study participants for the gwas were drawn from two studies , the shanxi upper gastrointestinal cancer genetics project ( shanxi ) and the linxian nutrition intervention trial ( nit ) , a prospective cohort .
for the second phase , we genotyped additional subjects from shanxi and nit as well as subjects from the shanghai men 's health study ( smhs ) , the shanghai women 's health study ( smhs ) , and the singapore chinese health study ( schs ) ( supplementary table 1 ) .
the shanxi study controls were matched on age and sex for the case - control portion , while for the nit controls were selected as a case - cohort and frequency matched on age and sex . for the smhs , swhs , and schs cohorts ,
controls were alive , free of upper gastrointestinal tract cancer , and matched to cases as described in supplementary table 1 . for the shanxi and nit study ,
tumor anatomic location was known for all cases and > 85% of cases had pathologic confirmation .
for the three cohorts added in the second phase , the proportion with anatomic location in the stomach is given in supplementary table 1 and pathologic confirmation was available for > 95% of cases .
all examined esophageal cancers were squamous cell carcinomas ( escc ) and all examined gastric cancers ( gc ) were adenocarcinomas .
cardia cancers were located in the proximal 3 cm of the stomach , while noncardia cancers were those in the remainder of the stomach .
gastric cancers without location information were included in total gc analyses but excluded from gc anatomic subsite analyses .
each of the five participating studies obtained informed consent from subjects and from their studies institutional review board(s ) .
genome - wide scanning was attempted on 6,384 samples using the illumina 660w quad chip . after excluding 8 samples with no observed intensity data ,
the 6,376 remaining samples were analyzed , including 4,987 from the shanxi study and 1,389 from the nit .
clustering was performed with 1,270 previously scanned caucasian samples in order to improve calling for low maf snps in the east asian samples .
participants were excluded because of : 1 ) completion rate lower than 94% ( n=485 samples ) ; 2 ) abnormal heterozygosity values of less than 25% or greater than 30% ( n=53 , among which 36 were also excluded for low completion rates ; 3 ) discordant expected duplicates ( n=3 pairs ) ; 4 ) concordant unexpected duplicates ( n=5 pairs , all from shanxi ) ; 5 ) gender discordance ( n=55 , all from shanxi ) ; 6 ) phenotype exclusions ( due to ineligibility or incomplete information ) ( n=46 ) .
we checked for relatedness among study subjects using genotypes for all subject pairs with identity - by - state greater than 45% .
these were input into glu qc.ibds module ( http://code.google.com/p/glu-genetics/ ) to estimate the identity - by - degree ratio and infer the degree of relatedness ( 12nd degree ) .
we found 20 full sibling pairs , 2 parent - child pairs , and 22 half - sibling pairs .
this level of relatedness was not surprising because of the geographic proximity of subjects accrued in the two studies .
we selected and retained one from each of the 1st degree relative pair and excluded the other ( n=22 ) for the pca but included all for the association analyses .
for the 132 known duplicate pairs the concordance was 99.98% . using 12,000 snps in low linkage disequilibrium ( pair - wise r<0.004)11 , we identified and excluded two subjects with less than 90% asian ancestry based on structure analysis ( http://pritch.bsd.uchicago.edu/structure.html)26 ( supplementary fig .
for all subjects in the genome - wide scan phase , we attempted 657,364 genotype assays . for analysis , we removed snps with a call rate < 90% .
4 ) for case - control analyses were separately examined for gc and escc and there was no evidence for significant problems with population substructure or case - control matching : the unscaled  for gc and escc were 0.990 and 0.989 respectively , while 1000 for gc and escc were 0.995 and 0.994 , respectively28 .
the illumina infinium genotype probe cluster plots for select snps ( rs2274223 and rs3781264 ) are shown in supplementary figure 5 .
after completion of the genome - wide phase , we selected six snps at10q23 , two at 1q22 , and two at 22q12 for taqman genotyping in our second phase .
all ten snps were at or near genome - wide significance for total gc , escc , or both .
for the selected snps , we successfully optimized eight taqman assays ( abi ) , while two failed manufacturing or validation .
for the second phase using taqman , we included samples from the shanxi and nit study that had not been scanned or failed qc metrics in the genome - wide phase as well as samples from three prospective cohort studies of subjects of chinese ethnicity ( smhs , swhs , and schs ) ( supplementary table 1 ) . in total
after standard quality control metrics were applied , the sample completion rate overall was 98.8.% .
we report trend models ( tables 1 , 2 ) , but also fit genotype models for comparison ( supplementary table 3 ) .
all reported p - values are based on two - sided tests . in the second and combined phases , logistic regression models were adjusted for age , sex , and study . because previous studies reported an interaction between risk of escc , alcohol or tobacco consumption , and variants marking the adh1b or aldh2 gene loci , we fit models both adjusted for and stratified on these factors ( supplementary table 4 ) .
data analysis and management was performed with glu ( genotyping library and utilities version 1.0 ) , a suite of tools available as an open - source application for management , storage and analysis of gwas data .
study participants for the gwas were drawn from two studies , the shanxi upper gastrointestinal cancer genetics project ( shanxi ) and the linxian nutrition intervention trial ( nit ) , a prospective cohort .
for the second phase , we genotyped additional subjects from shanxi and nit as well as subjects from the shanghai men 's health study ( smhs ) , the shanghai women 's health study ( smhs ) , and the singapore chinese health study ( schs ) ( supplementary table 1 ) .
the shanxi study controls were matched on age and sex for the case - control portion , while for the nit controls were selected as a case - cohort and frequency matched on age and sex . for the smhs , swhs , and schs cohorts ,
controls were alive , free of upper gastrointestinal tract cancer , and matched to cases as described in supplementary table 1 . for the shanxi and nit study ,
tumor anatomic location was known for all cases and > 85% of cases had pathologic confirmation .
for the three cohorts added in the second phase , the proportion with anatomic location in the stomach is given in supplementary table 1 and pathologic confirmation was available for > 95% of cases .
all examined esophageal cancers were squamous cell carcinomas ( escc ) and all examined gastric cancers ( gc ) were adenocarcinomas .
cardia cancers were located in the proximal 3 cm of the stomach , while noncardia cancers were those in the remainder of the stomach .
gastric cancers without location information were included in total gc analyses but excluded from gc anatomic subsite analyses .
each of the five participating studies obtained informed consent from subjects and from their studies institutional review board(s ) .
genome - wide scanning was attempted on 6,384 samples using the illumina 660w quad chip . after excluding 8 samples with no observed intensity data ,
the 6,376 remaining samples were analyzed , including 4,987 from the shanxi study and 1,389 from the nit .
clustering was performed with 1,270 previously scanned caucasian samples in order to improve calling for low maf snps in the east asian samples .
participants were excluded because of : 1 ) completion rate lower than 94% ( n=485 samples ) ; 2 ) abnormal heterozygosity values of less than 25% or greater than 30% ( n=53 , among which 36 were also excluded for low completion rates ; 3 ) discordant expected duplicates ( n=3 pairs ) ; 4 ) concordant unexpected duplicates ( n=5 pairs , all from shanxi ) ; 5 ) gender discordance ( n=55 , all from shanxi ) ; 6 ) phenotype exclusions ( due to ineligibility or incomplete information ) ( n=46 ) .
we checked for relatedness among study subjects using genotypes for all subject pairs with identity - by - state greater than 45% .
these were input into glu qc.ibds module ( http://code.google.com/p/glu-genetics/ ) to estimate the identity - by - degree ratio and infer the degree of relatedness ( 12nd degree ) .
we found 20 full sibling pairs , 2 parent - child pairs , and 22 half - sibling pairs .
this level of relatedness was not surprising because of the geographic proximity of subjects accrued in the two studies .
we selected and retained one from each of the 1st degree relative pair and excluded the other ( n=22 ) for the pca but included all for the association analyses .
for the 132 known duplicate pairs the concordance was 99.98% . using 12,000 snps in low linkage disequilibrium ( pair - wise r<0.004)11 , we identified and excluded two subjects with less than 90% asian ancestry based on structure analysis ( http://pritch.bsd.uchicago.edu/structure.html)26 ( supplementary fig .
for all subjects in the genome - wide scan phase , we attempted 657,364 genotype assays . for analysis , we removed snps with a call rate < 90% .
4 ) for case - control analyses were separately examined for gc and escc and there was no evidence for significant problems with population substructure or case - control matching : the unscaled  for gc and escc were 0.990 and 0.989 respectively , while 1000 for gc and escc were 0.995 and 0.994 , respectively28 .
the illumina infinium genotype probe cluster plots for select snps ( rs2274223 and rs3781264 ) are shown in supplementary figure 5 .
after completion of the genome - wide phase , we selected six snps at10q23 , two at 1q22 , and two at 22q12 for taqman genotyping in our second phase .
all ten snps were at or near genome - wide significance for total gc , escc , or both .
for the selected snps , we successfully optimized eight taqman assays ( abi ) , while two failed manufacturing or validation .
for the second phase using taqman , we included samples from the shanxi and nit study that had not been scanned or failed qc metrics in the genome - wide phase as well as samples from three prospective cohort studies of subjects of chinese ethnicity ( smhs , swhs , and schs ) ( supplementary table 1 ) . in total
after standard quality control metrics were applied , the sample completion rate overall was 98.8.% .
we report trend models ( tables 1 , 2 ) , but also fit genotype models for comparison ( supplementary table 3 ) .
all reported p - values are based on two - sided tests . in the second and combined phases , logistic regression models were adjusted for age , sex , and study . because previous studies reported an interaction between risk of escc , alcohol or tobacco consumption , and variants marking the adh1b or aldh2 gene loci , we fit models both adjusted for and stratified on these factors ( supplementary table 4 ) . data analysis and management was performed with glu ( genotyping library and utilities version 1.0 ) , a suite of tools available as an open - source application for management , storage and analysis of gwas data .
 we conducted a genome - wide association study of gastric cancer ( gc ) and esophageal squamous cell carcinoma ( escc ) in ethnic chinese subjects in which we genotyped 551,152 single nucleotide polymorphisms ( snps ) . 
 we report a combined analysis of 2,240 gc cases , 2,115 escc cases , and 3,302 controls drawn from five studies . in logistic regression models adjusted for age , sex , and study , multiple variants at 10q23 had genome - wide significance for gc and escc independently . 
 a notable signal was rs2274223 , a nonsynonymous snp located in plce1 , for gc ( p=8.40109 ; per allele odds ratio ( or ) = 1.31 ) and escc ( p=3.85109 ; or = 1.34 ) . 
 the association with gc differed by anatomic subsite . for tumors located in the cardia the association was stronger ( p=4.19  1015 ; or= 1.57 ) and for those located in the noncardia stomach it was absent ( p=0.44 ; or=1.05 ) . 
 our findings at 10q23 could provide insight into the high incidence rates of both cancers in china . 
ONLINE METHODS
Study participants
Genotyping and quality control
Association analysis
Supplementary Material