Table 1.

Contributing consortia and characteristics of datasets

GAME-ON/GECCO analysisReplication stage (European ancestry)Generalizability (other ancestry)
Cancer site (consortium)No. of studiesCasesControlsaVariantsbGenotyping platformImputation thresholdcStudyCasesControlsaStudyCasesControlsa
Lung (TRICL; ref. 10)612,16016,8388492272IlluminaR2 > 0.3deCODE (10, 13)3,865196,658Nanjing (18)2,3313,077
Harvard (14, 15)984970
 Adenocarcinoma3,71815,8718472145deCODE1,434198,663Nanjing1,3043,077
Harvard597970Japan (17)1,5753,363
 SqCC3,42216,0158478230deCODE784171,059Nanjing8223,077
Harvard216970
Colorectal (CORECT; ref. 11)65,1004,8317229595Affymetrix AxiomNonedeCODE3,546236,404
Colorectal (GECCO; ref. 5)1310,31412,8579193926Illumina, AffymetrixR2 > 0.3
Prostate (ELLIPSE)614,16012,7249084781Illumina, AffymetrixR2 > 0.3deCODE4,85883,103LAPC/MEC (20)1,0341,046
iCOGS (16)20,21920,440AAPC (23)4,8534,678
JAPC/MEC (20)9801,005
 Prostate aggressive64,45012,7249003304
Breast (DRIVE; refs. 7, 9)1115,74818,0849331393Illumina, AffymetrixR2 > 0.3deCODE5,318280,808Shanghai (19)2,8672,285
iCOGS (7)46,78542,892LABC/MEC, SF (21)1,4973,213
AABC (22)3,0152,743
 Breast ER (6)84,93913,1289250406
Ovary (FOCI; ref. 8)34,3699,1239911464IlluminaR2 > 0.3deCODE716111,373
iCOGS (8)16,28323,491
 Ovary - serous32,5569,1239911279iCOGS10,31623,491
 Ovary - endometrial37159,1239910229iCOGS2,33823,491
Totala4561,85161,820991656455,789330,49018,15221,410
  • Abbreviations: AABC, African American Breast Cancer GWAS Consortium; AAPC, African Ancestry Prostate Cancer GWAS Consortium, SqCC, squamous cell carcinoma; ER, estrogen receptor negative.

  • aThe number of unique individuals after accounting for cancer subtypes and overlapping controls. Breast iCOGS included only 1q22 variants, so total for replicates without breast iCOGS is shown.

  • bSubset meta-analyses were performed for a specific variant if at least 3 sites (i.e., three of lung, colorectal, prostate, breast, or ovary) contributed data.

  • cImputation performed using the 1000 genome reference panel. Exclusion threshold is shown.