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Table S3: Description of samples included in the GWA meta-analysis (Stage 1) and follow-up studies (stage 2). | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9
Study Name | Study design | Sample Size for Phenotype |  |  |  |  | Reference | Study participants | Specific comments
 |  | WC | WHR |  | BIA | DXA
Stage 1: Genome-wide association studies
British 1958 [NAME] discovery samples | population-based | 1422 | 1422 |  | 0 | 0 | 41, 42 | 1) UK population random sample, 2) followed at age 44-45, n=1,502 as WTCCC controls
Cohorte Lausannoise (CoLaus) Study | population-based | 5434 | 5434 |  | 5389 | 0 | 43 | 1) randomly selected from 56,694 individuals, 2) 35 -75 years of age, 3) permanent residents of the City of Lausanne, Switzerland, 4) four grandparents of European origin | adjusted for principal components of GWA genotypes using EIGENSOFT (ref 10 from bmi paper); all individuals informed about sponsorship by [NAME]
deCODE genetics discovery samples | population-based | 5784 | 5784 |  | 2715 | 560 | 25 | Individuals participating in deCODE studies on obesity and cardiovascular phenotypes. | DXA information was obtained through population- and family studies on Osteoporosis.
Diabetes [NAME] (DGI) Cases | type 2 diabetes cases | 1258 | 957 |  | 0 | 0 | 44, 45 | 1) 1,588 type 2 diabetes cases, 2) European ancestry from Sweden and Finland
Diabetes [NAME] (DGI) Controls | type 2 diabetes controls | 1067 | 469 |  | 0 | 0 | 44, 45 | 1) 1,523 matched type 2 diabetes controls, 2) European ancestry from Sweden and Finland
European Prospective Investigation of Cancer (EPIC-Norfolk) Obesity Study | population-based | 2417 | 2417 |  | 0 | 0 | 23, 46 | 1) 2,566 randomly selected from the EPIC-Norfork Study (25,663 subjects), 2) European descent, 3) 39-75 years of age, 4) recruited between 1993- 1997
Finland-United States Investigation of NIDDM Genetics (FUSION) Cases | type 2 diabetes cases | 1088 | 1087 |  | 0 | 0 | 11, 47, 48 | 1) 1,161 Finnish type 2 diabetes cases, 2) additional 1 offspring of case/control pair 3) frequency matched cases and controls regarding 5-year age category, sex, and birth province in Finland | SNPs excluded when total number of duplicate pair discrepancies in 79 duplicate sample pairs and Mendelian inheritance inconsistencies in 122 parent-offspring sets was >3
Finland-United States Investigation of NIDDM Genetics (FUSION) Controls | type 2 diabetes controls | 1289 | 1288 |  | 0 | 0 | 11, 48 | 1) 1,174 normal glucose tolerant controls, 2) 119 offspring of case/control pair 3) frequency matched cases and controls regarding 5-year age category, sex, and birth province in Finland | SNPs excluded when total number of duplicate pair discrepancies in 79 duplicate sample pairs and Mendelian inheritance inconsistencies in 122 parent-offspring sets was >3
Invecchiare in Chianti/aging in the Chianti area (InCHIANTI) | population-based | 1146 | 1146 |  | 0 | 0 | 5, 49 | 1) random selected from population registries of two small towns in Tuscany, Italy, 2) clinic visit for evaluation of health status
KOoperative gesundheitsforschung in der Region Augsburg (KORA), Survey 3 | population-based | 1639 | 1638 |  | 0 | 0 | 50, 51 | 1) n=3,996 subjects andom sample from general population of the South-German city of Augsburg and surrounding counties, 2) subjects had German passport and were of European origin, 3) recruited 1994/95, 4) subsample n=1,642 with 10-year-follow-up genotyped
Northern Finnish Birth Cohort (NFBC) 1966 | population-based | 4505 | 4505 |  | 0 | 0 | 52 | 1) Mothers living in Northern-most provinces of Finland, 2) expected delivery dates during 1966, 3) 12,059 live-births were in the study, 4) at age 31, individuals still living in Helsinki area or Northern Finland were asked to participate, 5) detailed biological and medical examinations and questionnaire | to study factors affecting pre-term birth, low birth weight and subsequent morbidity and mortality
Nurses Health Study | breast cancer controls | 1639 | 1632 |  | 0 | 0 | 53 | 1) recruited 1976 (n=121,700, 30-55 years of age), 2) CGEMS (Cancer Cenetic Markers of Susceptivbility nested case-control study (n=32,826 with blood available, recruited 1989/90, free of breast cancer, 3) 1.133 breast cancer controls GWA genotyped with height and weight available
SardiNIA Study of Aging | population-based | 4302 | 4301 |  | 0 | 0 | 11, 54 | 1) 4,301 related inviduals, 2) in the Ogliastra region of Sardinia, Italy, 2) four grandparents from Sardinia | adjusted for four principal components of GWA genotypes using EIGENSTRAT(ref 10 from bmi paper); aimed at age-related quantitative traits; 1,412 subjects genotyped by Affymetrix 500k, additional 2,893 subjects genotyped with Affymetrix 10k using relatedness with subjects among the 1,412 subjects to impute HapMap genotypes
Twins UK discovery samples | population-based | 1714 | 1714 |  | 1748 | 1748 | 55 | 1) 2218 women included in analysis, 2) 1018 singletons (754 twin memebers from monozygotic pairs, 253 from dizygotic pairs, 11 of pairs with unknown zygosity) and 1200 siblings from 600 dizygotic paris.
WTCCC Hypertension Cases | hypertension cases | 1952 | 1952 |  | 0 | 0 | 41, 56 | 1) several hypertensive subjects, 2) from families with multiplex affected sibships or parent-offspring trios, 2) British ancestry, 3) recruited from Medical Research Council General Practice Framework and other primary care practices (UK77 study)
WTCCC Type 2 Diabetes Cases | type 2 diabetes cases | 1924 | 1924 |  | 0 | 0 | 41 | 1) British/Irish descent, 2) n=1,999 from the Diabetes UK Warren 2 repository, 3) 25-75 years of age at diagnosis, 4) diabetes medication or laboratory evidence of hyperglycemia, 5) 30% part of mulitplex sibship, 25% representing the offspring within trios or duos, isolated cases ascertained for early age at diagnosis and a high proportion of diabetic relatives
Stage 2a: Replication studies in-silico
[NAME] study (ERF) | population-based | 1231 | 1231 |  | 0 | 1236 | 57 | 1) Related individuals from an isolated Dutch population located in the south-west of the Netherlands
[NAME] (ERGO) | population-based | 5471 | 5468 |  | 0 | 2438 | 58, 59 | 1) ethically homogeneous population of Dutch Caucasian origin, 2) 7983 mean and women aged 55 years, 3) living in Ommoord, a suburb of Rotterdam, Netherlands | focussing on chronic disabling conditions in the elderly
Fenland study | population-based | 1402 | 1402 |  | 0 | 1312 |  | 1) 1,500 individuals from the population-based Fenland study, 2) European descent, 3) 29.4 - 57.7 years of age, 4) recruited between  Jan 2005- Nov 2007
Genetic Epidemiology of Metabolic Syndrome (GEMS) Cases | type 2 diabetes cases | 903 | 903 |  | 0 | 0 | 60 | 1)a multinational, family-based study to explore the genetic basis of the metabolic syndrome 2) One thousand four hundred thirty-six (854 men/582 women) affected patients (metabolic syndrome) 3) 1,672 (737 men/935 women) unaffected persons
Genetic Epidemiology of Metabolic Syndrome (GEMS) Controls | type 2 diabetes controls | 919 | 919 |  | 0 | 0 | 60 | 1)a multinational, family-based study to explore the genetic basis of the metabolic syndrome 2) One thousand four hundred thirty-six (854 men/582 women) affected patients (metabolic syndrome) 3) 1,672 (737 men/935 women) unaffected persons
London Life Sciences Population Study - Northern Europeans (LOLIPOP-NE) | population-based | 1584 | 1584 |  | 1438 | 0 | 24 | 1) LOLIPOP is an ongoing population based cohort study of ~30,000  Indian Asian and European white men and women, aged 35-75 years, recruited from the  lists of 58 General Practitioners in West London, United Kingdom
Precocious Coronary Artery Disease (ProCARDIS) | coronary artery disease cases and controls | 960 | 960 |  | 0 | 0 | 61
Twins UK replication samples | population-based | 1360 | 1360 |  | 0 | 1240 | 55 | The replication sample includes 1072 DZ twins from 727 families (869 females and 203 males) and 288 MZ twins from 255 families (231 females and 57 males). [NAME] are unrelated with GWAS sample.
Stage 2b: Replication studies bespoke genotyping
Prevalence, Prediction and Prevention of Diabetes in the Botnia study (BPPP) | population-based | 3425 | 3424 |  | 1846 | 0 | 62 | sample of the Botnia population | aims to study diabetes prevalence in the Botnia population, to test whether genetic and metbolic risk factors previously identified in the Botnia study can be used to identify high risk individuals, and to study whether incidence o fT2DM can be prevented in these high risk groups using intervention programs
British 1958 [NAME] replication samples | population-based | 4882 | 4882 |  | 0 | 0 | 41, 42 | 1) UK population random sample, 2) followed at age 44-45, n=1,502 as WTCCC controls
British Women Health Study (BWHS) | population-based | 3654 | 3660 |  | 0 | 0 | 63 | 1)a randomly selected sample of women aged 60–79 drawn from 23 towns in England, Scotland, and Wales. 2) Of 7173 women invited and eligible to participate, any phenotype information was obtained on 4286 (60%)
deCODE genetics replication samples | population-based | 7807 | 7807 |  | 3657 | 4614 | 25 | Individuals participating in deCODE studies on obesity and cardiovascular phenotypes. | DXA information was obtained through population- and family studies on Osteoporosis.
National FINRISK study, 1997 | population-based | 7884 | 7882 |  | 0 | 0 | 64 | 1) sample from National Population registry 1997, 2) from five geographical areas (North Karelia, Juopio, Oulu province, Helsinki, Vantaa, Turku/Loimaa), 3) 250 per sec, 10-year-age group and study area, 4) age range 25-64 years, 5) additional senior sample including 250 men and 500 women age 65-74 years from North Karelia and Helsinki/vantaa, 6) 11,500 invited and 8.447 (73.5%) participated
Finland-United States Investigation of NIDDM Genetics Stage 2 (FUSION S2) Cases | type 2 diabetes cases | 1113 | 1113 |  | 0 | 0 | 47 | 1) these FUSION samples do not overlap with FUSION sample in the GWA stage, 2) frequency matched cases and controls regarding 5-year age category, sex, and birth province in Finland
Finland-United States Investigation of NIDDM Genetics Stage 2 (FUSION S2) Controls | type 2 diabetes controls | 1233 | 1233 |  | 0 | 0 | 47 | 1) these FUSION samples do not overlap with FUSION sample in the GWA stage, 2) frequency matched cases and controls regarding 5-year age category, sex, and birth province in Finland
Hertfortshire Cohort Study | population-based | 2137 | 2136 |  | 2135 | 0 | 65 | 1) subjects born in the English county of Hertfordshire during 1931- 1939, 2) still resident today, 3) aged 60-75 years at follow-up, 4) participants attended a clinic for detailed physiological investigations
KOoperative gesundheitsforschung in der Region Augsburg (KORA), [NAME] | population-based | 4039 | 4039 |  | 3990 | 0 | 66 | 1)a population-based survey in southern Germany (the Kooperative Gesundheitsforschung in der Region Augsburg [KORA] [Cooperative Health Research in the Region of Augsburg] Survey S4, 1999-2001)
Metabolic Syndrome in Men (METSIM) | population-based | 6225 | 6224 |  | 6213 | 0 | 11 | 1) men, 2) randomly selected from the population of the town of Kuopio in Eastern Finland, 3) aged 49-72 years of age | aims to investigate the metabolic syndrome, type 2 diabetes, cardiovascular disease, and cardiovascular risk factors, on-going study with the goal of collecting 10,000 men
MRC [NAME] | population-based | 1674 | 1671 |  | 1655 | 0 | 67-69 | 1) randomly selected from the population living in [NAME] and surrounding villages (East Anglia, UK), 2) ethically homogeneous Euroid population, 3) 35-79 years of age
Nurses Health Study (NHS) - Cases | type 2 diabetes cases | 1868 | 1868 |  | 0 | 0 | 53, 70 | 1) The Nurses’ Health Studies are among the largest and longest running investigations of factors that influence women’s health. Started in 1976 and expanded in 1989, 2) it is based on the information provided by the 238,000 dedicated nurse-participants
Nurses Health Study (NHS) - Controls | type 2 diabetes controls | 1846 | 1846 |  | 0 | 0 | 53, 70 | 1) The Nurses’ Health Studies are among the largest and longest running investigations of factors that influence women’s health. Started in 1976 and expanded in 1989, 2) it is based on the information provided by the 238,000 dedicated nurse-participants
UK Type 2 Diabetes Genetics Consortium collection replication set 1 Cases | type 2 diabetes cases | 1984 | 0 |  | 0 | 0 | 71 | 1) All cases and controls were of European White descent, living in the Tayside region of Dundee when recruited. 2) Cases had T2D diagnosed between the  ages of 35-70 years (inclusive)
UK Type 2 Diabetes Genetics Consortium collection replication set 1 Controls | type 2 diabetes controls | 2006 | 0 |  | 0 | 0 | 71 | 1) All cases and controls were of European White descent, living in the Tayside region of Dundee when recruited. 2)Controls were aged below 80 years  and had not been diagnosed with diabetes at the time of recruitment (or  subsequently). Control subjects were excluded from analysis if laboratory  investigations at the time of recruitment provided evidence of hyperglycaemia  (fasting glucose >7.0 mmol/l, HbA1c >6.4%)
UK Type 2 Diabetes Genetics Consortium collection replication set 3 Cases | type 2 diabetes cases | 1080 | 0 |  | 0 | 0 | 71 | 1) All cases and controls were of European White descent, living in the Tayside region of Dundee when recruited.  2) Cases had T2D diagnosed between the  ages of 35-70 years (inclusive)
UK Type 2 Diabetes Genetics Consortium collection replication set 3 Controls | type 2 diabetes controls | 1539 | 0 |  | 0 | 0 | 71 | 1) All cases and controls were of European White descent, living in the Tayside region of Dundee when recruited. 2) Controls were aged below 80 years  and had not been diagnosed with diabetes at the time of recruitment (or  subsequently). Control subjects were excluded from analysis if laboratory  investigations at the time of recruitment provided evidence of hyperglycaemia  (fasting glucose >7.0 mmol/l, HbA1c >6.4%)
UK Type 2 Diabetes Genetics Consortium collection replication set 4 Cases | type 2 diabetes cases | 977 | 0 |  | 0 | 0 | 71 | 1) All cases and controls were of European White descent, living in the Tayside region of Dundee when recruited.  2) Cases had T2D diagnosed between the  ages of 35-70 years (inclusive)
UK Type 2 Diabetes Genetics Consortium collection replication set 4 Controls | type 2 diabetes controls | 1486 | 0 |  | 0 | 0 | 71 | 1) All cases and controls were of European White descent, living in the Tayside region of Dundee when recruited. 2) Controls were aged below 80 years  and had not been diagnosed with diabetes at the time of recruitment (or  subsequently). Control subjects were excluded from analysis if laboratory  investigations at the time of recruitment provided evidence of hyperglycaemia  (fasting glucose >7.0 mmol/l, HbA1c >6.4%)
[NAME] of Obesity (UGO) | population-based | 0 | 0 |  | 0 | 2114 | 72 | This was a cross-sectional study where DEXA measurements of regional fat mass were performed on all subjects, who subsequently participated in a community intervention program. | Waist measurements were available on less than 15% of the individuals and thus not analysed.
sum stage 1* |  | 38580 | 37670 |  | 9852 | 2308
sum stage 2 |  | 70689 | 61612 |  | 20934 | 12954
sum across stage 1 and stage2 |  | 109269 | 99282 |  | 30786 | 15262