Predicting multiallelic HLA markers for Han Chinese population using unphased and flanking single nucleotide polymorphisms
學年 102
學期 1
出版（發表）日期 2014-01-29
作品名稱 Predicting multiallelic HLA markers for Han Chinese population using unphased and flanking single nucleotide polymorphisms
作品名稱（其他語言）
著者 Hsieh Ai-Ru; Chang SW; Chen PL; Chu CC; Hsiao CL; Yang WS; Chang CC; Wu JY; Chen YT; Chang TC; Fann Cathy SJ
單位
出版者
著錄名稱、卷期、頁數 BMC Genomics 15, p,81
摘要 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.
關鍵字 Major histocompatibility complex (MHC);Human leukocyte antigen (HLA);Single-nucleotide polymorphisms (SNPs)
語言 zh_TW
ISSN
期刊性質 國內
收錄於
產學合作
通訊作者
審稿制度 否
國別 TWN
公開徵稿
出版型式 ,電子版
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機構典藏連結 ( http://tkuir.lib.tku.edu.tw:8080/dspace/handle/987654321/117008 )