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Single nucleotide polymorphisms in telomere length-related genes are associated with hepatocellular carcinoma risk in the Chinese Han population.

ABSTRACT: Background:Single nucleotide polymorphisms (SNPs) in telomere-related genes are associated with a high risk of hepatocellular carcinoma (HCC). In this study, we investigated the SNPs of telomere length-related genes and their correlation with HCC risk in the Chinese Han population. Materials and methods:A total of 473 HCC patients and 564 healthy volunteers were recruited. Overall, 42 SNPs distributed in telomere-related genes were selected and identified. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated. Results:We found rs6713088 (OR?=?1.27, 95% CI?=?1.07-1.52, p?=?0.007), rs843711 (OR?=?1.29, 95% CI?=?1.09-1.54, p?=?0.004) and rs843706 (OR?=?1.30, 95% CI?=?1.09-1.55, p?=?0.003) in the ACYP2 gene, rs10936599 (OR?=?1.21, 95% CI?=?1.02-1.44, p?=?0.032) in the TERC gene and rs7708392 (OR?=?1.24, 95% CI?=?1.00-1.52, p?=?0.042) in the TNIP1 gene were associated with high HCC risk (OR?>?1). In contrast, rs1682111 (OR?=?0.77, 95% CI?=?0.64-0.94, p?=?0.008) in the ACYP2 gene, rs2320615 (OR?=?0.79, 95% CI?=?0.64-0.99, p?=?0.038) in the NAF1 gene, rs10069690 (OR?=?0.75, 95% CI?=?0.59-0.96, p?=?0.021) and rs2242652 (OR?=?0.70, 95% CI?=?0.55-0.90, p?=?0.004) in the TERT gene were associated with low HCC risk (OR?

SUBMITTER: Huang P

PROVIDER: S-EPMC7290267 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Single nucleotide polymorphisms in telomere length-related genes are associated with hepatocellular carcinoma risk in the Chinese Han population.

Huang Peng P Li Rong R Shen Lin L He Weizhou W Chen Shuo S Dong Yu Y Ma Jiancang J Chen Xi X Xu Meng M

Therapeutic advances in medical oncology 20200610

<h4>Background</h4>Single nucleotide polymorphisms (SNPs) in telomere-related genes are associated with a high risk of hepatocellular carcinoma (HCC). In this study, we investigated the SNPs of telomere length-related genes and their correlation with HCC risk in the Chinese Han population.<h4>Materials and methods</h4>A total of 473 HCC patients and 564 healthy volunteers were recruited. Overall, 42 SNPs distributed in telomere-related genes were selected and identified. Odds ratios (ORs) and 95 ...[more]

PMID: 32577134

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Project description:BACKGROUND: Genetic variation associated with human leukocyte antigen (HLA) genes has immunological functions and is associated with autoimmune diseases. To date, large-scale studies involving classical HLA genes have been limited by time-consuming and expensive HLA-typing technologies. To reduce these costs, single-nucleotide polymorphisms (SNPs) have been used to predict HLA-allele types. Although HLA allelic distributions differ among populations, most prediction model of HLA genes are based on Caucasian samples, with few reported studies involving non-Caucasians. RESULTS: Our sample consisted of 437 Han Chinese with Affymetrix 5.0 and Illumina 550 K SNPs, of whom 214 also had data on Affymetrix 6.0 SNPs. All individuals had HLA typings at a 4-digit resolution. Using these data, we have built prediction model of HLA genes that are specific for a Han Chinese population. To optimize our prediction model of HLA genes, we analyzed a number of critical parameters, including flanking-region size, genotyping platform, and imputation. Predictive accuracies generally increased both with sample size and SNP density. CONCLUSIONS: SNP data from the HapMap Project are about five times more dense than commercially available genotype chip data. Using chips to genotype our samples, however, only reduced the accuracy of our HLA predictions by only ~3%, while saving a great deal of time and expense. We demonstrated that classical HLA alleles can be predicted from SNP genotype data with a high level of accuracy (80.37% (HLA-B) ~95.79% (HLA-DQB1)) in a Han Chinese population. This finding offers new opportunities for researchers in obtaining HLA genotypes via prediction using their already existing chip datasets. Since the genetic variation structure (e.g. SNP, HLA, Linkage disequilibrium) is different between Han Chinese and Caucasians, and has strong impact in building prediction models for HLA genes, our findings emphasize the importance of building ethnic-specific models when analyzing human populations.

Dataset Information

Single nucleotide polymorphisms in telomere length-related genes are associated with hepatocellular carcinoma risk in the Chinese Han population.

Publications

Single nucleotide polymorphisms in telomere length-related genes are associated with hepatocellular carcinoma risk in the Chinese Han population.

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