ID

45782

Description

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.

Link

dbGaP-study=phs001095

Keywords

Versions (1)
  1. 6/21/23 6/21/23 - Chiara Middel
Copyright Holder

David Altshuler, Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA

Uploaded on

June 21, 2023

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License

Creative Commons BY 4.0
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dbGaP phs001095 T2D-GENES Multi-Ethnic Exome Sequencing Study: Ashkenazi

English

Eligibility Criteria

5 forms  
Inclusion and exclusion criteria
Description

Inclusion and exclusion criteria

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C0680251
Cases were ascertained according to the following criteria:
Description

Elig.phs001095.v1.p1.1

Data type

boolean

Alias
UMLS CUI [1,1]
C1706256
UMLS CUI [1,2]
C1512693
UMLS CUI [1,3]
C0243161
Ashkenazi Jewish origin, defined as having all four grandparents born in Northern or Eastern Europe; subjects with known or suspected Sephardic Jewish or non-Jewish ancestry were excluded.
Description

Elig.phs001095.v1.p1.2

Data type

boolean

Alias
UMLS CUI [1,1]
C2135555
UMLS CUI [1,2]
C1704788
UMLS CUI [1,3]
C0444868
UMLS CUI [1,4]
C0337471
UMLS CUI [1,5]
C1300001
UMLS CUI [1,6]
C0028413
UMLS CUI [1,7]
C0015177
UMLS CUI [2,1]
C0680251
UMLS CUI [2,2]
C0750491
UMLS CUI [2,3]
C0205309
UMLS CUI [2,4]
C0574825
UMLS CUI [2,5]
C1298908
UMLS CUI [2,6]
C0178443
UMLS CUI [2,7]
C3841890
T2D defined according to the World Health Organization criteria (fasting glucose >140 mg/dl on two or more occasions or random glucose >200mg/dl).
Description

Elig.phs001095.v1.p1.3

Data type

boolean

Alias
UMLS CUI [1,1]
C0011860
UMLS CUI [1,2]
C1704788
UMLS CUI [1,3]
C0043237
UMLS CUI [1,4]
C0243161
To avoid late-onset T1D, patients who became insulin-dependent within 2 years of diagnosis were excluded; anti-GAD or anti-islet cell antibody titers were not routinely measured.
Description

Elig.phs001095.v1.p1.4

Data type

boolean

Alias
UMLS CUI [1,1]
C0870186
UMLS CUI [1,2]
C0376415
UMLS CUI [1,3]
C0011854
UMLS CUI [2,1]
C0680251
UMLS CUI [2,2]
C0030705
UMLS CUI [2,3]
C0011860
UMLS CUI [2,4]
C1524063
UMLS CUI [2,5]
C0021641
UMLS CUI [2,6]
C0332285
UMLS CUI [2,7]
C0205448
UMLS CUI [2,8]
C0439234
UMLS CUI [2,9]
C0011900
UMLS CUI [3,1]
C1298908
UMLS CUI [3,2]
C0205547
UMLS CUI [3,3]
C0242485
UMLS CUI [3,4]
C1167897
UMLS CUI [3,5]
C0063900
T2D cases were selected from two separate DNA collections:
Description

Elig.phs001095.v1.p1.5

Data type

boolean

Alias
UMLS CUI [1,1]
C1706256
UMLS CUI [1,2]
C0011860
UMLS CUI [1,3]
C0242802
UMLS CUI [1,4]
C0205448
UMLS CUI [1,5]
C0443299
UMLS CUI [1,6]
C0012854
UMLS CUI [1,7]
C0010995
Genome-wide, affected-sibling-pair linkage study (Permutt et al. Diabetes 2001). Families in which both parents were known to have diabetes were excluded. One affected individual selected from each family and, wherever possible, sibling with youngest age of diagnosis selected.
Description

Elig.phs001095.v1.p1.6

Data type

boolean

Alias
UMLS CUI [1,1]
C3640076
UMLS CUI [1,2]
C0522476
UMLS CUI [1,3]
C0037047
UMLS CUI [1,4]
C1709450
UMLS CUI [1,5]
C0796345
UMLS CUI [2,1]
C0680251
UMLS CUI [2,2]
C1706086
UMLS CUI [2,3]
C0030551
UMLS CUI [2,4]
C0522476
UMLS CUI [2,5]
C0011849
Study to determine genetic risk for diabetic complications (Blech et al. PLoS One 2011). Patients ascertained by the Israel Diabetes Research Group between 2002 and 2004 from 15 diabetes clinics throughout Israel. Primary selection criteria: (1) known T1D or T2D for more than 10 years, (2) 4 grandparents being either Ashkenazi or Sephardic-North African Jewish. For this study, only T2D patients with all 4 grandparents of Ashkenazi Jewish origin and age of diagnosis between 35 and 60 were selected. Controls were determined according to the following criteria:
Description

Elig.phs001095.v1.p1.7

Data type

boolean

Alias
UMLS CUI [1,1]
C0008976
UMLS CUI [1,2]
C1148554
UMLS CUI [1,3]
C0314603
UMLS CUI [1,4]
C0035647
UMLS CUI [1,5]
C0342257
UMLS CUI [2,1]
C0242802
UMLS CUI [2,2]
C0022271
UMLS CUI [2,3]
C0011849
UMLS CUI [2,4]
C0242481
UMLS CUI [2,5]
C0441833
UMLS CUI [2,6]
C0442592
UMLS CUI [3,1]
C0205225
UMLS CUI [3,2]
C0242801
UMLS CUI [3,3]
C0205309
UMLS CUI [3,4]
C0011860
UMLS CUI [3,5]
C0011854
UMLS CUI [3,6]
C0449238
UMLS CUI [3,7]
C0444868
UMLS CUI [3,8]
C0337471
UMLS CUI [3,9]
C0337704
UMLS CUI [3,10]
C0574825
UMLS CUI [4,1]
C0242802
UMLS CUI [4,2]
C0205171
UMLS CUI [4,3]
C0030705
UMLS CUI [4,4]
C0011860
UMLS CUI [4,5]
C0444868
UMLS CUI [4,6]
C0337471
UMLS CUI [4,7]
C0337704
UMLS CUI [4,8]
C1828181
UMLS CUI [5,1]
C0009932
UMLS CUI [5,2]
C1512693
UMLS CUI [5,3]
C0243161
Fasting blood glucose <7 mmol/l.
Description

Elig.phs001095.v1.p1.8

Data type

boolean

Alias
UMLS CUI [1,1]
C0583513
No personal history of diabetes.
Description

Elig.phs001095.v1.p1.9

Data type

boolean

Alias
UMLS CUI [1,1]
C1298908
UMLS CUI [1,2]
C0262926
UMLS CUI [1,3]
C0011849
No anti-diabetic medications.
Description

Elig.phs001095.v1.p1.10

Data type

boolean

Alias
UMLS CUI [1,1]
C1298908
UMLS CUI [1,2]
C0935929
UMLS CUI [1,3]
C0013227
Patients who became insulin-dependent within 2 years of diagnosis were excluded.
Description

Elig.phs001095.v1.p1.11

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C0011860
UMLS CUI [1,3]
C1524063
UMLS CUI [1,4]
C0021641
UMLS CUI [1,5]
C0332285
UMLS CUI [1,6]
C0205448
UMLS CUI [1,7]
C0439234
UMLS CUI [1,8]
C0011900
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Similar models

Eligibility Criteria

5 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Inclusion and exclusion criteria
C1512693 (UMLS CUI [1,1])
C0680251 (UMLS CUI [1,2])
Elig.phs001095.v1.p1.1
Item
Cases were ascertained according to the following criteria:
boolean
C1706256 (UMLS CUI [1,1])
C1512693 (UMLS CUI [1,2])
C0243161 (UMLS CUI [1,3])
Elig.phs001095.v1.p1.2
Item
Ashkenazi Jewish origin, defined as having all four grandparents born in Northern or Eastern Europe; subjects with known or suspected Sephardic Jewish or non-Jewish ancestry were excluded.
boolean
C2135555 (UMLS CUI [1,1])
C1704788 (UMLS CUI [1,2])
C0444868 (UMLS CUI [1,3])
C0337471 (UMLS CUI [1,4])
C1300001 (UMLS CUI [1,5])
C0028413 (UMLS CUI [1,6])
C0015177 (UMLS CUI [1,7])
C0680251 (UMLS CUI [2,1])
C0750491 (UMLS CUI [2,2])
C0205309 (UMLS CUI [2,3])
C0574825 (UMLS CUI [2,4])
C1298908 (UMLS CUI [2,5])
C0178443 (UMLS CUI [2,6])
C3841890 (UMLS CUI [2,7])
Elig.phs001095.v1.p1.3
Item
T2D defined according to the World Health Organization criteria (fasting glucose >140 mg/dl on two or more occasions or random glucose >200mg/dl).
boolean
C0011860 (UMLS CUI [1,1])
C1704788 (UMLS CUI [1,2])
C0043237 (UMLS CUI [1,3])
C0243161 (UMLS CUI [1,4])
Elig.phs001095.v1.p1.4
Item
To avoid late-onset T1D, patients who became insulin-dependent within 2 years of diagnosis were excluded; anti-GAD or anti-islet cell antibody titers were not routinely measured.
boolean
C0870186 (UMLS CUI [1,1])
C0376415 (UMLS CUI [1,2])
C0011854 (UMLS CUI [1,3])
C0680251 (UMLS CUI [2,1])
C0030705 (UMLS CUI [2,2])
C0011860 (UMLS CUI [2,3])
C1524063 (UMLS CUI [2,4])
C0021641 (UMLS CUI [2,5])
C0332285 (UMLS CUI [2,6])
C0205448 (UMLS CUI [2,7])
C0439234 (UMLS CUI [2,8])
C0011900 (UMLS CUI [2,9])
C1298908 (UMLS CUI [3,1])
C0205547 (UMLS CUI [3,2])
C0242485 (UMLS CUI [3,3])
C1167897 (UMLS CUI [3,4])
C0063900 (UMLS CUI [3,5])
Elig.phs001095.v1.p1.5
Item
T2D cases were selected from two separate DNA collections:
boolean
C1706256 (UMLS CUI [1,1])
C0011860 (UMLS CUI [1,2])
C0242802 (UMLS CUI [1,3])
C0205448 (UMLS CUI [1,4])
C0443299 (UMLS CUI [1,5])
C0012854 (UMLS CUI [1,6])
C0010995 (UMLS CUI [1,7])
Elig.phs001095.v1.p1.6
Item
Genome-wide, affected-sibling-pair linkage study (Permutt et al. Diabetes 2001). Families in which both parents were known to have diabetes were excluded. One affected individual selected from each family and, wherever possible, sibling with youngest age of diagnosis selected.
boolean
C3640076 (UMLS CUI [1,1])
C0522476 (UMLS CUI [1,2])
C0037047 (UMLS CUI [1,3])
C1709450 (UMLS CUI [1,4])
C0796345 (UMLS CUI [1,5])
C0680251 (UMLS CUI [2,1])
C1706086 (UMLS CUI [2,2])
C0030551 (UMLS CUI [2,3])
C0522476 (UMLS CUI [2,4])
C0011849 (UMLS CUI [2,5])
Elig.phs001095.v1.p1.7
Item
Study to determine genetic risk for diabetic complications (Blech et al. PLoS One 2011). Patients ascertained by the Israel Diabetes Research Group between 2002 and 2004 from 15 diabetes clinics throughout Israel. Primary selection criteria: (1) known T1D or T2D for more than 10 years, (2) 4 grandparents being either Ashkenazi or Sephardic-North African Jewish. For this study, only T2D patients with all 4 grandparents of Ashkenazi Jewish origin and age of diagnosis between 35 and 60 were selected. Controls were determined according to the following criteria:
boolean
C0008976 (UMLS CUI [1,1])
C1148554 (UMLS CUI [1,2])
C0314603 (UMLS CUI [1,3])
C0035647 (UMLS CUI [1,4])
C0342257 (UMLS CUI [1,5])
C0242802 (UMLS CUI [2,1])
C0022271 (UMLS CUI [2,2])
C0011849 (UMLS CUI [2,3])
C0242481 (UMLS CUI [2,4])
C0441833 (UMLS CUI [2,5])
C0442592 (UMLS CUI [2,6])
C0205225 (UMLS CUI [3,1])
C0242801 (UMLS CUI [3,2])
C0205309 (UMLS CUI [3,3])
C0011860 (UMLS CUI [3,4])
C0011854 (UMLS CUI [3,5])
C0449238 (UMLS CUI [3,6])
C0444868 (UMLS CUI [3,7])
C0337471 (UMLS CUI [3,8])
C0337704 (UMLS CUI [3,9])
C0574825 (UMLS CUI [3,10])
C0242802 (UMLS CUI [4,1])
C0205171 (UMLS CUI [4,2])
C0030705 (UMLS CUI [4,3])
C0011860 (UMLS CUI [4,4])
C0444868 (UMLS CUI [4,5])
C0337471 (UMLS CUI [4,6])
C0337704 (UMLS CUI [4,7])
C1828181 (UMLS CUI [4,8])
C0009932 (UMLS CUI [5,1])
C1512693 (UMLS CUI [5,2])
C0243161 (UMLS CUI [5,3])
Elig.phs001095.v1.p1.8
Item
Fasting blood glucose <7 mmol/l.
boolean
C0583513 (UMLS CUI [1,1])
Elig.phs001095.v1.p1.9
Item
No personal history of diabetes.
boolean
C1298908 (UMLS CUI [1,1])
C0262926 (UMLS CUI [1,2])
C0011849 (UMLS CUI [1,3])
Elig.phs001095.v1.p1.10
Item
No anti-diabetic medications.
boolean
C1298908 (UMLS CUI [1,1])
C0935929 (UMLS CUI [1,2])
C0013227 (UMLS CUI [1,3])
Elig.phs001095.v1.p1.11
Item
Patients who became insulin-dependent within 2 years of diagnosis were excluded.
boolean
C0680251 (UMLS CUI [1,1])
C0011860 (UMLS CUI [1,2])
C1524063 (UMLS CUI [1,3])
C0021641 (UMLS CUI [1,4])
C0332285 (UMLS CUI [1,5])
C0205448 (UMLS CUI [1,6])
C0439234 (UMLS CUI [1,7])
C0011900 (UMLS CUI [1,8])
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