Single nucleotide polymorphisms associated with colorectal cancer susceptibility and loss of heterozygosity in a Taiwanese population

Autor: Chien-Hsing Lin, Shung Haur Yang, Chih-Hung Jen, Chi Hung Lin, Chien-Yi Tung, Ruey-Hwa Lu, Chih-Yung Yang, Jeng-Kai Jiang, Jen-Kou Lin
Jazyk: angličtina
Rok vydání: 2014
Předmět:
Genotyping Techniques
Population
DNA transcription
Taiwan
Loss of Heterozygosity
lcsh:Medicine
Single-nucleotide polymorphism
Genome-wide association study
Biology
Polymorphism
Single Nucleotide
Loss of heterozygosity
Genetic variation
Molecular Cell Biology
Genetic predisposition
Ethnicity
Genome-Wide Association Studies
Genetics
Medicine and Health Sciences
Humans
Genetic Predisposition to Disease
Allele
education
lcsh:Science
neoplasms
Genetic association
education.field_of_study
Evolutionary Biology
Multidisciplinary
Biology and life sciences
Population Biology
Cancer Risk Factors
lcsh:R
Computational Biology
Human Genetics
Cell Biology
Genomics
Genome Analysis
digestive system diseases
Oncology
Case-Control Studies
Genetic Polymorphism
lcsh:Q
Gene expression
Colorectal Neoplasms
Population Genetics
Research Article
Zdroj: PLoS ONE, Vol 9, Iss 6, p e100060 (2014)
PLoS ONE
ISSN: 1932-6203
Popis: Given the significant racial and ethnic diversity in genetic variation, we are intrigued to find out whether the single nucleotide polymorphisms (SNPs) identified in genome-wide association studies of colorectal cancer (CRC) susceptibility in East Asian populations are also relevant to the population of Taiwan. Moreover, loss of heterozygosity (LOH) may provide insight into how variants alter CRC risk and how regulatory elements control gene expression. To investigate the racial and ethnic diversity of CRC-susceptibility genetic variants and their relevance to the Taiwanese population, we genotyped 705 CRC cases and 1,802 healthy controls (Taiwan Biobank) for fifteen previously reported East Asian CRC-susceptibility SNPs and four novel genetic variants identified by whole-exome sequencing. We found that rs10795668 in FLJ3802842 and rs4631962 in CCND2 were significantly associated with CRC risk in the Taiwanese population. The previously unreported rs1338565 was associated with a significant increased risk of CRC. In addition, we also genotyped tumor tissue and paired adjacent normal tissues of these 705 CRC cases to search for LOH, as well as risk-associated and protective alleles. LOH analysis revealed preferential retention of three SNPs, rs12657484, rs3802842, and rs4444235, in tumor tissues. rs4444235 has been recently reported to be a cis-acting regulator of BMP4 gene; in this study, the C allele was preferentially retained in tumor tissues (p = 0.0023). rs4631962 and rs10795668 contribute to CRC risk in the Taiwanese and East Asian populations, and the newly identified rs1338565 was specifically associated with CRC, supporting the ethnic diversity of CRC-susceptibility SNPs. LOH analysis suggested that the three CRC risk variants, rs12657484, rs3802842, and rs4444235, exhibited somatic allele-specific imbalance and might be critical during neoplastic progression.
Databáze: OpenAIRE
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