教師資料查詢 | 類別: 期刊論文 | 教師: 謝璦如 HSIEH, AI-RU (瀏覽個人網頁)

標題: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)
語言中文
ISSN
期刊性質國內
收錄於
產學合作
通訊作者
審稿制度
國別中華民國
公開徵稿
出版型式,電子版
相關連結
Google+ 推薦功能,讓全世界都能看到您的推薦!