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postgraduate thesis: Genome-wide association study on colorectal cancer in the Hong Kong Chinese population

TitleGenome-wide association study on colorectal cancer in the Hong Kong Chinese population
Authors
Issue Date2012
PublisherThe University of Hong Kong (Pokfulam, Hong Kong)
Citation
Choi, S. [蔡兆聰]. (2012). Genome-wide association study on colorectal cancer in the Hong Kong Chinese population. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b4852156
AbstractColorectal cancer (CRC) is the second most common cancer in Hong Kong. While high-penetrance germline mutations account for up to 6% of cases, much of the variation in genetic risk may be attributable to multiple low-penetrance variants. Previous genome wide association studies (GWAS) have identified a number of CRC susceptibility alleles in Caucasian populations. Our GWAS investigated the association between genetic variants with CRC risk in the Han Chinese population in Hong Kong. In Stage I, genomic DNA samples from 455 female Chinese CRC subjects were genotyped using the Illumina 610 Quad SNP chip. Association analysis was performed on 439 cases and 771 general population female controls recruited for a study on bone mineral density. Population stratification was examined through principal components analysis using EIGENSTRAT version 2.0. From the association results, 46 SNPs (Group 1) were selected for follow-up replication (Stage II), together with 10 SNPs (Group 2) from previous GWAS studies. Genomic DNA samples from 3,571 Chinese subjects were genotyped using Sequenom MassARRAY system. Association analysis was performed on 1,505 cases and 1,452 controls. 5 SNPs (rs835378, rs2652007, rs2139273, rs2139273 and rs9286410) exceeded the genome-wide significance level in stage I, although none replicated in Stage 2, suggesting genotyping error. Results from stage II showed that the three most significant SNP were among those selected from the previous studies, yet their significance levels in Stage I were very weak . None of the SNPs selected from Stage I was significant at p<0.01 in Stage 2. Two composite scores of genetic susceptibility, one for each group of SNPs, were calculated in stage II genotype data, as the total number of high-risk alleles (according to the direction of effect in Stage I results or previous GWAS) present in an individual. Both composite scores were significantly associated with CRC risk in Stage 2 (Group 1, p=2.38 x 10-5, beta=0.046, SE=0.012; Group 2 p=1.06 x 10-7, beta=0.10, SE=0.019), suggesting that while we had insufficient power to confirm individual SNPs identified in our GWAS and the previous GWAS, these findings indicate that the SNP sets selected from Stage I results, as well as those selected from previous GWAS, contain SNPs with genuine effects on CRC risk. One SNP, rs10795668 (OR = 0.79 [CI] 95%:0.71 – 0.87 p=3.78 x 10-6), was significantly associated with CRC risk in Stage II after adjustment for multiple testing. Two further SNPs, rs6983267 and rs4939827, also achieved suggestive p-values in Stage II. All these SNPs were selected from previous GWAS in the Caucasian population, demonstrating that shared genetic factors operate for CRC in diverse populations.
DegreeMaster of Philosophy
SubjectChinese - Health and hygiene - China - Hong Kong
Colon (Anatomy) - Cancer - Genetic aspects
Rectum - Cancer - Genetic aspects
Dept/ProgramPsychiatry
Persistent Identifierhttp://hdl.handle.net/10722/193016

 

DC FieldValueLanguage
dc.contributor.authorChoi, Siu-chung-
dc.contributor.author蔡兆聰-
dc.date.accessioned2013-12-14T10:12:15Z-
dc.date.available2013-12-14T10:12:15Z-
dc.date.issued2012-
dc.identifier.citationChoi, S. [蔡兆聰]. (2012). Genome-wide association study on colorectal cancer in the Hong Kong Chinese population. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b4852156-
dc.identifier.urihttp://hdl.handle.net/10722/193016-
dc.description.abstractColorectal cancer (CRC) is the second most common cancer in Hong Kong. While high-penetrance germline mutations account for up to 6% of cases, much of the variation in genetic risk may be attributable to multiple low-penetrance variants. Previous genome wide association studies (GWAS) have identified a number of CRC susceptibility alleles in Caucasian populations. Our GWAS investigated the association between genetic variants with CRC risk in the Han Chinese population in Hong Kong. In Stage I, genomic DNA samples from 455 female Chinese CRC subjects were genotyped using the Illumina 610 Quad SNP chip. Association analysis was performed on 439 cases and 771 general population female controls recruited for a study on bone mineral density. Population stratification was examined through principal components analysis using EIGENSTRAT version 2.0. From the association results, 46 SNPs (Group 1) were selected for follow-up replication (Stage II), together with 10 SNPs (Group 2) from previous GWAS studies. Genomic DNA samples from 3,571 Chinese subjects were genotyped using Sequenom MassARRAY system. Association analysis was performed on 1,505 cases and 1,452 controls. 5 SNPs (rs835378, rs2652007, rs2139273, rs2139273 and rs9286410) exceeded the genome-wide significance level in stage I, although none replicated in Stage 2, suggesting genotyping error. Results from stage II showed that the three most significant SNP were among those selected from the previous studies, yet their significance levels in Stage I were very weak . None of the SNPs selected from Stage I was significant at p<0.01 in Stage 2. Two composite scores of genetic susceptibility, one for each group of SNPs, were calculated in stage II genotype data, as the total number of high-risk alleles (according to the direction of effect in Stage I results or previous GWAS) present in an individual. Both composite scores were significantly associated with CRC risk in Stage 2 (Group 1, p=2.38 x 10-5, beta=0.046, SE=0.012; Group 2 p=1.06 x 10-7, beta=0.10, SE=0.019), suggesting that while we had insufficient power to confirm individual SNPs identified in our GWAS and the previous GWAS, these findings indicate that the SNP sets selected from Stage I results, as well as those selected from previous GWAS, contain SNPs with genuine effects on CRC risk. One SNP, rs10795668 (OR = 0.79 [CI] 95%:0.71 – 0.87 p=3.78 x 10-6), was significantly associated with CRC risk in Stage II after adjustment for multiple testing. Two further SNPs, rs6983267 and rs4939827, also achieved suggestive p-values in Stage II. All these SNPs were selected from previous GWAS in the Caucasian population, demonstrating that shared genetic factors operate for CRC in diverse populations.-
dc.languageeng-
dc.publisherThe University of Hong Kong (Pokfulam, Hong Kong)-
dc.relation.ispartofHKU Theses Online (HKUTO)-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.rightsThe author retains all proprietary rights, (such as patent rights) and the right to use in future works.-
dc.subject.lcshChinese - Health and hygiene - China - Hong Kong-
dc.subject.lcshColon (Anatomy) - Cancer - Genetic aspects-
dc.subject.lcshRectum - Cancer - Genetic aspects-
dc.titleGenome-wide association study on colorectal cancer in the Hong Kong Chinese population-
dc.typePG_Thesis-
dc.identifier.hkulb4852156-
dc.description.thesisnameMaster of Philosophy-
dc.description.thesislevelMaster-
dc.description.thesisdisciplinePsychiatry-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.5353/th_b4852156-
dc.date.hkucongregation2012-

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