Spreadsheet: 5aa7295f-73d3-4003-ab00-141c76c16843
Sheet: Sheet1

Unnamed: 0 | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10 | Unnamed: 11
A.
 | Genotyping |  |  |  |  |  | Imputation |  |  | Association analyses
 |  |  | Inclusion criteria |  |  |  |  | Inclusion criteria
Cohort | Platform | Genotype calling algorithm | MAF | Call rate* | p for HWE | SNPs that met [NAME] criteria | Imputation software | MAF | Imputation quality* | SNPs in meta-analysis | Analyses software
Follow-Up Stage - Insilico
LifeLines | [NAME] v2 | GenomeStudio | [NAME] 1% | ≥ 95% | > 10-4 | 257.581 | BEAGLE v3.1.0 | >0% | no filtering on imputation quality | 2472812 | SNPtest
PLCO2 controls | [NAME]; [NAME]K | [NAME] | [NAME]. [NAME] | ≥ 90% | - | 525262 | IMPUTE | ≥1% | proper-info ≥ 0.40 | 2538067 | SNPtest
PLCO2 cases | [NAME]; [NAME]K | [NAME] | [NAME]. [NAME] | ≥ 90% | - | 525262 | IMPUTE | ≥1% | proper-info ≥ 0.40 | 2564030 | SNPtest
PREVEND | [NAME] | GenomeStudio | [NAME] 1% | >95% | 0.0001 | 232571 | BEAGLE | ≥1% | at meta-level | 2289210 | PLINK
QIMR | [NAME] 370 or 610 | BeadStudio | [NAME] 1% | ≥ 95% | > 10-6 | 271069 | MACH |  |  | 2543887 | PLINK
B.
 |  |  | Inclusion criteria
Cohort | [NAME] | Genotype calling algorithm | MAF | Call rate* | p for HWE | SNPs that met [NAME] criteria | Analyses software
Follow-Up Stage - Metabochip:
ADVANCE-CAD cases (females) | [NAME] |  | > 0% |  | > 0.001 | 195827 | PLINK
ADVANCE-CAD cases (males) | [NAME] |  | > 0% |  | > 0.001 | 195050 | PLINK
ADVANCE-CAD controls (females) | [NAME] |  | > 0% |  | > 0.001 | 195679 | PLINK
ADVANCE-CAD controls (males) | [NAME] |  | > 0% |  | > 0.001 | 195405 | PLINK
AMC-PAS | Metabochip | GenoSNP | none | ≥ 98% | > 10-4 | 169807 | PLINK
B58C nonGWAS | [NAME] | GeneCall | >=1% | >=95% | >10-6 | 180655 | SNPTEST
BHS nonGWAS metabochip | [NAME] | GeneCall | none | none | none | 129565 | GenABEL
CARDIOGENICS | Metabochip | GenoSNP | none | ≥ 98% | > 10-5 | 177614 | PLINK
D2D2007, DPS, DR'S EXTRA, FUSION stage 2, and METSIM  cases | [NAME] | BeadStudio version 3.3.7, Gentrain version 1.0 | > 0% | ≥ 98.15% | provided p for all SNPs but did not exclude | 138569 | EMMAX
D2D2007, DPS, DR'S EXTRA, FUSION stage 2, and METSIM  controls | [NAME] | BeadStudio version 3.3.7, Gentrain version 1.0 | > 0% | ≥ 98.15% | provided p for all SNPs but did not exclude | 145465 | EMMAX
DILGOM | Metabochip | GenCall | none | ≥ 95% | none | 183872 | PLINK
EAS | [NAME] | GenomeStudio | > 0% | ≥ 90% | > 10-6 | 184559 | PLINK
EGCUT metabochip CAD cases | [NAME] | GeneCall | > 0% | ≥ 84.6% | > 10-7 | 182516 | GenABEL
EGCUT metabochip controls | [NAME] | GeneCall | > 0% | ≥ 84.6% | > 10-7 | 182516 | GenABEL
EGCUT metabochip DB cases | [NAME] | GeneCall | > 0% | ≥ 84.6% | > 10-7 | 182516 | GenABEL
ELY | [NAME] | GeneCall | > 0% | ≥ 90% | > 10-6 | 149302 | PLINK
EPIC Controls & cases | [NAME] | GeneCall | > 0% | ≥ 90% | > 10-6 | 143294 | PLINK
Fenland | [NAME] | GeneCall | > 0% | ≥ 90% | > 10-6 | 167085 | PLINK
GLACIER | [NAME] | Illuminus | >0% | ≥ 95% | >0.00001 | 149782 | PLINK
GO-DARTS cases | [NAME] | GeneCall | >=1% | >=95% | >10-6 | 180399 | SNPTEST
GO-DARTS controls | [NAME] | GeneCall | >=1% | >=95% | >10-6 | 180399 | SNPTEST
Heinz Nixdorf Recall Study | Metabochip | GenomeStudioV2010.2 | none | ≥ 95% | > 10-6 | 192261 | [NAME]
HUNT2 and TROMSO cases | [NAME] | BeadStudio version 3.3.7, Gentrain version 1.0 | > 0% | ≥ 98.15% | provided p for all SNPs but did not exclude | 139415 | EMMAX
HUNT2 and TROMSO controls | [NAME] | BeadStudio version 3.3.7, Gentrain version 1.0 | > 0% | ≥ 98.15% | provided p for all SNPs but did not exclude | 143806 | EMMAX
IMPROVE | [NAME] | GeneCall | > 0% | ≥ 95% | > 10-6 | 185704 | PLINK
KORA S3 | Metabochip | Genome Studio | none | none | none | 185781 | ProbABEL/PLINK
KORA S4 | Metabochip | Genome Studio | none | none | none | 185781 | ProbABEL/PLINK
LURIC cases | [NAME] | GeneTrain 2 | - | ≥ 90% | > 10-6 | 191341 | PLINK
LURIC controls | [NAME] | GeneTrain 2 | - | ≥ 90% | > 10-6 | 191341 | PLINK
MORGAM | Metabochip | GenCall | none | none | none | 196725 | PLINK
MORGAM cases | Metabochip | GenCall | none | none | none | 196725 | PLINK
NSHD | [NAME] | GeneCall | > 0% | ≥ 90% | > 10-6 | 146474 | PLINK
PIVUS | [NAME] | GenCall | > 0% | ≥ 90% | > 10-6 | 185450 | PLINK
PIVUS | [NAME] | GenCall | > 0% | ≥ 90% | > 10-6 | 185450 | PLINK
SCARFSHEEP | [NAME] | GeneCall | > 0% | ≥ 95% | > 10-6 | 185704 | PLINK
STR | [NAME] | GenCall | > 0% | ≥ 90% | > 10-6 | 183961 | Merlin
[NAME] nonGWAS | [NAME] | GeneCall | >=1% | >=95% | >10-6 | 180655 | SNPTEST
THISEAS | Metabochip | GenoSNP | none | ≥ 98% | > 10-7 | 169779 | PLINK
ULSAM | [NAME] | GenCall | > 0% | ≥ 90% | > 10-6 | 183357 | PLINK
ULSAM | [NAME] | GenCall | > 0% | ≥ 90% | > 10-6 | 183357 | PLINK
WHITEHALL | [NAME] | GeneCall | > 0% | ≥ 90% | > 10-6 | 171257 | PLINK