Spreadsheet: c5c125a0-02ac-448f-a3a6-68b3e69926d1
Sheet: Sheet1

Study | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Sample QC | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8
Short name | Full name | Design | Total Sample size (N) | Call rate* | Other exclusions | Samples in analyses (N) | Anthropometric assessment method | References
Follow-Up Stage - Insilico:
LifeLines | LifeLines | Population-based | 3900 | ≥ 95% [exclude if <95%] | 1) non-Caucasian (Principle Components Analysis); 2) related individuals (pi-hat > 0.4);   3) unexpected duplicates;  4) gender mismatch | 3367 | measured | 1
PREVEND | Prevention of Renal and Vascular Endstage Disease | Population-based | 3920 | ≥95% | 1) ethnic outliers;  2) related individuals and duplicates;  3) missing phenotype | 3622 | measured | 2
QIMR | Twin study at Queensland Instutite of Medical Rearch | Population-based | 11930 | ≥ 95% | 1) age < 18; 2) ethnic outliers; 3) related individuals and duplicates; 4) Missing body weight and height | 3627 | measured  or self-reported | 3
PLCO2 controls | Prostate, [NAME], Colorectal, and Ovarian Cancer Screening Trial | Population-based case-control | 1216 | >98% | 1) sex discordance with genetic data; 2) heterozygosity; 3) ancestry outliers; 4) related individuals and duplicates; 5) missing phenotype data | 1193 | self-report | 4
PLCO2 cases | Prostate, [NAME], Colorectal, and Ovarian Cancer Screening Trial | Population-based case-control | 3003 | >98% | 1) sex discordance with genetic data; 2) heterozygosity; 3) ancestry outliers; 4) related individuals and duplicates; 5) missing phenotype data | 2976 | self-report | 4
Follow-Up Stage - MetaboChip:
ADVANCE-CAD cases | Atherosclerotic Disease, VAscular FuNction, & GenetiC Epidemiology study | Population-based case control study of CAD | 974 | ≥ 95% | 1) sex discrepancies | 663 | measured | 5-8
ADVANCE-CAD controls | Atherosclerotic Disease, VAscular FuNction, & GenetiC Epidemiology study | Population-based case control study of CAD | 705 | ≥ 95% | 1) sex discrepancies | 895 | measured | 5-8
AMC-PAS | Academic Medical Centre Amsterdam Premature Atherosclerosis Study | CAD cases | 706 | 0.97 | 1) heterozygosity; 2) ethnic outliers;  3) duplicates;  4) missing phenotypes;  5) call rate< 0.95 | 490 | measured | 9
B58C nonGWAS | 1958 British Birth Cohort | Population-based | 2359 | For SNPs with MAF >=5%: >=95%;  For SNPs with >=1% MAF<5%: >=99% | 1) MAF>=1%;  2) genotype clustering; 3) call rate; 4) HWE; 5) MI of alleles;  6) concordance rate;  7) correct SNP mapping | 2211 | measured | 10-13
BHS nonGWAS metabochip | Busselton Health Study | Population-based | 270 | ≥99% | 1) Relatedness | 267 | measured | 14
CARDIOGENICS | CARDIOGENICS | CAD case-control | 806 | 0.98 | 1) heterozygosity;  2) ethnic outliers;  3) duplicates;  4) missing phenotypes;  5) call rate< 0.95 | 754 | measured | 15
D2D2007 cases | FIN-D2D study | Population-based | 457 | ≥ 98.15% | 1) Missing BMI, age, age<18, or is not T2D;  2) Gender discrepancy or anomaly;  3) Unexplained duplicate sample | 457 | measured | 16
D2D2007 controls | FIN-D2D study | Population-based | 2231 | ≥ 98.15% | 1) Missing BMI, age, age<18., or has diabetes;  2) Gender discrepancy or anomaly;  3) Unexplained duplicate sample | 2231 | measured | 16
DILGOM | Dietary, life style, and genetic determinants of obesity and metabolic syndrome | Population-based | 3997 | ≥ 95% | 1) heterozygosity <23.9% or >27.6%; 2) ethnic outliers; 3) related individuals and duplicates | 3938 | measured | 17,18
DPS cases | Diabetes Prevention Study | Population-based | 89 | ≥ 98.15% | 1) Missing BMI, age, age<18, or is not T2D;  2) Gender discrepancy or anomaly;  3) Unexplained duplicate sample | 89 | measured | 19
DPS controls | Diabetes Prevention Study | Population-based | 383 | ≥ 98.15% | 1) Missing BMI, age, age<18., or has diabetes;  2) Gender discrepancy or anomaly;  3) Unexplained duplicate sample | 383 | measured | 19
DR'S EXTRA cases | DR'S EXTRA | Population-based | 111 | ≥ 98.15% | 1) Missing BMI, age, age<18, or is not T2D;  2) Gender discrepancy or anomaly;  3) Unexplained duplicate sample | 121 | measured | 20
DR'S EXTRA controls | DR'S EXTRA | Population-based | 1174 | ≥ 98.15% | 1) Missing BMI, age, age<18., or has diabetes;  2) Gender discrepancy or anomaly;  3) Unexplained duplicate sample | 1174 | measured | 20
EAS | Edinburgh Artery Study | Population-based | 750 | ≥ 95% | 1) Missing body weight and height | 729 | Measured | 21
EGCUT metabochip CAD cases | Estonian Genome Center of University of Tartu - Cardiovascular Disease cases | Case-Controls | 700 | ≥ 84.6% | 1) Missing body weight and height;  2) Cryptic relatedness |  | measured | 22
EGCUT metabochip controls | Estonian Genome Center of University of Tartu - Controls | Case-Controls | 942 | ≥ 84.6% | 1) Missing body weight and height;  2) Cryptic relatedness |  | measured | 22
EGCUT metabochip DB cases | Estonian Genome Center of University of Tartu - Type 2 Diabetes cases | Case-Controls | 968 | ≥ 84.6% | 1) Missing body weight and height;  2) Cryptic relatedness |  | measured | 22
ELY | Ely Study | Population-based | 1625 | ≥ 95% | 1) Missing body weight and height;  2) Heterozygosity;  3) gender check | 1600 | measured | 23
EPIC cases | EPIC (European Prospective Investigation into Cancer) Norfolk Cohort, DM cases | Population-based | 735 | ≥ 95% | 1) Missing body weight and height, or case-control status;  2) Heterozygosity;  3) gender check | 727 | measured | 24
EPIC controls | EPIC (European Prospective Investigation into Cancer) Norfolk [NAME], non-DM controls | Population-based | 978 | ≥ 95% | 1) Missing body weight and height, or case-control status;  2) Heterozygosity;  3) gender check | 963 | measured | 24
Fenland | Fenland Study | Population-based | 3251 | ≥ 95% | 1) Missing body weight and height;  2) Heterozygosity;  3) gender check | 3186 | measured | 25
FUSION stage 2 cases | FUSION stage 2 | case-control | 1039 | ≥ 98.15% | 1) Missing BMI, age, age<18, or is not T2D;  2) Gender discrepancy or anomaly;  3) Unexplained duplicate sample | 1039 | measured | 26
FUSION stage 2 controls | FUSION stage 2 | case-control | 1890 | ≥ 98.15% | 1) Missing BMI, age, age<18., or has diabetes;  2) Gender discrepancy or anomaly; 3) Unexplained duplicate sample | 1890 | measured | 26
GLACIER | Gene x Lifestyle interactions And Complex traits Involved in Elevated disease Risk | Prospective cohort study | 6311 | ≥ 95% | 1) Missing phenotype;  2) Duplicates;  3) Call rate;  4) Heterozygosoty;  5) Gender fails | 6047 | measured | 27,28
GO-DARTS cases | GO-DARTS cases | Population-based | 3582 | For SNPs with MAF >=5% : >=95%;  For SNPs with >=1% MAF<5%:  >=99% | 1) MAF>=1%;  2) genotype clustering;  3) call rate;  4) HWE;  5) MI of alleles;  6) concordance rate;  7) correct SNP mapping | 3313 | measured | 29
GO-DARTS controls | GO-DARTS controls | Population-based | 3962 | For SNPs with MAF >=5% : >=95%;  For SNPs with >=1% MAF<5%:  >=99% | 1) MAF>=1%;  2) genotype clustering;  3) call rate;  4) HWE;  5) MI of alleles;  6) concordance rate;  7) correct SNP mapping | 3709 | measured | 29
Heinz Nixdorf Recall Study | Heinz Nixdorf Recall Study | Population-based | 4570 | ≥ 97% | 1) heterozygosity <21% or >26%;  2) ethnic outliers = 15;  3) related individuals and duplicates = 37;  4) Missing body weight = 26 and height = 18 | 4518 |  | 30
HUNT cases | HUNT2 | Population-based, although [NAME] samples selected for metabochip typing | 578 | ≥ 98.15% | 1) Missing BMI, age, age<18, or is not T2D;  2) Gender discrepancy or anomaly;  3) Unexplained duplicate sample | 578 | measured | 31
HUNT controls | HUNT2 | Population-based, although [NAME] samples selected for metabochip typing | 756 | ≥ 98.15% | 1) Missing BMI, age, age<18, or is T2D;  2) Gender discrepancy or anomaly;  3) Unexplained duplicate sample | 756 | measured | 31
IMPROVE |  | Population-based | 3426 | ≥ 95% | 1) ambiguous sex;  2) cryptic relatedness;  3) non-european descent | 3426 | measured | 32
KORA S3 | Cooperative Health Research in the Region of Augsburg (third survey), [NAME] in der Region Augsburg (dritte [NAME]) | Population-based | 3113 | 0.93 | none | 3113 | measured | 33
KORA S4 | Cooperative Health Research in the Region of Augsburg (forth survey), [NAME] in der Region Augsburg (vierte [NAME]) | Population-based | 3028 | 0.93 | none | 3028 | measured | 33
LURIC cases | [NAME] and Cardiovascular Health Study | case-control | 2281 | ≥ 95% | 1) Gender ambiguity;  2) Missing hip and waist measurement, age < 18 | 2251 | measured | 34
LURIC controls | [NAME] and Cardiovascular Health Study | case-control | 648 | ≥ 95% | 1) Gender ambiguity;  2) Missing hip and waist measurement, age < 18 | 644 | measured | 34
METSIM cases | Metabolic Syndrome In Men | Population-based, although [NAME] samples selected for metabochip typing | 1214 | ≥ 98.15% | 1) Missing BMI, age, age<18, or is not T2D;  2) Gender discrepancy or anomaly;  3) Unexplained duplicate sample | 1214 | measured | 35
METSIM controls | Metabolic Syndrome In Men | Population-based, although [NAME] samples selected for metabochip typing | 957 | ≥ 98.15% | 1) Missing BMI, age, age<18, or has diabetes  2) Gender discrepancy or anomaly;  3) Unexplained duplicate sample | 957 | measured | 35
MORGAM | [NAME], Genetics, Archiving and Monograph | Population-based | ~2,650 | ≥ 95% | 1) heterozygosity <18.1% or >20.7%; 2) >10.0% discordance with Sequenom genotypes;  3) ethnic outliers;  4) related individuals and duplicates | 2528 | measured | 36-39
MORGAM cases | [NAME], Genetics, Archiving and Monograph | CVD cases from population-based follow-up cohorts. Baseline and incident cases. | ~2,150 | ≥ 95% | 1) heterozygosity <18.1% or >20.7%; 2) >10.0% discordance with Sequenom genotypes;  3) ethnic outliers;  4) related individuals and duplicates | 2065 | measured | 36-39
NSHD | MRC National Survey of Health & Development | Birth cohort | 5362 | ≥ 95% | 1) Missing body weight and height;  2) Heterozygosity;  3) gender check | 988 | measured | 40,41
PIVUS | Prospective Investigation of the Vasculature in Uppsala Seniors | Population-based | 999 | ≥90% | 1) Related individuals and duplicates;  2) Heterozygosity, (F-mean(F))/sd(Z) [NAME] 5;  3) Missing all phenotypes | 978 | measured | 42
SCARFSHEEP |  | case-control | 2899 | ≥ 95% | 1) ambiguous sex;  2) cryptic relatedness;  3) non-european descent | 3201 | measured
STR | Swedish Twin Registry | Population-based | 2702 | ≥90% | 1) Heterozygosity, (F-mean(F))/sd(Z) [NAME] 5;  2) Missing all phenotypes | 2430 | measured | 43
T2D – WTCCC nonGWAS | Wellcome Trust Case Control Consortium - T2D non GWAS | Population-based | 1335 | For SNPs with MAF >=5% : >=95%;  For SNPs with >=1% MAF<5%:  >=99% | 1) MAF>=1%;  2) genotype clustering;  3) call rate;  4) HWE;  5) MI of alleles; 6) concordance rate;  7) correct SNP mapping | 1077 | measured
THISEAS | The Hellenic study of Interactions between Snps and Eating in Atherosclerosis Susceptibility | CAD case-control | 1887 | 0.97 | 1) heterozygosity;  2) ethnic outliers;  3) duplicates;  4) missing phenotypes;  5) call rate < 0.95 | 1413 | measured | 44
Tromsø cases | Tromsø | Population-based, although [NAME] samples selected for metabochip typing | 709 | ≥ 98.15% | 1) Missing BMI, age, age<18, or is not T2D;  2) Gender discrepancy or anomaly;  3) Unexplained duplicate sample | 709 | measured | 45
Tromsø controls | Tromsø | Population-based, although [NAME] samples selected for metabochip typing | 709 | ≥ 98.15% | 1) Missing BMI, age, age<18, or is T2D;  2) Gender discrepancy or anomaly;  3) Unexplained duplicate sample | 709 | measured | 45
ULSAM | Uppsala Longitudinal Study of Adult Men | Population-based | 1221 | ≥90% | 1) Related individuals and duplicates;  2) Heterozygosity, (F-mean(F))/sd(Z) [NAME] 5;  3) Missing all phenotypes | 1116 | measured | 46
WHITEHALL | The Whitehall II study | Cohort of London-based civil servants | 3413 | ≥ 95% | 1) Missing body weight and height;  2) Heterozygosity;  3) gender check | 3377 | measured | 47,48.