GoT2D
Ontology highlight
ABSTRACT: The Genetics of Type 2 Diabetes Consortium (GoT2D) is a collaboration between the University of Michigan, the Broad Institute and the Wellcome Trust Centre for Human Genetics. The overall aim is to extend upon recent efforts, such as genome-wide association studies (GWAS) and large scale meta-analyses. While they have proved successful at mapping genomic loci that influence human diseases, like type 2 diabetes, much of the heritability remains unexplained. In this study, we use next generation sequencing and genotyping technologies to query for lower frequency variants in the human genome. Thereby, allowing a deeper characterization of the spectrum of alleles associated with type 2 diabetes risk, and a better assessment of the genes that play a role in the etiology of type 2 diabetes development. We studied 1,326 T2D cases and 1,331 normoglycemic controls from Northern and Central Europe (Sweden, Finland, UK, and Germany). To efficiently characterize the entire genome sequence of each individual, we performed low-coverage (~5x) whole-genome sequencing, augmented by deep coverage (~100x) sequencing of the exome (Fuchsberger et al, 2016), and dense (2.5M) single nucleotide polymorphism (SNP) genotyping using the HumanOmni2.5 array. The data deposited in dbGaP will include all the Swedish, Finnish, and UK samples, but the German data will be deposited in the European Genome-phenome Archive (EGA), by virtue of the project specific funding requirements.
SECONDARY ACCESSION(S): PRJNA268369PRJNA268370
REPOSITORIES: dbGaP
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| GapExchange_phs000840.v1.p1.xml | Xml | |||
| dbGaPEx2.1.5.xsd | Other | |||
| Study_Report.phs000840.GoT2D.v1.p1.MULTI.pdf | ||||
| manifest_phs000840.GoT2D.v1.p1.c1.DS-T2D-IRB-RD.pdf | ||||
| datadict_v2.xsl | Other |
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Project description:The Genetics of Type 2 Diabetes Consortium (GoT2D) is a collaboration between the University of Michigan, the Broad Institute and the Wellcome Trust Centre for Human Genetics. The overall aim is to extend upon recent efforts, such as genome-wide association studies (GWAS) and large scale meta-analyses. While they have proved successful at mapping genomic loci that influence human diseases, like type 2 diabetes, much of the heritability remains unexplained. In this study, we use next generation sequencing and genotyping technologies to query for lower frequency variants in the human genome. Thereby, allowing a deeper characterization of the spectrum of alleles associated with type 2 diabetes risk, and a better assessment of the genes that play a role in the etiology of type 2 diabetes development. We studied 1,326 T2D cases and 1,331 normoglycemic controls from Northern and Central Europe (Sweden, Finland, UK, and Germany). To efficiently characterize the entire genome sequence of each individual, we performed low-coverage (~5x) whole-genome sequencing, augmented by deep coverage (~100x) sequencing of the exome, and dense (2.5M) single nucleotide polymorphism (SNP) genotyping using the HumanOmni2.5 array. The data deposited in EGA will include all the Swedish, Finnish, UK, and German samples.
| EGAS00001001459 | EGA
Project description:The aim of this study was to identify proteomic alterations associated with functional dysregulation of the retina with diabetes that could eventually be used as surrogate endpoints in preclinical drug testing studies. A multi-modal approach of antibody (Luminex)-, electrophoresis (2-DIGE)-, and LC-MS (iTRAQ)-based quantitation methods was used to provide broad coverage of the retinal proteome. Transcriptional profiling through microarray analysis was also included to increase coverage and provide insight into potential regulation of protein expression changes at the mRNA level. The different technologies proved complementary, with limited coverage overlap between methods.
2010-06-01 | GSE20886 | GEO
Project description:<p>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: <ul> <li>Type 2 Diabetes Genetic Exploration by Next-generation sequencing in multi-Ethnic Samples (T2D-GENES)</li> <li>Genetics of Type 2 Diabetes (GoT2D)</li> <li>Exome Sequencing Project (ESP)</li> <li>Slim Initiative in Genomic Medicine for the Americas: Type 2 Diabetes (SIGMA T2D)</li> <li>Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention, and Care (LuCAMP)</li> <li>Progress in Diabetes Genetics in Youth (ProDIGY)</li> </ul> </p> <p>This data generated from the SIGMA Diabetes in Mexico Study (DMS) 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.</p> <p>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: <a href="https://esp.gs.washington.edu/drupal/dbGaP_Releases">https://esp.gs.washington.edu/drupal/dbGaP_Releases</a>. </p> <p><table style="width:100%" border="1"> <caption>Table 1. 52,000 sample T2D Case/Control Whole Exome Sequencing Studies</caption> <tr> <th>Ancestry</th> <th>Consortia</th> <th>Study</th> <th>Countries of Origin</th> <th># Cases</th> <th># Controls</th> </tr> <tr> <td>African American</td> <td>T2D-GENES Project 1</td> <td>Jackson Heart Study</td> <td>US</td> <td>500</td> <td>526</td> </tr> <tr> <td>African American</td> <td>T2D-GENES Project 1</td> <td>Wake Forest School of Medicine Study</td> <td>US</td> <td>518</td> <td>530</td> </tr> <tr> <td>African American</td> <td>ESP</td> <td>Exome Sequencing Project (ESP)</td> <td>US</td> <td>467</td> <td>1374</td> </tr> <tr> <td>African American</td> <td>T2D-GENES Follow up study</td> <td>BioMe Biobank Program (BioMe)</td> <td>US</td> <td>1297</td> <td>1256</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Project 1</td> <td>Korea Association Research Project</td> <td>Korea</td> <td>526</td> <td>561</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Project 1& Follow up Study</td> <td>Singapore Diabetes Cohort Study; Singapore Prospective Study Program</td> <td>Singapore (Chinese)</td> <td>1486</td> <td>1568</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Follow up study</td> <td>Korea SNUH</td> <td>South Korea</td> <td>450</td> <td>475</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Follow up study</td> <td>Research Studies in Hong Kong (Hong Kong)</td> <td>Hong Kong</td> <td>493</td> <td>485</td> </tr> <tr> <td>European</td> <td>T2D-GENES Project 1</td> <td>Ashkenazi</td> <td>US, Israel</td> <td>506</td> <td>355</td> </tr> <tr> <td>European</td> <td>T2D-GENES Project 1</td> <td>Metabolic Syndrome in Men Study (METSIM)</td> <td>Finland</td> <td>484</td> <td>498</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>Finland-United States Investigation of NIDDM Genetics (FUSION) Study</td> <td>Finland</td> <td>472</td> <td>476</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>Kooperative Gesundheitsforschung in der Region Augsburg (KORA)</td> <td>Germany</td> <td>97</td> <td>90</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>UK Type 2 Diabetes Genetics Consortium (UKT2D)</td> <td>UK</td> <td>322</td> <td>320</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>Malmo-Botnia Study</td> <td>Finland, Sweden</td> <td>478</td> <td>443</td> </tr> <tr> <td>European</td> <td>LuCamp</td> <td>Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention, and Care (LuCamp)</td> <td>Denmark</td> <td>997</td> <td>997</td> </tr> <tr> <td>European</td> <td>ESP</td> <td>Exome Sequencing Project (ESP)</td> <td>US</td> <td>390</td> <td>2843</td> </tr> <tr> <td>European</td> <td>T2D-GENES Follow up study</td> <td>Genetics of Diabetes and Audit Research Tayside Study (GoDARTS)</td> <td>Scotland, UK</td> <td>960</td> <td>966</td> </tr> <tr> <td>European</td> <td>T2D-GENES Follow up study</td> <td>Framingham Heart Study (FHS)</td> <td>US</td> <td>396</td> <td>596</td> </tr> <tr> <td>Hispanic</td> <td>T2D-GENES Project 1</td> <td>San 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> <td>US</td> <td>272</td> <td>218</td> </tr> <tr> <td>Hispanic</td> <td>T2D-GENES Project 1 & SIGMAv2</td> <td>Starr County, Texas</td> <td>US</td> <td>1762</td> <td>1738</td> </tr> <tr> <td>Hispanic</td> <td>SIGMAv1</td> <td>Mexico City Diabetes Study</td> <td>Mexico</td> <td>281</td> <td>549</td> </tr> <tr> <td>Hispanic</td> <td>SIGMAv1 & v2</td> <td>Multiethnic Cohort (MEC)</td> <td>US</td> <td>1476</td> <td>1443</td> </tr> <tr> <td>Hispanic</td> <td>SIGMAv1 & v2</td> <td>UNAM/INCMNSZ Diabetes Study (UIDS)</td> <td>Mexico</td> <td>1998</td> <td>1977</td> </tr> <tr> <td>Hispanic</td> <td>SIGMAv1 & v2</td> <td>Diabetes in Mexico Study (DMS)</td> <td>Mexico</td> <td>1522</td> <td>1546</td> </tr> <tr> <td>Multi ethnic</td> <td>ProDIGY</td> <td>Treatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY)</td> <td>US</td> <td>3097</td> <td>0</td> </tr> <tr> <td>Multi ethnic</td> <td>ProDIGY</td> <td>SEARCH for Diabetes in Youth (SEARCH)</td> <td>US</td> <td>553</td> <td>0</td> </tr> <tr> <td>South Asian</td> <td>T2D-GENES Project 1</td> <td>London Life Sciences Population Study (LOLIPOP)</td> <td>UK (Indian Asian)</td> <td>531</td> <td>538</td> </tr> <tr> <td>South Asian</td> <td>T2D-GENES Project 1 & Follow up study</td> <td>Singapore Indian Eye Study</td> <td>Singapore (Indian Asian)</td> <td>1640</td> <td>1478</td> </tr> <tr> <td>South Asian</td> <td>T2D-GENES Follow up study</td> <td>Pakistan Genomic Resource (PGR)</td> <td>Pakistan</td> <td>914</td> <td>932</td> </tr> </table> </p> <p>The Diabetes in Mexico Study (DMS) study contributed 1,522 cases and 1,546 controls to the 52k T2D exome sequencing study.</p>
| phs001388 | dbGaP
Project description: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: <ul> <li>Type 2 Diabetes Genetic Exploration by Next-generation sequencing in Multi-Ethnic Samples (T2D-GENES)</li> <li>Genetics of Type 2 Diabetes (GoT2D)</li> <li>Exome Sequencing Project (ESP)</li> <li>Slim Initiative in Genomic Medicine for the Americas (SIGMA)</li> <li>Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention, and Care (LuCAMP)</li> <li>Progress in Diabetes Genetics in Youth (ProDIGY)</li> </ul> <p>This data generated from the BioMe Biobank cohort was part of the T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-generation sequencing in multi-Ethnic Samples) consortium, which is a NIDDK-funded international research consortium that seeks to identify genetic variants for type 2 diabetes (T2D) through multiethnic sequencing studies. The T2D-GENES Project 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. </p> <p>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. </p> <p><b>Table 1.</b> 52,000 sample T2D Case/Control Whole Exome Sequencing Studies</p> <table border="1"> <tr> <th><b>Ancestry</b></th> <th>Consortia</th> <th><b>Study</b></th> <th><b>Countries of Origin</b></th> <th><b># Cases</b></th> <th><b># Controls</b></th> </tr> <tr> <td>African American</td> <td>T2D-GENES Project 1</td> <td>Jackson Heart Study</td> <td>US</td> <td>502</td> <td>527</td> </tr> <tr> <td>African American</td> <td>T2D-GENES Project 1</td> <td>Wake Forest School of Medicine Study</td> <td>US</td> <td>518</td> <td>532</td> </tr> <tr> <td>African American</td> <td>ESP</td> <td>Exome Sequencing Project (ESP)</td> <td>US</td> <td>467</td> <td>1374</td> </tr> <tr> <td>African American</td> <td>T2D-GENES Follow-Up Study</td> <td>BioMe Biobank Program (BioMe)</td> <td>US</td> <td>1294</td> <td>1254</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Project 1</td> <td>Korea Association Research Project</td> <td>Korea</td> <td>526</td> <td>561</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Project 1 and Follow-Up Study</td> <td>Singapore Diabetes Cohort Study; Singapore Prospective Study Program</td> <td>Singapore (Chinese)</td> <td>1486</td> <td>1568</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Follow-Up Study</td> <td>Korea SNUH</td> <td>South Korea</td> <td>450</td> <td>475</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Follow-Up Study</td> <td>Research Studies in Hong Kong (Hong Kong)</td> <td>Hong Kong</td> <td>493</td> <td>485</td> </tr> <tr> <td>European</td> <td>T2D-GENES Project 1</td> <td>Ashkenazi</td> <td>US, Israel</td> <td>506</td> <td>355</td> </tr> <tr> <td>European</td> <td>T2D-GENES Project 1</td> <td>Metabolic Syndrome in Men Study (METSIM)</td> <td>Finland</td> <td>484</td> <td>498</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>Finland-United States Investigation of NIDDM Genetics (FUSION) Study</td> <td>Finland</td> <td>472</td> <td>476</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>Kooperative Gesundheitsforschung in der Region Augsburg (KORA)</td> <td>Germany</td> <td>97</td> <td>90</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>UK Type 2 Diabetes Genetics Consortium (UKT2D)</td> <td>UK</td> <td>322</td> <td>320</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>Malmö-Botnia Study</td> <td>Finland, Sweden</td> <td>478</td> <td>443</td> </tr> <tr> <td>European</td> <td>LuCamp</td> <td>Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention, and Care (LuCamp)</td> <td>Denmark</td> <td>997</td> <td>997</td> </tr> <tr> <td>European</td> <td>ESP</td> <td>Exome Sequencing Project (ESP)</td> <td>US</td> <td>390</td> <td>2843</td> </tr> <tr> <td>European</td> <td>T2D-GENES Follow-Up Study</td> <td>Genetics of Diabetes and Audit Research Tayside Study (GoDARTS)</td> <td>Scotland, UK</td> <td>960</td> <td>966</td> </tr> <tr> <td>European</td> <td>T2D-GENES Follow-Up Study</td> <td>Framingham Heart Study (FHS)</td> <td>US</td> <td>396</td> <td>596</td> </tr> <tr> <td>Hispanic</td> <td>T2D-GENES Project 1</td> <td>San 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> <td>US</td> <td>272</td> <td>218</td> </tr> <tr> <td>Hispanic</td> <td>T2D-GENES Project 1 and SIGMA v2</td> <td>Starr County, Texas</td> <td>US</td> <td>1762</td> <td>1738</td> </tr> <tr> <td>Hispanic</td> <td>SIGMA v1</td> <td>Mexico City Diabetes Study</td> <td>Mexico</td> <td>281</td> <td>549</td> </tr> <tr> <td>Hispanic</td> <td>SIGMA v1 and SIGMA v2</td> <td>Multiethnic Cohort (MEC)</td> <td>US</td> <td>1476</td> <td>1443</td> </tr> <tr> <td>Hispanic</td> <td>SIGMA v1 and SIGMA v2</td> <td>UNAM/INCMNSZ Diabetes Study (UIDS)</td> <td>Mexico</td> <td>1998</td> <td>1977</td> </tr> <tr> <td>Hispanic</td> <td>SIGMA v1 and SIGMA v2</td> <td>Diabetes in Mexico Study (DMS)</td> <td>Mexico</td> <td>1522</td> <td>1546</td> </tr> <tr> <td>Multiethnic</td> <td>ProDIGY</td> <td>Treatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY)</td> <td>US</td> <td>3097</td> <td>0</td> </tr> <tr> <td>Multiethnic</td> <td>ProDIGY</td> <td>SEARCH for Diabetes in Youth (SEARCH)</td> <td>US</td> <td>553</td> <td>0</td> </tr> <tr> <td>South Asian</td> <td>T2D-GENES Project 1</td> <td>London Life Sciences Population Study (LOLIPOP)</td> <td>UK (Indian Asian)</td> <td>531</td> <td>538</td> </tr> <tr> <td>South Asian</td> <td>T2D-GENES Project 1 and Follow-Up Study</td> <td>Singapore Indian Eye Study</td> <td>Singapore (Indian Asian)</td> <td>1640</td> <td>1478</td> </tr> <tr> <td>South Asian</td> <td>T2D-GENES Follow-Up Study</td> <td>Pakistan Genomic Resource (PGR)</td> <td>Pakistan</td> <td>914</td> <td>932</td> </tr> </table> <p>The BioMe Biobank study contributed 1294 cases and 1254 controls to T2D-GENES Follow-Up Study. </p>
| phs001490 | dbGaP
Project description: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: <ul> <li>Type 2 Diabetes Genetic Exploration by Next-generation sequencing in Multi-Ethnic Samples (T2D-GENES)</li> <li>Genetics of Type 2 Diabetes (GoT2D)</li> <li>Exome Sequencing Project (ESP)</li> <li>Slim Initiative in Genomic Medicine for the Americas (SIGMA)</li> <li>Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention, and Care (LuCAMP)</li> <li>Progress in Diabetes Genetics in Youth (ProDIGY)</li> </ul> <p>This data generated from the Hong Kong cohort was part of the T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-generation sequencing in multi-Ethnic Samples) consortium, which is a NIDDK-funded international research consortium that seeks to identify genetic variants for type 2 diabetes (T2D) through multiethnic sequencing studies. The T2D-GENES Project 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. </p> <p>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. </p> <p><b>Table 1.</b> 52,000 sample T2D Case/Control Whole Exome Sequencing Studies</p> <table border="1"> <tr> <th><b>Ancestry</b></th> <th>Consortia</th> <th><b>Study</b></th> <th><b>Countries of Origin</b></th> <th><b># Cases</b></th> <th><b># Controls</b></th> </tr> <tr> <td>African American</td> <td>T2D-GENES Project 1</td> <td>Jackson Heart Study</td> <td>US</td> <td>500</td> <td>526</td> </tr> <tr> <td>African American</td> <td>T2D-GENES Project 1</td> <td>Wake Forest School of Medicine Study</td> <td>US</td> <td>518</td> <td>530</td> </tr> <tr> <td>African American</td> <td>ESP</td> <td>Exome Sequencing Project (ESP)</td> <td>US</td> <td>467</td> <td>1374</td> </tr> <tr> <td>African American</td> <td>T2D-GENES Follow-Up Study</td> <td>BioMe Biobank Program (BioMe)</td> <td>US</td> <td>1297</td> <td>1256</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Project 1</td> <td>Korea Association Research Project</td> <td>Korea</td> <td>526</td> <td>561</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Project 1 and Follow-Up Study</td> <td>Singapore Diabetes Cohort Study; Singapore Prospective Study Program</td> <td>Singapore (Chinese)</td> <td>1486</td> <td>1568</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Follow-Up Study</td> <td>Korea SNUH</td> <td>South Korea</td> <td>450</td> <td>475</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Follow-Up Study</td> <td>Research Studies in Hong Kong (Hong Kong)</td> <td>Hong Kong</td> <td>493</td> <td>485</td> </tr> <tr> <td>European</td> <td>T2D-GENES Project 1</td> <td>Ashkenazi</td> <td>US, Israel</td> <td>506</td> <td>352</td> </tr> <tr> <td>European</td> <td>T2D-GENES Project 1</td> <td>Metabolic Syndrome in Men Study (METSIM)</td> <td>Finland</td> <td>484</td> <td>498</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>Finland-United States Investigation of NIDDM Genetics (FUSION) Study</td> <td>Finland</td> <td>472</td> <td>476</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>Kooperative Gesundheitsforschung in der Region Augsburg (KORA)</td> <td>Germany</td> <td>97</td> <td>90</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>UK Type 2 Diabetes Genetics Consortium (UKT2D)</td> <td>UK</td> <td>322</td> <td>320</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>Malmö-Botnia Study</td> <td>Finland, Sweden</td> <td>478</td> <td>443</td> </tr> <tr> <td>European</td> <td>LuCamp</td> <td>Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention, and Care (LuCamp)</td> <td>Denmark</td> <td>997</td> <td>997</td> </tr> <tr> <td>European</td> <td>ESP</td> <td>Exome Sequencing Project (ESP)</td> <td>US</td> <td>390</td> <td>2843</td> </tr> <tr> <td>European</td> <td>T2D-GENES Follow-Up Study</td> <td>Genetics of Diabetes and Audit Research Tayside Study (GoDARTS)</td> <td>Scotland, UK</td> <td>960</td> <td>966</td> </tr> <tr> <td>European</td> <td>T2D-GENES Follow-Up Study</td> <td>Framingham Heart Study (FHS)</td> <td>US</td> <td>396</td> <td>596</td> </tr> <tr> <td>Hispanic</td> <td>T2D-GENES Project 1</td> <td>San 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> <td>US</td> <td>272</td> <td>218</td> </tr> <tr> <td>Hispanic</td> <td>T2D-GENES Project 1 and SIGMA v2</td> <td>Starr County, Texas</td> <td>US</td> <td>1762</td> <td>1738</td> </tr> <tr> <td>Hispanic</td> <td>SIGMA v1</td> <td>Mexico City Diabetes Study</td> <td>Mexico</td> <td>281</td> <td>549</td> </tr> <tr> <td>Hispanic</td> <td>SIGMA v1 and SIGMA v2</td> <td>Multiethnic Cohort (MEC)</td> <td>US</td> <td>1476</td> <td>1443</td> </tr> <tr> <td>Hispanic</td> <td>SIGMA v1 and SIGMA v2</td> <td>UNAM/INCMNSZ Diabetes Study (UIDS)</td> <td>Mexico</td> <td>1998</td> <td>1977</td> </tr> <tr> <td>Hispanic</td> <td>SIGMA v1 and SIGMA v2</td> <td>Diabetes in Mexico Study (DMS)</td> <td>Mexico</td> <td>1522</td> <td>1546</td> </tr> <tr> <td>Multiethnic</td> <td>ProDIGY</td> <td>Treatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY)</td> <td>US</td> <td>3097</td> <td>0</td> </tr> <tr> <td>Multiethnic</td> <td>ProDIGY</td> <td>SEARCH for Diabetes in Youth (SEARCH)</td> <td>US</td> <td>553</td> <td>0</td> </tr> <tr> <td>South Asian</td> <td>T2D-GENES Project 1</td> <td>London Life Sciences Population Study (LOLIPOP)</td> <td>UK (Indian Asian)</td> <td>531</td> <td>538</td> </tr> <tr> <td>South Asian</td> <td>T2D-GENES Project 1 and Follow-Up Study</td> <td>Singapore Indian Eye Study</td> <td>Singapore (Indian Asian)</td> <td>1640</td> <td>1478</td> </tr> <tr> <td>South Asian</td> <td>T2D-GENES Follow-Up Study</td> <td>Pakistan Risk of Myocardial Infarction Study (PROMIS)</td> <td>Pakistan</td> <td>914</td> <td>932</td> </tr> </table> <p>The research studies in Hong Kong contributed 493 cases and 485 controls to T2D-GENES Follow-Up study.</p>
| phs001504 | dbGaP
Project description: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: <ul> <li>Type 2 Diabetes Genetic Exploration by Next-generation sequencing in Multi-Ethnic Samples (T2D-GENES)</li> <li>Genetics of Type 2 Diabetes (GoT2D)</li> <li>Exome Sequencing Project (ESP)</li> <li>Slim Initiative in Genomic Medicine for the Americas (SIGMA)</li> <li>Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention, and Care (LuCAMP)</li> <li>Progress in Diabetes Genetics in Youth (ProDIGY)</li> </ul> <p>This data generated from the Pakistan Genomic Resource (PGR) cohort was part of the T2-GENES (Type 2 Diabetes Genetic Exploration by Next-generation sequencing in multi-Ethnic Samples) consortium, which is a NIDDK-funded international research consortium that seeks to identify genetic variants for type 2 diabetes (T2D) through multiethnic sequencing studies. The T2D-GENES Project 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. </p> <p>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. </p> <p><b>Table 1.</b> 52,000 sample T2D Case/Control Whole Exome Sequencing Studies</p> <table border="1"> <tr> <th><b>Ancestry</b></th> <th>Consortia</th> <th><b>Study</b></th> <th><b>Countries of Origin</b></th> <th><b># Cases</b></th> <th><b># Controls</b></th> </tr> <tr> <td>African American</td> <td>T2D-GENES Project 1</td> <td>Jackson Heart Study</td> <td>US</td> <td>502</td> <td>527</td> </tr> <tr> <td>African American</td> <td>T2D-GENES Project 1</td> <td>Wake Forest School of Medicine Study</td> <td>US</td> <td>518</td> <td>532</td> </tr> <tr> <td>African American</td> <td>ESP</td> <td>Exome Sequencing Project (ESP)</td> <td>US</td> <td>467</td> <td>1374</td> </tr> <tr> <td>African American</td> <td>T2D-GENES Follow-Up Study</td> <td>BioMe Biobank Program (BioMe)</td> <td>US</td> <td>1297</td> <td>1256</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Project 1</td> <td>Korea Association Research Project</td> <td>Korea</td> <td>526</td> <td>561</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Project 1 and Follow-Up Study</td> <td>Singapore Diabetes Cohort Study; Singapore Prospective Study Program</td> <td>Singapore (Chinese)</td> <td>1486</td> <td>1568</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Follow-Up Study</td> <td>Korea SNUH</td> <td>South Korea</td> <td>450</td> <td>475</td> </tr> <tr> <td>East Asian</td> <td>T2D-GENES Follow-Up Study</td> <td>Research Studies in Hong Kong (Hong Kong)</td> <td>Hong Kong</td> <td>493</td> <td>485</td> </tr> <tr> <td>European</td> <td>T2D-GENES Project 1</td> <td>Ashkenazi</td> <td>US, Israel</td> <td>506</td> <td>355</td> </tr> <tr> <td>European</td> <td>T2D-GENES Project 1</td> <td>Metabolic Syndrome in Men Study (METSIM)</td> <td>Finland</td> <td>484</td> <td>498</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>Finland-United States Investigation of NIDDM Genetics (FUSION) Study</td> <td>Finland</td> <td>472</td> <td>476</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>Kooperative Gesundheitsforschung in der Region Augsburg (KORA)</td> <td>Germany</td> <td>97</td> <td>90</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>UK Type 2 Diabetes Genetics Consortium (UKT2D)</td> <td>UK</td> <td>322</td> <td>320</td> </tr> <tr> <td>European</td> <td>GoT2D</td> <td>Malmö-Botnia Study</td> <td>Finland, Sweden</td> <td>478</td> <td>443</td> </tr> <tr> <td>European</td> <td>LuCamp</td> <td>Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention, and Care (LuCamp)</td> <td>Denmark</td> <td>997</td> <td>997</td> </tr> <tr> <td>European</td> <td>ESP</td> <td>Exome Sequencing Project (ESP)</td> <td>US</td> <td>390</td> <td>2843</td> </tr> <tr> <td>European</td> <td>T2D-GENES Follow-Up Study</td> <td>Genetics of Diabetes and Audit Research Tayside Study (GoDARTS)</td> <td>Scotland, UK</td> <td>960</td> <td>966</td> </tr> <tr> <td>European</td> <td>T2D-GENES Follow-Up Study</td> <td>Framingham Heart Study (FHS)</td> <td>US</td> <td>396</td> <td>596</td> </tr> <tr> <td>Hispanic</td> <td>T2D-GENES Project 1</td> <td>San 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> <td>US</td> <td>272</td> <td>218</td> </tr> <tr> <td>Hispanic</td> <td>T2D-GENES Project 1 and SIGMA v2</td> <td>Starr County, Texas</td> <td>US</td> <td>1762</td> <td>1738</td> </tr> <tr> <td>Hispanic</td> <td>SIGMA v1</td> <td>Mexico City Diabetes Study</td> <td>Mexico</td> <td>281</td> <td>549</td> </tr> <tr> <td>Hispanic</td> <td>SIGMA v1 and SIGMA v2</td> <td>Multiethnic Cohort (MEC)</td> <td>US</td> <td>1476</td> <td>1443</td> </tr> <tr> <td>Hispanic</td> <td>SIGMA v1 and SIGMA v2</td> <td>UNAM/INCMNSZ Diabetes Study (UIDS)</td> <td>Mexico</td> <td>1998</td> <td>1977</td> </tr> <tr> <td>Hispanic</td> <td>SIGMA v1 and SIGMA v2</td> <td>Diabetes in Mexico Study (DMS)</td> <td>Mexico</td> <td>1522</td> <td>1546</td> </tr> <tr> <td>Multiethnic</td> <td>ProDIGY</td> <td>Treatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY)</td> <td>US</td> <td>3097</td> <td>0</td> </tr> <tr> <td>Multiethnic</td> <td>ProDIGY</td> <td>SEARCH for Diabetes in Youth (SEARCH)</td> <td>US</td> <td>553</td> <td>0</td> </tr> <tr> <td>South Asian</td> <td>T2D-GENES Project 1</td> <td>London Life Sciences Population Study (LOLIPOP)</td> <td>UK (Indian Asian)</td> <td>531</td> <td>538</td> </tr> <tr> <td>South Asian</td> <td>T2D-GENES Project 1 and Follow-Up Study</td> <td>Singapore Indian Eye Study</td> <td>Singapore (Indian Asian)</td> <td>1640</td> <td>1478</td> </tr> <tr> <td>South Asian</td> <td>T2D-GENES Follow-Up Study</td> <td>Pakistan Genomic Resource (PGR)</td> <td>Pakistan</td> <td>903</td> <td>930</td> </tr> </table> <p>The PGR study contributed 903 cases and 930 controls to T2D-GENES Follow-Up Study. </p>
| phs001552 | dbGaP
Project description:The aim of this study was to identify proteomic alterations associated with functional dysregulation of the retina with diabetes that could eventually be used as surrogate endpoints in preclinical drug testing studies. A multi-modal approach of antibody (Luminex)-, electrophoresis (2-DIGE)-, and LC-MS (iTRAQ)-based quantitation methods was used to provide broad coverage of the retinal proteome. Transcriptional profiling through microarray analysis was also included to increase coverage and provide insight into potential regulation of protein expression changes at the mRNA level. The different technologies proved complementary, with limited coverage overlap between methods. Diabetes was induced in Sprague-Dawley male rats (Charles River Laboratories, Wilmington, MA) by intraperitoneal injection of 65 mg/kg streptozotocin (STZ) (Sigma-Aldrich, St. Louis, MO) in 10mM sodium citrate pH 4.5 vehicle. Control rats were injected with an equal dose of vehicle only. Rats had free access to food and water, and were maintained on a 12 hour light/dark cycle. Blood glucose level and body weight were measured 6 days post-STZ or vehicle injection, and biweekly throughout the experiment. Only rats with blood glucose levels >250 mg/dL at the time of the original test and throughout the experiment were included in the diabetic groups. At the time of retina harvest, rats were given a lethal dose of pentobarbital, 100 mg/kg, (Ovation Pharmaceuticals Inc., Deerfield, IL) by intraperitoneal injection and sacrificed by decapitation. Retinas were rapidly excised snap- frozen in liquid nitrogen for subsequent experimentation.
2010-06-01 | E-GEOD-20886 | biostudies-arrayexpress
Project description:The link between the gut microbiota and type 2 diabetes (T2D) warrants further investigation because of known confounding effects from antidiabetic treatment. Here we profiled the gut microbiome in a discovery (n=1011) and validation (n=484) cohort comprising Swedish subjects naive for diabetes treatment and grouped by glycemic status.
| EGAS00001004480 | EGA
Project description:WTCCC genome-wide case-control association study for Type 2 Diabetes (T2D) using the 1958 British Birth Cohort and the UK National Blood Service collections as controls.
| EGAS00000000016 | EGA
Project description:WTCCC genome-wide case-control association study for Type 1 Diabetes (T1D) using the 1958 British Birth Cohort and the UK National Blood Service collections as controls.
| EGAS00000000014 | EGA