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Selection of human p75NTR tag SNPs and its biological significance for clinical association studies

Issue title: Frontiers in Biomedical Engineering and Biotechnology – Proceedings of the 3rd International Conference on Biomedical Engineering and Biotechnology, 25–28 September 2014, Beijing, China

Article type: Research Article

Authors: Wang, Yong-Tang; | Lu, Xiu-Min; | Shu, Ya-Hai | Xiao, Lan | Chen, Kai-Ting

Affiliations: State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 400042, China | College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China

Note: [] Corresponding authors: Yong-Tang Wang, Institute of Surgery Research, Daping Hospital, Third Military Medical University, 10 Changjiang Sub-Road, Chongqing 400042, China. Tel.: +86 023 68757435; E-mail: [email protected]. Xiu-Min Lu, College of Pharmacy and Bioengineering, Chongqing University of Technology, 69 Hongguang Road, Chongqing 400054, China. Tel.: +86 023 62563190; E-mail: [email protected].

Note: [] Corresponding authors: Yong-Tang Wang, Institute of Surgery Research, Daping Hospital, Third Military Medical University, 10 Changjiang Sub-Road, Chongqing 400042, China. Tel.: +86 023 68757435; E-mail: [email protected]. Xiu-Min Lu, College of Pharmacy and Bioengineering, Chongqing University of Technology, 69 Hongguang Road, Chongqing 400054, China. Tel.: +86 023 62563190; E-mail: [email protected].

Keywords: p75NTR, haplotype block, tag SNP, haplotype, bioinformatics analysis

DOI: 10.3233/BME-141213

Journal: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3833-3839, 2014

Published: 2014
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Abstract

To select tag single nucleotide polymorphisms (SNPs) within and around human p75 neurotrophin receptor (p75NTR) gene in Chinese Han population, the sequence involving p75NTR gene as well as the upstream and downstream of the gene was identified according to the data from National Center for Biotechnology Information (NCBI) GenBank database, and the SNP genotype data involving 63 SNPs in the regions were obtained from Chinese Han Beijing (CHB) population of HapMap database. Then, Haploview (version 4.2) was used to calculate linkage disequilibrium (LD) statistics for the selected 32 common SNPs with a minor allele frequence (MAF) more than 0.05. Haplotype blocks were constructed throughout the p75NTR gene according to the upper and the lower 95% confidence bound of D' value, and the tag SNPs were selected based on the r2 and LOD values between SNPs as well as the results of bioinformatics analysis. The results indicated that five haplotype blocks were constructed within and around p75NTR gene and 12 tag SNPs including rs2537710, rs603769, rs614455, rs2537706, rs534561, rs2072445, rs2072446, rs7219709, rs734194, rs741071, rs741073 and rs2671641 were selected to represent the other 51 SNPs in p75NTR gene. Therefore, the 12 selected SNPs may act as tag SNPs for the entire p75NTR gene in Chinese Han population, which will provide an effective way to select tag SNPs in a whole gene, and its biological significance is to further guide the clinical association studies between the candidate gene and disease susceptibility.

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