Abstract
Genome-wide association studies have identified susceptibility loci for esophageal squamous cell carcinoma (ESCC). We conducted a meta-analysis of all single-nucleotide polymorphisms (SNPs) that showed nominally significant P-values in two previously published genome-wide scans that included a total of 2961 ESCC cases and 3400 controls. The meta-analysis revealed five SNPs at 2q33 with P< 5 × 10 -8, and the strongest signal was rs13016963, with a combined odds ratio (95% confidence interval) of 1.29 (1.19-1.40) and P= 7.63 × 10 -10. An imputation analysis of 4304 SNPs at 2q33 suggested a single association signal, and the strongest imputed SNP associations were similar to those from the genotyped SNPs. We conducted an ancestral recombination graph analysis with 53 SNPs to identify one or more haplotypes that harbor the variants directly responsible for the detected association signal. This showed that the five SNPs exist in a single haplotype along with 45 imputed SNPs in strong linkage disequilibrium, and the strongest candidate was rs10201587, one of the genotyped SNPs. Our meta-analysis found genome-wide significant SNPs at 2q33 that map to the CASP8/ALS2CR12/TRAK2 gene region. Variants in CASP8 have been extensively studied across a spectrum of cancers with mixed results. The locus we identified appears to be distinct from the widely studied rs3834129 and rs1045485 SNPs in CASP8. Future studies of esophageal and other cancers should focus on comprehensive sequencing of this 2q33 locus and functional analysis of rs13016963 and rs10201587 and other strongly correlated variants. Published by Oxford University Press 2012.
| Original language | English (US) |
|---|---|
| Article number | dds029 |
| Pages (from-to) | 2132-2141 |
| Number of pages | 10 |
| Journal | Human molecular genetics |
| Volume | 21 |
| Issue number | 9 |
| DOIs | |
| State | Published - May 1 2012 |
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All Science Journal Classification (ASJC) codes
- Molecular Biology
- Genetics
- Genetics(clinical)
Cite this
}
Genotypic variants at 2q33 and risk of esophageal squamous cell carcinoma in China : A meta-analysis of genome-wide association studies. / Abnet, Christian C.; Wang, Zhaoming; Song, Xin; Hu, Nan; Zhou, Fu You; Freedman, Neal D.; Li, Xue Min; Yu, Kai; Shu, Xiao Ou; Yuan, Jian Min; Zheng, Wei; Dawsey, Sanford M.; Liao, Linda M.; Lee, Maxwell P.; Ding, Ti; Qiao, You Lin; Gao, Yu Tang; Koh, Woon Puay; Xiang, Yong Bing; Tang, Ze Zhong; Fan, Jin Hu; Chung, Charles C.; Wang, Chaoyu; Wheeler, William; Yeager, Meredith; Yuenger, Jeff; Hutchinson, Amy; Jacobs, Kevin B.; Giffen, Carol A.; Burdett, Laurie; Fraumeni, Joseph F.; Tucker, Margaret A.; Chow, Wong Ho; Zhao, Xue Ke; Li, Jiang Man; Li, Ai Li; Sun, Liang Dan; Wei, Wu; Li, Ji Lin; Zhang, Peng; Li, Hong Lei; Cui, Wen Yan; Wang, Wei Peng; Liu, Zhi Cai; Yang, Xia; Fu, Wen Jing; Cui, Ji Li; Lin, Hong Li; Zhu, Wen Liang; Liu, Min; Chen, Xi; Chen, Jie; Guo, Li; Han, Jing Jing; Zhou, Sheng Li; Huang, Jia; Wu, Yue; Yuan, Chao; Huang, Jing; Ji, Ai Fang; Kul, Jian Wei; Fan, Zhong Min; Wang, Jian Po; Zhang, Dong Yun; Zhang, Lian Qun; Zhang, Wei; Chen, Yuan Fang; Ren, Jing Li; Li, Xiu Min; Dong, Jin Cheng; Xing, Guo Lan; Guo, Zhi Gang; Yang, Jian Xue; Mao, Yi Ming; Yuan, Yuan; Guo, Er Tao; Zhang, Wei; Hou, Zhi Chao; Liu, Jing; Li, Yan; Tang, Sa; Chang, Jia; Peng, Xiu Qin; Han, Min; Yin, Wan Li; Liu, Ya Li; Hu, Yan Long; Liu, Yu; Yang, Liu Qin; Zhu, Fu Guo; Yang, Xiu Feng; Feng, Xiao Shan; Wang, Zhou; Li, Yin; Gao, She Gan; Liu, Hai Lin; Yuan, Ling; Jin, Yan; Zhang, Yan Rui; Sheyhidin, Ilyar; Li, Feng; Chen, Bao Ping; Ren, Shu Wei; Liu, Bin; Li, Dan; Zhang, Gao Fu; Yue, Wen Bin; Feng, Chang Wei; Qige, Qirenwang; Zhao, Jian Ting; Yang, Wen Jun; Lei, Guang Yan; Chen, Long Qi; Li, En Min; Xu, Li Yan; Wu, Zhi Yong; Bao, Zhi Qin; Chen, Ji Li; Li, Xian Chang; Zhuang, Xiang; Zhou, Ying Fa; Zuo, Xian Bo; Dong, Zi Ming; Wang, Lu Wen; Fan, Xue Pin; Wang, Jin; Zhou, Qi; Ma, Guo Shun; Zhang, Qin Xian; Liu, Hai; Jian, Xin Ying; Lian, Sin Yong; Wang, Jin Sheng; Chang, Fu Bao; Lu, Chang Dong; Miao, Jian Jun; Chen, Zhi Guo; Wang, Ran; Guo, Ming; Fan, Zeng Lin; Tao, Ping; Liu, Tai Jing; Wei, Jin Chang; Kong, Qing Peng; Fan, Lei; Wang, Xian Zeng; Gao, Fu Sheng; Wang, Tian Yun; Xie, Dong; Wang, Li; Chen, Shu Qing; Yang, Wan Cai; Hong, Jun Yan; Wang, Liang; Qiu, Song Liang; Goldstein, Alisa M.; Yuan, Zhi Qing; Chanock, Stephen J.; Zhang, Xue Jun; Taylor, Philip R.; Wang, Li Dong.
In: Human molecular genetics, Vol. 21, No. 9, dds029, 01.05.2012, p. 2132-2141.Research output: Contribution to journal › Article
TY - JOUR
T1 - Genotypic variants at 2q33 and risk of esophageal squamous cell carcinoma in China
T2 - A meta-analysis of genome-wide association studies
AU - Abnet, Christian C.
AU - Wang, Zhaoming
AU - Song, Xin
AU - Hu, Nan
AU - Zhou, Fu You
AU - Freedman, Neal D.
AU - Li, Xue Min
AU - Yu, Kai
AU - Shu, Xiao Ou
AU - Yuan, Jian Min
AU - Zheng, Wei
AU - Dawsey, Sanford M.
AU - Liao, Linda M.
AU - Lee, Maxwell P.
AU - Ding, Ti
AU - Qiao, You Lin
AU - Gao, Yu Tang
AU - Koh, Woon Puay
AU - Xiang, Yong Bing
AU - Tang, Ze Zhong
AU - Fan, Jin Hu
AU - Chung, Charles C.
AU - Wang, Chaoyu
AU - Wheeler, William
AU - Yeager, Meredith
AU - Yuenger, Jeff
AU - Hutchinson, Amy
AU - Jacobs, Kevin B.
AU - Giffen, Carol A.
AU - Burdett, Laurie
AU - Fraumeni, Joseph F.
AU - Tucker, Margaret A.
AU - Chow, Wong Ho
AU - Zhao, Xue Ke
AU - Li, Jiang Man
AU - Li, Ai Li
AU - Sun, Liang Dan
AU - Wei, Wu
AU - Li, Ji Lin
AU - Zhang, Peng
AU - Li, Hong Lei
AU - Cui, Wen Yan
AU - Wang, Wei Peng
AU - Liu, Zhi Cai
AU - Yang, Xia
AU - Fu, Wen Jing
AU - Cui, Ji Li
AU - Lin, Hong Li
AU - Zhu, Wen Liang
AU - Liu, Min
AU - Chen, Xi
AU - Chen, Jie
AU - Guo, Li
AU - Han, Jing Jing
AU - Zhou, Sheng Li
AU - Huang, Jia
AU - Wu, Yue
AU - Yuan, Chao
AU - Huang, Jing
AU - Ji, Ai Fang
AU - Kul, Jian Wei
AU - Fan, Zhong Min
AU - Wang, Jian Po
AU - Zhang, Dong Yun
AU - Zhang, Lian Qun
AU - Zhang, Wei
AU - Chen, Yuan Fang
AU - Ren, Jing Li
AU - Li, Xiu Min
AU - Dong, Jin Cheng
AU - Xing, Guo Lan
AU - Guo, Zhi Gang
AU - Yang, Jian Xue
AU - Mao, Yi Ming
AU - Yuan, Yuan
AU - Guo, Er Tao
AU - Zhang, Wei
AU - Hou, Zhi Chao
AU - Liu, Jing
AU - Li, Yan
AU - Tang, Sa
AU - Chang, Jia
AU - Peng, Xiu Qin
AU - Han, Min
AU - Yin, Wan Li
AU - Liu, Ya Li
AU - Hu, Yan Long
AU - Liu, Yu
AU - Yang, Liu Qin
AU - Zhu, Fu Guo
AU - Yang, Xiu Feng
AU - Feng, Xiao Shan
AU - Wang, Zhou
AU - Li, Yin
AU - Gao, She Gan
AU - Liu, Hai Lin
AU - Yuan, Ling
AU - Jin, Yan
AU - Zhang, Yan Rui
AU - Sheyhidin, Ilyar
AU - Li, Feng
AU - Chen, Bao Ping
AU - Ren, Shu Wei
AU - Liu, Bin
AU - Li, Dan
AU - Zhang, Gao Fu
AU - Yue, Wen Bin
AU - Feng, Chang Wei
AU - Qige, Qirenwang
AU - Zhao, Jian Ting
AU - Yang, Wen Jun
AU - Lei, Guang Yan
AU - Chen, Long Qi
AU - Li, En Min
AU - Xu, Li Yan
AU - Wu, Zhi Yong
AU - Bao, Zhi Qin
AU - Chen, Ji Li
AU - Li, Xian Chang
AU - Zhuang, Xiang
AU - Zhou, Ying Fa
AU - Zuo, Xian Bo
AU - Dong, Zi Ming
AU - Wang, Lu Wen
AU - Fan, Xue Pin
AU - Wang, Jin
AU - Zhou, Qi
AU - Ma, Guo Shun
AU - Zhang, Qin Xian
AU - Liu, Hai
AU - Jian, Xin Ying
AU - Lian, Sin Yong
AU - Wang, Jin Sheng
AU - Chang, Fu Bao
AU - Lu, Chang Dong
AU - Miao, Jian Jun
AU - Chen, Zhi Guo
AU - Wang, Ran
AU - Guo, Ming
AU - Fan, Zeng Lin
AU - Tao, Ping
AU - Liu, Tai Jing
AU - Wei, Jin Chang
AU - Kong, Qing Peng
AU - Fan, Lei
AU - Wang, Xian Zeng
AU - Gao, Fu Sheng
AU - Wang, Tian Yun
AU - Xie, Dong
AU - Wang, Li
AU - Chen, Shu Qing
AU - Yang, Wan Cai
AU - Hong, Jun Yan
AU - Wang, Liang
AU - Qiu, Song Liang
AU - Goldstein, Alisa M.
AU - Yuan, Zhi Qing
AU - Chanock, Stephen J.
AU - Zhang, Xue Jun
AU - Taylor, Philip R.
AU - Wang, Li Dong
PY - 2012/5/1
Y1 - 2012/5/1
N2 - Genome-wide association studies have identified susceptibility loci for esophageal squamous cell carcinoma (ESCC). We conducted a meta-analysis of all single-nucleotide polymorphisms (SNPs) that showed nominally significant P-values in two previously published genome-wide scans that included a total of 2961 ESCC cases and 3400 controls. The meta-analysis revealed five SNPs at 2q33 with P< 5 × 10 -8, and the strongest signal was rs13016963, with a combined odds ratio (95% confidence interval) of 1.29 (1.19-1.40) and P= 7.63 × 10 -10. An imputation analysis of 4304 SNPs at 2q33 suggested a single association signal, and the strongest imputed SNP associations were similar to those from the genotyped SNPs. We conducted an ancestral recombination graph analysis with 53 SNPs to identify one or more haplotypes that harbor the variants directly responsible for the detected association signal. This showed that the five SNPs exist in a single haplotype along with 45 imputed SNPs in strong linkage disequilibrium, and the strongest candidate was rs10201587, one of the genotyped SNPs. Our meta-analysis found genome-wide significant SNPs at 2q33 that map to the CASP8/ALS2CR12/TRAK2 gene region. Variants in CASP8 have been extensively studied across a spectrum of cancers with mixed results. The locus we identified appears to be distinct from the widely studied rs3834129 and rs1045485 SNPs in CASP8. Future studies of esophageal and other cancers should focus on comprehensive sequencing of this 2q33 locus and functional analysis of rs13016963 and rs10201587 and other strongly correlated variants. Published by Oxford University Press 2012.
AB - Genome-wide association studies have identified susceptibility loci for esophageal squamous cell carcinoma (ESCC). We conducted a meta-analysis of all single-nucleotide polymorphisms (SNPs) that showed nominally significant P-values in two previously published genome-wide scans that included a total of 2961 ESCC cases and 3400 controls. The meta-analysis revealed five SNPs at 2q33 with P< 5 × 10 -8, and the strongest signal was rs13016963, with a combined odds ratio (95% confidence interval) of 1.29 (1.19-1.40) and P= 7.63 × 10 -10. An imputation analysis of 4304 SNPs at 2q33 suggested a single association signal, and the strongest imputed SNP associations were similar to those from the genotyped SNPs. We conducted an ancestral recombination graph analysis with 53 SNPs to identify one or more haplotypes that harbor the variants directly responsible for the detected association signal. This showed that the five SNPs exist in a single haplotype along with 45 imputed SNPs in strong linkage disequilibrium, and the strongest candidate was rs10201587, one of the genotyped SNPs. Our meta-analysis found genome-wide significant SNPs at 2q33 that map to the CASP8/ALS2CR12/TRAK2 gene region. Variants in CASP8 have been extensively studied across a spectrum of cancers with mixed results. The locus we identified appears to be distinct from the widely studied rs3834129 and rs1045485 SNPs in CASP8. Future studies of esophageal and other cancers should focus on comprehensive sequencing of this 2q33 locus and functional analysis of rs13016963 and rs10201587 and other strongly correlated variants. Published by Oxford University Press 2012.
UR - http://www.scopus.com/inward/record.url?scp=84859258707&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84859258707&partnerID=8YFLogxK
U2 - 10.1093/hmg/dds029
DO - 10.1093/hmg/dds029
M3 - Article
C2 - 22323360
AN - SCOPUS:84859258707
VL - 21
SP - 2132
EP - 2141
JO - Human Molecular Genetics
JF - Human Molecular Genetics
SN - 0964-6906
IS - 9
M1 - dds029
ER -