Spreadsheet: b0bd1ef9-a74b-46a5-a694-6536c848e850
Sheet: Sheet1

Table S5:  Information on genotyping methods, quality control of SNPs, imputation, and statistical analysis for Stage 1 and 2 study cohorts | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10 | Unnamed: 11
Study | Genotyping |  |  | SNP inclusion criteria |  |  | Study-specific Exclusions | Imputation |  | Association analysis
 | Platform | Calling algorithm | Observed Call Rate Minimum | MAF | Call rate | HWE P-value |  | SNPs for imputation | Software | SNPs for analysis* | Software
Stage 1: Genome-wide association studies
British 1958 [NAME] discovery samples | Affymetrix 500K Array Set | CHIAMO | 0.97 | > 0% |  |  | 1) contamination;  2) non-European identity; | 490032 | IMPUTE | 2236936 | SNPTEST
Cohorte Lausannoise (CoLaus) Study | Affymetrix 500K Array Set | BRLMM | 0.9 | > 0% | ≥ 70% | > 10-7 | 1) gender discrepancy with genetic data from X-linked markers;  2) inconsistent genotypes when compared with control markers;  3) duplicates and first and second degree relatives; | 390631 | IMPUTE | 2199156 | SNPTEST
deCODE genetics discovery samples | [NAME] 300 and 370 | Illumina BeadStudio clustering based on deCODE data | ≥ 95% | >1% | > 96% | > 10-6 | 1) excluded samples with < 95% yield | 290447 | IMPUTE | 2338257 | SNPTEST
Diabetes [NAME] (DGI) Cases | Affymetrix 500K Array Set | BRLMM | 0.95 | > 5% | ≥ 95% | > 10-6 | 1) gender discrepancy with X-linked markers;  2) first degree relatives | 347010 | MACH | 2375043 | Merlin
Diabetes [NAME] (DGI) Controls | Affymetrix 500K Array Set | BRLMM | 0.95 | > 5% | ≥ 95% | > 10-6 | 1) gender discrepancy with X-linked markers;  2) first degree relatives | 347010 | MACH | 2375043 | Merlin
European Prospective Investigation of Cancer (EPIC-Norfolk) Obesity Study | Affymetrix 500K Array Set | BRLMM | 0.94 | [NAME] 1% | ≥ 90% | > 10-6 | 1) heterozygosity <23% or >30%; 2) >5.0% discordance in SNP pairs with r2= 1 in HapMap;  3) ethnic outliers;  4) related individuals and duplicates | 397438 | IMPUTE | 2175428 | SNPTEST
Finland-United States Investigation of NIDDM Genetics (FUSION) Cases | [NAME] | [NAME] clustering with FUSION data | 0.975 | >1% | ≥ 90% | > 10-6 | 1) likely first or second degree relatives | 304581 | MACH | 2420814 | MerlinOffline
Finland-United States Investigation of NIDDM Genetics (FUSION) Controls | [NAME] | [NAME] clustering with FUSION data | 0.975 | >1% | ≥ 90% | > 10-6 | 1) likely first or second degree relatives 2) impaired fasting glucose samples. | 304581 | MACH | 2420814 | MerlinOffline
Invecchiare in Chianti/aging in the Chianti area (InCHIANTI) | [NAME] 550 V.1 & V.3 | Standard Illumina BeadStudio | 0.97 | >1% | ≥ 99% | > 10-4 | 1) gender discrepancy with genetic data from X-linked markers 2) heterozygosity <30% | 495343 | MACH | 2461088 | MerlinOffline
KOoperative gesundheitsforschung in der Region Augsburg (KORA), Survey 3 | Affymetrix 500K Array Set | BRLMM | 0.93 | >5% |  |  | 1) discrepancy for one of the 50 SNPs common to both chips; 2)gender discrepancy with X-linked markers. | 380407 | MACH | 2211280 | MACH2QTL
Northern Finnish Birth Cohort (NFBC) 1966 | Illumina HumanCNV-370DUO Analysis BeadChip | Standard Illumina BeadStudio | 0.95 | ≥ 5% | ≥ 95% | > 10-4 | 1) gender discrepancy with genetic data from X-linked markers;  2) withdrawn consent; 3) duplicates and first and second degree relatives; 4) contaminated samples | 328007 | IMPUTE | 2314061 | SNPTEST
Nurses Health Study | Illumina HumanHap550 | Standard Illumina BeadStudio | 0.9 | [NAME] 1% | ≥ 90% |  | 1) Low genotyping completion (<90%); 2) Unclear identity and admixed origin; | 510073 | MACH | 2458400 | MACH2QTL
SardiNIA Study of Aging | Affymetrix 500K Array Set & Affymetrix 10K Array Set | BRLMM | 0.95 | > 5% | > 90% | > 10-6 | 1) Not belonging to families where at least one member was genotyped with the 500K Affymetrix chip. | 356359 | MACH | 2251301 | Merlin
Twins UK discovery samples | [NAME] | Standard Illumina BeadStudio | 0.95 | ≥ 5% | ≥ 95% | > 10-6 (in singletons) | 1) heterozygosity <33% or >37%; 2) ethnic outliers (using STRUCTURE) | 307040 | IMPUTE | 2136866 | Merlin
WTCCC Hypertension Cases | Affymetrix 500K Array Set | CHIAMO | 0.97 | > 5% | ≥ 95% | > 10-6 | 1) heterozygosity <23% or >30%; 2) discrepancy with external identifying information;   3) ethnic outliers;  4) related individuals and duplicates 5) Missing body weight and height | 387667 | IMPUTE | 2207989 | SNPTEST
WTCCC Type 2 Diabetes Cases | Affymetrix 500K Array Set | CHIAMO | 0.97 | > 5% | ≥ 95% | > 10-6 | 1) heterozygosity <23% or >30%; 2) discrepancy with external identifying information;   3) ethnic outliers;  4) related individuals and duplicates | 387667 | IMPUTE | 2206690 | SNPTEST
Stage 2a: Replication studies in-silico
[NAME] study (ERF) | 1) Illumina 318K 2) Illumina 6K 3) Illumina 370K 4) Affymetrix 250K | [NAME] | 0.98 | >1% | ≥ 90% | > 10-6 |  | up to 427922 | MACH | 29 | ProbABEL
[NAME] (ERGO) | [NAME] 550 V.3 | Standard Illumina BeadStudio | 0.975 | ≥ 5% | ≥ 98% | > 10-4 | 1) gender discrepancy with genetic data from X-linked markers;  2) excess autosomal heterozygosity > 0.336 ~FDR<0.1%; 3) duplicates and/or 1st or 2nd degree relatives with IBS; probabilities > 97%; 4) ethnic outliers | 512349 | MACH | 30 | MACH2QTL
Fenland study | Affymetrix SNP5.0  chip | BRLMM | 0.907 | [NAME] 1% | ≥ 90% | > 10-6 | 1)  Failed heterozygosity check: upperbound 0.2882 lowerbound 0.2735 2)  Failed ralatedness check (sample with lower call rate in related samples) 3) Failed duplicate check (sample with lower call rate in duplicates) | 433312 | IMPUTE | 32 | SNPTEST
Genetic Epidemiology of Metabolic Syndrome (GEMS) Cases | Affymetrix GeneChip Human Mapping 500K array | BRLMM | 0.9 | [NAME] 1% | ≥ 95% | >10-7 | 1)any participant whose sex was inconsistent with genetic data from X-linked SNPs, 2)inconsistent genotypes when compared with duplicate samples | 359052 | IMPUTE | 32 | PLINK version 1.0
Genetic Epidemiology of Metabolic Syndrome (GEMS) Controls | Affymetrix GeneChip Human Mapping 500K array | BRLMM | 0.9 | [NAME] 1% | ≥ 95% | >10-7 | 1)any participant whose sex was inconsistent with genetic data from X-linked SNPs, 2)inconsistent genotypes when compared with duplicate samples | 359052 | IMPUTE | 32 | PLINK version 1.0
London Life Sciences Population Study - Northern Europeans (LOLIPOP-NE) | HumanHap300 BeadChips | [NAME] software | not reported | > 1% | ≥ 90% | >10-3 |  |  | IMPUTE | 32 | SNPTEST
Precocious Coronary Artery Disease (ProCARDIS) | HumanHap300 BeadChips | [NAME] software | >95% | > 0.o5% | ≥ 95% | >5x10-7 |  |  | IMPUTE | 32 | SNPTEST
Twins UK replication samples | HumanHap 300k duo chip | Standard Illumina BeadStudio | 0.842 | > 0% | ≥ 90% | >10-3 |  |  |  | 27 | Merlin
Stage 2b: Replication studies bespoke genotyping
Prevalence, Prediction and Prevention of Diabetes in the Botnia study (BPPP) | Sequenom iPLEX | TYPER | 0.579 | > 0% | ≥ 90% | >10-3 |  |  |  | 26 | SAS 9.1
British 1958 [NAME] replication samples | TaqMan | ABI PRISM 7700 | 0.666 | > 0% | ≥ 90% | >10-3 |  |  |  | 6
British Women Health Study (BWHS) | KASPar | [NAME] | 0.97 | > 0% | ≥ 90% | >10-3 |  |  |  | 11 | STATA
deCODE genetics replication samples | Centaurus |  | ≥ 95% | > 0% | ≥ 90% | >10-3 |  |  |  | 30 | SNPTEST
National FINRISK study, 1997 | Sequenom iPLEX | TYPER | 0.504 | > 0% | ≥ 90% | >10-3 |  |  |  | 28 | SAS 9.1
Finland-United States Investigation of NIDDM Genetics Stage 2 (FUSION S2) Cases | Sequenom | TYPER | 0.783 | > 0% | ≥ 90% | >10-3 |  |  |  | 25 | Merlin
Finland-United States Investigation of NIDDM Genetics Stage 2 (FUSION S2) Controls | Sequenom | TYPER | 0.783 | > 0% | ≥ 90% | >10-3 |  |  |  | 25 | Merlin
Hertfortshire Cohort Study | Sequenom/TaqMan | TYPER | 0.796 | > 0% | ≥ 90% | >10-3 |  |  |  | 23
KOoperative gesundheitsforschung in der Region Augsburg (KORA), [NAME] | Sequenom | TYPER | 0.894 | > 0% | ≥ 90% | >10-3 | 1) gender discrepancy with X-linked markers. |  |  | 15 | R
Metabolic Syndrome in Men (METSIM) | Sequenom | TYPER | 0.934 | > 0% | ≥ 90% | >10-3 |  |  |  | 22 | Merlin
MRC [NAME] | Sequenom | TYPER | 0.91 | > 0% | ≥ 90% | >10-3 |  |  |  | 30 | SAS 9.1
Nurses Health Study (NHS) - Cases | Biotrove | Biotrove OpenArray SNP Genotyping Analysis Software v.1.0.2 | 0.939 | > 0% | ≥ 90% | >10-3 |  |  |  | 23 | SAS 9.1
Nurses Health Study (NHS) - Controls | Biotrove | Biotrove OpenArray SNP Genotyping Analysis Software v.1.0.2 | 0.939 | > 0% | ≥ 90% | >10-3 |  |  |  | 22 | SAS 9.1
UK Type 2 Diabetes Genetics Consortium collection replication set 1 Cases | TaqMan | ABI PRISM 7700 | 0.94115 | > 0% | ≥ 90% | >10-3 |  |  |  | 6 | SNPTEST
UK Type 2 Diabetes Genetics Consortium collection replication set 1 Controls | TaqMan | ABI PRISM 7700 | 0.94944 | > 0% | ≥ 90% | >10-3 |  |  |  | 7 | SNPTEST
UK Type 2 Diabetes Genetics Consortium collection replication set 3 Cases | TaqMan | ABI PRISM 7700 | 0.8994 | > 0% | ≥ 90% | >10-3 |  |  |  | 5 | SNPTEST
UK Type 2 Diabetes Genetics Consortium collection replication set 3 Controls | TaqMan | ABI PRISM 7700 | 0.8877 | > 0% | ≥ 90% | >10-3 |  |  |  | 6 | SNPTEST
UK Type 2 Diabetes Genetics Consortium collection replication set 4 Cases | TaqMan | ABI PRISM 7700 | 0.92893 | > 0% | ≥ 90% | >10-3 |  |  |  | 7 | SNPTEST
UK Type 2 Diabetes Genetics Consortium collection replication set 4 Controls | TaqMan | ABI PRISM 7700 | 0.94323 | > 0% | ≥ 90% | >10-3 |  |  |  | 6 | SNPTEST
[NAME] of Obesity (UGO) | Sequenom iPLEX | TYPER | 0.98 | > 5% | ≥ 94% | >10-3 | 1) discrepancy in duplicates < 3% |  |  | 20 | SAS 9.1
*The data here presents all markers that passed QC criteria and was subsequently used in association analysis. Some studies sent one or more proxies for the follow-up markers which is why the N deviates from the reported N of 26 markers we followed up.