Diabetes in Mexico Study SIGMA Exome Sequencing Project
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PROVIDER: PRJNA391221 | ENA |
REPOSITORIES: ENA
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Project description:Mexico City Diabetes Study SIGMA Exome Sequencing Project
| PRJNA389148 | ENA
Project description:UNAM/INCMNSZ Diabetes Study (UIDS) SIGMA Exome Sequencing Project
| PRJNA392111 | ENA
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:Multiethnic Cohort (MEC) SIGMA Exome Sequencing Project
| PRJNA398435 | ENA
Project description:Mexico City Diabetes Study SIGMA Exome Sequencing Project
| PRJNA389149 | ENA
Project description:Diabetes in Mexico Study SIGMA Exome Sequencing Project
| PRJNA391222 | ENA
Project description:With an escalating global burden, T2DM is associated to long-term complications that have contributed to the burden of morbidity and mortality worldwide. The objective of this manuscript is to conduct an Exome-Wide Association Study (EWAS) on T2DM Emirati individuals to improve our understanding on diabetes-related complications for a more enhanced disease management and improve therapeutic targets.
2023-04-12 | GSE226084 | GEO
Project description:Sigma factors are master regulators of bacterial transcription which direct gene expression of specific subsets of genes. In particular, alternative sigma factors are well-known to be key players of bacterial adaptation to changing environments. To elucidate the regulatory network of sigma factors in P. aeruginosa, an integrative approach including ChIP-seq of 11 polyhistidine-tag sigma factors was performed to define the primary regulon of each sigma factor.
2015-02-12 | GSE54997 | GEO
Project description:The GoDARTS T2D-GENES Exome sequencing study is a subset of a larger Type 2 Diabetes Exome Sequencing project. This effort 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 and includes samples from: T2D-GENES, GoT2D, ESP, SIGMA T2D, LuCAMP, and ProDIGY.
This data generated from the Genetics of Diabetes and Audit Research Tayside Study (GoDARTS) 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 T2D through multiethnic sequencing studies. Sequencing for the GoDARTS study was performed at the Broad Institute using Illumina Rapid Capture on Illumina HiSeq machines.
| EGAS00001002937 | EGA