title: Selection of human p75NTR tag SNPs and its biological significance for clinical association studies.
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.
authors.affiliation: State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 400042, China.
authors.forename: Yong-Tang
authors.initials: YT
authors.lastname: Wang
authors.affiliation: College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
authors.forename: Xiu-Min
authors.initials: XM
authors.lastname: Lu
authors.affiliation: College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
authors.forename: Ya-Hai
authors.initials: YH
authors.lastname: Shu
authors.affiliation: College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
authors.forename: Lan
authors.initials: L
authors.lastname: Xiao
authors.affiliation: College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
authors.forename: Kai-Ting
authors.initials: KT
authors.lastname: Chen
mesh_terms: D001483:Base Sequence; D002681:China / Q000453:epidemiology; D003863:Depression / Q000453:epidemiology* / Q000235:genetics*; D008040:Genetic Linkage / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000453:epidemiology / Q000235:genetics; D006801:Humans; D001523:Mental Disorders / Q000453:epidemiology* / Q000235:genetics*; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015995:Prevalence; D017475:Receptors, Nerve Growth Factor / Q000235:genetics*; D012307:Risk Factors; D013405:Suicide / Q000706:statistics & numerical data*
chemical_list: D005819:Genetic Markers; C484065:NGFR protein, human; D009419:Nerve Tissue Proteins; D017475:Receptors, Nerve Growth Factor
keywords: bioinformatics analysis; haplotype; haplotype block; p75NTR; tag SNP