中国北京汉族人群ABCA4基因的SNPs研究
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摘要
目的:研究北京汉族人群中ABCA4基因单核苷酸多态性,为病因学研究提供依据。方法:选取国际人类基因组单体型图计划(Hap Map)公布的北京汉族人群(Han Chinese in Beijing,China,CHB)ABCA4基因SNPs基因型数据,利用Haploview4.2软件对其进行分析。结果:Hapmap提供的343个ABCA4基因的SNPs中,有129个(37.6%)纯合基因型SNPs和214个(62.39%)合格SNPs。本研究共确定95个标签SNPs,构建了3个单体域,各单体域均以前2种单体型为主,累计频率在91.1%~94.0%之间。结论:通过分析北京汉族人群ABCA4基因SNPs数据,得到了标签SNPs、单体域和主要单体型,为进一步的病因学研究打下了基础。
Objective:To provide the basis of single nucleotide polymorphism( SNPs) for identification and analysis of ABCA4 gene related etiologic studies in Han Chinese in Beijing( CHB).Methods:SNPs of ABCA4 gene were analyzed for minor allele frequencies( MAFs),haplotype frequencies,linkage disequilibrium patterns,and tag SNPs by Haploview program using the Hap Map data.Results:129( 37.6%) of 343 SNPs were monotonic.95 tagging SNPs were identified in 214 eligible SNPs with 3 haplotype blocks identified.The frequencies of the top 2 haplotypes among each of the 3 haplotype blocks were between 91.1% and 94.0%.Conclusion:SNPs in ABCA4 gene were analyzed by Haploview program.The analysis provides clues for future studies involving this gene.
Objective:To provide the basis of single nucleotide polymorphism( SNPs) for identification and analysis of ABCA4 gene related etiologic studies in Han Chinese in Beijing( CHB).Methods:SNPs of ABCA4 gene were analyzed for minor allele frequencies( MAFs),haplotype frequencies,linkage disequilibrium patterns,and tag SNPs by Haploview program using the Hap Map data.Results:129( 37.6%) of 343 SNPs were monotonic.95 tagging SNPs were identified in 214 eligible SNPs with 3 haplotype blocks identified.The frequencies of the top 2 haplotypes among each of the 3 haplotype blocks were between 91.1% and 94.0%.Conclusion:SNPs in ABCA4 gene were analyzed by Haploview program.The analysis provides clues for future studies involving this gene.
引文
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[14]Barrett JC.Haploview:Visualization and analysis of SNP genotype data[J].Cold Spring Harb Protoc,2009,2009(10):pdb.ip71.
[15]Santana R,Mendiburu A,Zaitlen N,et al.Multi-marker tagging single nucleotide polymorphism selection using estimation of distribution algorithms[J].Artif Intell Med,2010,50(3):193-201.
[16]Zhang K,Calabrese P,Nordborg M,et al.Haplotype block structure and its applications to association studies:Power and study designs[J].Am J Hum Genet,2002,71(6):1386-394.
[2]Do CB,Hinds DA,Francke U,et al.Comparison of family history and SNPs for predicting risk of complex disease[J].PLo S Genet,2012,8(10):e1002973.
[3]金山,卢永平,李增健,等.BMP4基因T538C多态性与中国东北地区非综合征性唇腭裂的相关性研究[J].实用口腔医学杂志,2014,30(3):402-405.
[4]Burke TR,Tsang SH.Allelic and phenotypic heterogeneity in ABCA4 mutations[J].Ophthalmic Genet,2011,32(3):165-174.
[5]Beaty TH,Murray JC,Marazita ML,et al.A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4[J].Nat Genet,2010,42(6):525-529.
[6]Mostowska A,Hozyasz KK,Wojcicka K,et al.Polymorphic variants at 10q25.3 and 17q22 loci and the risk of non-syndromic cleft lip and palate in the Polish population[J].Birth Defects Res A Clin Mol Teratol,2012,94(1):42-46.
[7]Lennon CJ,Birkeland AC,Nuez JA,et al.Association of candidate genes with nonsyndromic clefts in Honduran and Colombian populations[J].Laryngoscope,2012,122(9):2082-2087.
[8]Fontoura C,Silva RM,Granjeiro JM,et al.Further evidence of association of the ABCA4 gene with cleft lip/palate[J].Eur J Oral Sci,2012,120(6):553-557.
[9]赵凯平,袁长征,王红.北京汉族人群ROR2基因SNPs等位基因及单体型频率研究[J].中国优生与遗传杂志,2011,19(6):11-13,129.
[10]Chen Q,Wang H,Hetmanski JB,et al.BMP4 was associated with NSCL/P in an Asian population[J].PLo S One,2012,7(4):e35347.
[11]Wang H,Zhang T,Wu T,et al.The FGF and FGFR gene family and risk of cleft lip with or without cleft palate[J].Cleft Palate Craniofac J,2013,50(1):96-103.
[12]Gabriel SB,Schaffner SF,Nguyen H,et al.The structure of haplotype blocks in the human genome[J].Science,2002,296(5576):2225-2229.
[13]Qin ZS,Niu T,Liu JS.Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms[J].Am J Hum Genet,2002,71(5):1242-1247.
[14]Barrett JC.Haploview:Visualization and analysis of SNP genotype data[J].Cold Spring Harb Protoc,2009,2009(10):pdb.ip71.
[15]Santana R,Mendiburu A,Zaitlen N,et al.Multi-marker tagging single nucleotide polymorphism selection using estimation of distribution algorithms[J].Artif Intell Med,2010,50(3):193-201.
[16]Zhang K,Calabrese P,Nordborg M,et al.Haplotype block structure and its applications to association studies:Power and study designs[J].Am J Hum Genet,2002,71(6):1386-394.