeles area. The baseline examination of the cohort included the euglycemic hyperinsulinemic clamp test from which the two key phenotypes were obtained: insulin sensitivity (M) and metabolic clearance rate of insulin (MCRI). Genome-wide genotyping was obtained under separate funding by NIDDK as a part of the GUARDIAN (Genetics Underlying Diabetes in Hispanics) Consortium.

pht008418.v1.p1

1 Itemgroep 9 Data-elementen

pht008419.v1.p1

1 Itemgroep 3 Data-elementen

Eligibility

1 Itemgroep 3 Data-elementen

pht008415.v1.p1

1 Itemgroep 3 Data-elementen

pht008416.v1.p1

1 Itemgroep 5 Data-elementen

dbGaP phs001188 The FUSION Study - Islet Expression and Regulation - Eligibility

- 01-06-23 - 5 Formulieren, 1 Itemgroep, 1 Data-element, 1 Taal
Itemgroep: IG.elig
Principal Investigator: Michael Boehnke, University of Michigan, Ann Arbor, MI, USA MeSH: Diabetes Mellitus, Type 2 https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001188 This study evaluates gene expression and its regulation in human pancreatic islets, a tissue relevant in the study of genetic risk factors contributing to diabetes. We obtained islets from deceased donors and generated data from genome-wide SNP chip, bulk RNA-Seq, microRNA (miRNA)-Seq, whole genome sequence, DNA methylation (methyl)-Seq, transcription initiation profiles using cap analysis of gene expression (CAGE)-Seq, single cell RNA-seq, and single nuclei ATAC-seq. These data include ATAC-seq of two islet subjects, RNA-seq of 31 additional subjects, genome-wide chip genotypes, and imputed genotypes of the 33 subjects released with phs001188.v1. For genotyping, 500-1000 islet equivalents (IEQ) were cultured as in Gershengorn (Science, 2004, PMID: 15564314); genomic DNA isolated from islet cultures. For RNA analyses, 2500-5000 IEQ from each islet source were used for bulk or single-cell RNA isolation. Messenger RNA was isolated with trizol extraction and 12-plex libraries were generated using the Illumina TruSeq directional mRNA-seq library protocol. Bulk RNA sequencing was performed on HiSeq2000/HiSeq2500 sequencers using paired-end reads at the NIH Intramural Sequencing Center (NISC). miRNA libraries were prepared from total RNA from 68 samples, pooled and sequenced 50bp single-end reads on Illumina HiSeq2500. CAGE libraries were prepared from total RNA samples using the nAnT-iCAGE protocol at DNAFORM, Japan. CAGE libraries were sequenced at the NIH Intramural Sequencing Center (NISC) on the HiSeq2000 sequencer. Genotyping on the Illumina Omni2.5M array was performed at the NHGRI Genomics Core facility. Genotypes were imputed using the HRC.r1.1.2016 reference panel. In order to assess regions of open chromatin in islets, we performed bulk ATAC-seq on HiSeq2000 sequencers using paired-end reads at NISC. Single-nuclei ATAC-seq libraries were prepared using single-cell-combinatorial-indexing (sci-) ATAC-seq protocol and sequenced on Illumina NextSeq using paired-end reads. scRNA-seq libraries were generated using the 10X Genomics platform and sequenced on Illumina HiSeq3000 at the Genomics Technology Core of the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS). Greater than 90% of the loci associated with T2D through genome-wide association studies occur in non-coding regions, suggesting a strong regulatory component to disease susceptibility. Therefore, there is a critical need to understand the full spectrum of genetic variation and regulatory element usage in T2D-relevant tissues. To that end, this study contains whole genome sequence and whole genome bisulfite sequence, and/or Illumina MethylationEPIC Array data, providing a comprehensive survey of both individual genetic variation as well as DNA methylation across different tissues from multiple individuals. In addition, we carried out sequencing of single cell RNAs (two subjects) and single cell nuclei (one subject) to characterize gene expression and chromatin accessibility of islets.

pht006300.v2.p1

1 Itemgroep 2 Data-elementen

pht006301.v2.p1

1 Itemgroep 12 Data-elementen

pht006302.v2.p1

1 Itemgroep 12 Data-elementen

pht006615.v2.p1

1 Itemgroep 2 Data-elementen

dbGaP phs001215 NHLBI TOPMed: San Antonio Family Heart Study (SAFHS) - Eligibility

- 16-05-23 - 6 Formulieren, 1 Itemgroep, 4 Data-elementen, 1 Taal
Itemgroep: IG.elig
Principal Investigator: John Blangero, PhD, University of Texas Rio Grande Valley, Brownsville, TX, USA MeSH: Cardiovascular Diseases,Body Height,Body Weight,Body Mass Index,Waist Circumference,Blood Glucose,Insulin,Diabetes Mellitus, Type 2,Blood Pressure,Cholesterol,Cholesterol, HDL,Triglycerides https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001215 The San Antonio Family Heart Study (SAFHS) is a complex pedigree-based mixed longitudinal study designed to identify low frequency or rare variants influencing susceptibility to cardiovascular disease, using whole genome sequence (WGS) information from 2,590 individuals in large Mexican American pedigrees from San Antonio, Texas. The major objectives of this study are to identify low frequency or rare variants in and around known common variant signals for CVD, as well as to find novel low frequency or rare variants influencing susceptibility to CVD. WGS of the SAFHS cohort has been obtained through three efforts. Approximately 540 WGS were performed commercially at 50X by Complete Genomics, Inc (CGI) as part of the large T2D-GENES Project. The phenotype and genotype data for this group is available at dbGaP under accession number phs000462. An additional ~900 WGS at 30X were obtained through Illumina as part of the R01HL113322 "Whole Genome Sequencing to Identify Causal Genetic Variants Influencing CVD Risk" project. Finally, ~1,150 WGS at 30X WGS were obtained through Illumina funded by a supplement as part of the NHLBI's TOPMed program. Extensive phenotype data are provided for sequenced individuals primarily obtained from the P01HL45522 "Genetics of Atherosclerosis in Mexican Americans" for adults and R01HD049051 for children in these same families. Phenotype information was collected between 1991 and 2016. For this dataset, the SAFHS appellation represents an amalgamation of the original SAFHS participants and an expansion that reexamined families previously recruited for the San Antonio Family Diabetes Study (R01DK042273) and the San Antonio Family Gall Bladder Study (R01DK053889). Due to this substantial examination history, participants may have information from up to five visits. The clinical variables reported are coordinated with TOPMed and include major adverse cardiac events (MACE), T2D status and age at diagnosis, glycemic traits (fasting glucose and insulin), blood pressure, blood lipids (total cholesterol, HDL cholesterol, calculated LDL cholesterol and triglycerides). Additional phenotype data include the medication status at each visit, classified in four categories as any current use of diabetes, hypertension or lipid-lowering medications, and, for females, current use of female hormones. Anthropometric measurements include age, sex, height, weight, hip circumference, waist circumference and derived ratios. PBMC derived gene expression assays for a subset of ~1,060 individuals obtained using the Illumina Sentrix-6 chip is also available from the baseline examination. The WGS data have been jointly called and are available in the current TOPMed accession (phs001215).

pht008628.v2.p2

1 Itemgroep 4 Data-elementen

pht008629.v2.p2

1 Itemgroep 6 Data-elementen

pht008631.v2.p2

1 Itemgroep 24 Data-elementen

pht008632.v2.p2

1 Itemgroep 10 Data-elementen

pht008630.v2.p2

1 Itemgroep 2 Data-elementen

dbGaP phs001375 Slim Initiative in Genomic Medicine for the Americas (SIGMA): Mexico City Diabetes Study (MCDS) - Eligibility

- 21-02-23 - 5 Formulieren, 1 Itemgroep, 5 Data-elementen, 1 Taal
Itemgroep: IG.elig
Principal Investigator: Jose Florez, Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA, and Massachusetts General Hospital, Boston, MA, USA MeSH: Diabetes Mellitus, Type 2 https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001375 The ~52,000 sample Type 2 Diabetes Exome Sequencing project is a collaboration of six consortia with various funding mechanisms that have joined together to investigate genetic variants for type 2 diabetes (T2D) using the largest T2D case/control sample set compiled to date. This includes samples from: - Type 2 Diabetes Genetic Exploration by Next-generation sequencing in multi-Ethnic Samples (T2D-GENES) - Genetics of Type 2 Diabetes (GoT2D) - Exome Sequencing Project (ESP) - Slim Initiative in Genomic Medicine for the Americas: Type 2 Diabetes (SIGMA T2D) - Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention, and Care (LuCAMP) - Progress in Diabetes Genetics in Youth (ProDIGY) This data generated from the SIGMA Mexico City Diabetes Study was part of the Slim Initiative in Genomic Medicine for the Americas: Type 2 Diabetes (SIGMA T2D), which is an international research consortium funded by the Carlos Slim Foundation that seeks to identify the genetic risk factors for type 2 diabetes (T2D) in Mexico and Latin America and translate those findings into improved treatment and prevention of diabetes. The SIGMA T2D project has sequenced and genotyped more than 13,000 samples from Mexican and Mexican Americans. The individuals were obtained from over 20 cohorts across the 6 consortia that are listed in Table 1. The strategy was to perform deep exome sequencing of individuals, 24,991 with T2D and 24,953 controls, divided among five ancestry groups: Europeans, East Asians, South Asians, American Hispanics, and African Americans. The T2D-GENES, ProDIGY and SIGMA studies, sequencing was performed at the Broad Institute using the Agilent v2 capture reagent or Illumina Rapid Capture on Illumina HiSeq machines. Please note that while we summarize the full sample list in publications and below, two of the cohorts below are not in dbGaP, due to the samples not being consented for deposition. This includes the Kooperative Gesundheitsforschung in der Region Augsburg (KORA) study and Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention, and Care (LuCamp) study. The Exome Sequencing Project (ESP) was deposited in dbGaP as part of their initial study and the phs numbers for that project can be found here: https://esp.gs.washington.edu/drupal/dbGaP_Releases table style="width:100%" border="1" captionTable 1. 52,000 sample T2D Case/Control Whole Exome Sequencing Studies/caption tbodytr thAncestry/th thConsortia/th thStudy/th thCountries of Origin/th th# Cases/th th# Controls/th /tr tr tdAfrican American/td tdT2D-GENES Project 1/td tdJackson Heart Study/td tdUS/td td500/td td526/td /tr tr tdAfrican American/td tdT2D-GENES Project 1/td tdWake Forest School of Medicine Study/td tdUS/td td518/td td530/td /tr tr tdAfrican American/td tdESP/td tdExome Sequencing Project (ESP)/td tdUS/td td467/td td1374/td /tr tr tdAfrican American/td tdT2D-GENES Follow up study/td tdBioMe Biobank Program (BioMe)/td tdUS/td td1297/td td1256/td /tr tr tdEast Asian/td tdT2D-GENES Project 1/td tdKorea Association Research Project/td tdKorea/td td526/td td561/td /tr tr tdEast Asian/td tdT2D-GENES Project 1& Follow up Study/td tdSingapore Diabetes Cohort Study; Singapore Prospective Study Program/td tdSingapore (Chinese)/td td1486/td td1568/td /tr tr tdEast Asian/td tdT2D-GENES Follow up study/td tdKorea SNUH/td tdSouth Korea/td td450/td td475/td /tr tr tdEast Asian/td tdT2D-GENES Follow up study/td tdResearch Studies in Hong Kong (Hong Kong)/td tdHong Kong/td td493/td td485/td /tr tr tdEuropean/td tdT2D-GENES Project 1/td tdAshkenazi/td tdUS, Israel/td td506/td td355/td /tr tr tdEuropean/td tdT2D-GENES Project 1/td tdMetabolic Syndrome in Men Study (METSIM)/td tdFinland/td td484/td td498/td /tr tr tdEuropean/td tdGoT2D/td tdFinland-United States Investigation of NIDDM Genetics (FUSION) Study/td tdFinland/td td472/td td476/td /tr tr tdEuropean/td tdGoT2D/td tdKooperative Gesundheitsforschung in der Region Augsburg (KORA)/td tdGermany/td td97/td td90/td /tr tr tdEuropean/td tdGoT2D/td tdUK Type 2 Diabetes Genetics Consortium (UKT2D)/td tdUK/td td322/td td320/td /tr tr tdEuropean/td tdGoT2D/td tdMalmo-Botnia Study/td tdFinland, Sweden/td td478/td td443/td /tr tr tdEuropean/td tdLuCamp/td tdLundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention, and Care (LuCamp)/td tdDenmark/td td997/td td997/td /tr tr tdEuropean/td tdESP/td tdExome Sequencing Project (ESP)/td tdUS/td td390/td td2843/td /tr tr tdEuropean/td tdT2D-GENES Follow up study/td tdGenetics of Diabetes and Audit Research Tayside Study (GoDARTS)/td tdScotland, UK/td td960/td td966/td /tr tr tdEuropean/td tdT2D-GENES Follow up study/td tdFramingham Heart Study (FHS)/td tdUS/td td396/td td596/td /tr tr tdHispanic/td tdT2D-GENES Project 1/td tdSan Antonio Family Heart Study, San Antonio Family Diabetes/ Gallbladder Study, Veterans Administration Genetic Epidemiology Study, and the Investigation of Nephropathy and Diabetes Study Family Component/td tdUS/td td272/td td218/td /tr tr tdHispanic/td tdT2D-GENES Project 1 & SIGMAv2/td tdStarr County, Texas/td tdUS/td td1762/td td1738/td /tr tr tdHispanic/td tdSIGMAv1/td tdMexico City Diabetes Study/td tdMexico/td td281/td td549/td /tr tr tdHispanic/td tdSIGMAv1 & v2/td tdMultiethnic Cohort (MEC)/td tdUS/td td1476/td td1443/td /tr tr tdHispanic/td tdSIGMAv1 & v2/td tdUNAM/INCMNSZ Diabetes Study (UIDS)/td tdMexico/td td1998/td td1977/td /tr tr tdHispanic/td tdSIGMAv1 & v2/td tdDiabetes in Mexico Study (DMS)/td tdMexico/td td1522/td td1546/td /tr tr tdMulti ethnic/td tdProDIGY/td tdTreatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY)/td tdUS/td td3097/td td0/td /tr tr tdMulti ethnic/td tdProDIGY/td tdSEARCH for Diabetes in Youth (SEARCH)/td tdUS/td td553/td td0/td /tr tr tdSouth Asian/td tdT2D-GENES Project 1/td tdLondon Life Sciences Population Study (LOLIPOP)/td tdUK (Indian Asian)/td td531/td td538/td /tr tr tdSouth Asian/td tdT2D-GENES Project 1 & Follow up study/td tdSingapore Indian Eye Study/td tdSingapore (Indian Asian)/td td1640/td td1478/td /tr tr tdSouth Asian/td tdT2D-GENES Follow up study/td tdPakistan Genomic Resource (PGR)/td tdPakistan/td td914/td td932/td /tr /tbody/table

pht006520.v1.p1

1 Itemgroep 4 Data-elementen

pht006521.v2.p1

1 Itemgroep 2 Data-elementen

pht006523.v1.p1

1 Itemgroep 5 Data-elementen

pht006522.v2.p1

1 Itemgroep 34 Data-elementen

dbGaP phs000583 Asian Indian Diabetic Heart Study (AIDHS) - Eligibility

- 13-01-23 - 6 Formulieren, 1 Itemgroep, 4 Data-elementen, 1 Taal
Itemgroep: IG.elig
Principal Investigator: Dharambir Sanghera, PhD, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA MeSH: Diabetes Mellitus, Type 2,Obesity https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000583 The Punjabi Sikh population is a well-defined, carefully collected homogeneous sample from northern India and the US. It has unique characteristics, which are ideal for genetic studies. Sikhs are *strictly* a non-smoking population and about 50% of participants are life-long vegetarians. All subjects included in the genome-wide association studies (GWAS) were recruited from one geographical location. Our population demonstrates a strong familial clustering of type 2 diabetes and related cardio-metabolic disorders that may be genetic and we believe that the contribution of alleles at specific loci are likely to be unique to Punjabi Asians compared to Europeans. Our group first showed that the association of a common variant at rs9939609 in the *FTO* (fat mass and obesity) gene in South Asians was independent of BMI (PMID:18598350) in contrast to Europeans where the association of same variant with T2D is mediated through obesity (PMID:17434869). These findings were later confirmed in an independent sample of South Indians (PMID:19005641), Pakistanis (PMID:21294771), and even East and South Asians in a large meta-analyses study comprising 96,551 individuals (PMID: 22109280). Earlier reported association of *MTNR1B* with fasting glucose concentrations and type 2 diabetes in European GWAS could not be confirmed in our Sikh cohort. On the other hand, our study revealed, for the first time, a significant protective association of another less common variant in *MTNR1B* with fasting glucose levels that was modulated by obesity. Ours was the first report that suggested that the low CETP activity was associated with higher CAD risk (PMID:22143414) in South Asians and that the genetic effects are significantly modulated by environmental factors (alcohol consumption). Our recent GWAS on type 2 diabetes has identified a novel locus at chromosome 13q12 in the *SGCG* gene (p=1.82x10sup-8/sup) associated with type 2 diabetes (PMID:23300278) in Punjabi Sikhs. From these findings, we are optimistic that our resource will provide new insights to gene functions in the diabetic pathway and better help researchers to understand and translate these insights to novel therapeutic treatment and early prevention to T2D that may be important beyond Indians.

pht003292.v1.p1

1 Itemgroep 5 Data-elementen

pht003293.v1.p1

1 Itemgroep 5 Data-elementen

pht003295.v1.p1

1 Itemgroep 5 Data-elementen

pht003296.v1.p1

1 Itemgroep 5 Data-elementen

pht003294.v1.p1

1 Itemgroep 5 Data-elementen

dbGaP phs000737 NIDDK Genetics of Metabolic Syndrome in an Island Population - Eligibility

- 28-12-22 - 6 Formulieren, 1 Itemgroep, 1 Data-element, 1 Taal
Itemgroep: IG.elig
Principal Investigator: Ranjan Deka, PhD, University of Cincinnati, Cincinnati, OH, USA MeSH: Metabolic Syndrome X,Diabetes mellitus type 2,Hypertension, Essential,Dyslipidemia,Coronary Heart Disease,Gout https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000737 The major objective of this study was to conduct a systematic genetic study of metabolic traits involved in metabolic syndrome through collection and analysis of epidemiological, demographic, environmental, and relevant biological and clinical data from a relatively isolated island population of the eastern Adriatic coast of Croatia. The population was chosen for the following reasons: 1) in spite of practicing a largely traditional life style and dietary habits, high rates of obesity, arterial hypertension, dyslipidemia and related metabolic abnormalities were found in previous studies; 2) the population was established by a relatively small number of founders, predominantly of Slavic descent from the mainland during 15th to 18th century AD, a genetically homogeneous population living in a homogeneous environment; 3) sharing a common European ancestry, a relevant population for study in the context of the general US population; 4) Croatian collaborators have been conducting anthropological and genetic studies in these communities for over three decades. There were two major aims of the study: 1) to recruit ~1200 adult participants and collect blood samples together with demographic, anthropometric, environmental and clinical data from the island of Hvar; to perform biochemical tests to measure glucose, insulin, uric acid and lipid levels; 2) conduct a genome-wide association analysis of metabolic traits and phenotypes using genome-wide SNP arrays (Affymetrix Genome-Wide Human SNP Array 5.0).

pht004443.v1.p1

1 Itemgroep 4 Data-elementen

pht004444.v1.p1

1 Itemgroep 5 Data-elementen

pht004445.v1.p1

1 Itemgroep 7 Data-elementen

pht004446.v1.p1

1 Itemgroep 52 Data-elementen

pht004447.v1.p1

1 Itemgroep 6 Data-elementen

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