基于毛干蛋白质组的族群推断技术的建立与验证
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摘要
毛干是一种案件现场常见的生物物证,由于核DNA含量极少且高度降解,难以采用现有的短串联重复序列(short tandem repeat,STR)检验方法进行个人识别鉴定,目前仅使用线粒体DNA检验进行母系亲缘关系的判定,利用率非常低.毛干中蛋白质非常稳定,而且具有遗传多态性,表现为基因组中的非同义单核苷酸多态性(non-synonymous single nucleotide polymorphisms,ns SNPs),转录翻译后形成蛋白质序列中的单氨基酸多态性(single amino acid polymorphisms,SAPs).充分利用毛干蛋白质中蕴含的遗传信息,为案件提供线索和证据,是实际公安业务的迫切需求,具有重要的应用价值.本文选取了104份中国汉族的毛干样本进行蛋白质组的检测,共获得了703个SAP位点,位于460个蛋白质上,共推导出552个nsSNP位点.进一步筛选在所有样本中检出率超过15%的位点,获得了88个nsSNP位点,使用毛干样本对应的口腔拭子DNA对88个ns SNP位点进行一代测序验证.为评估发现的nsSNP位点对于人群的区分能力,以千人数据库(1 000 Genome Project)为参考数据库,采用聚类分析和群体匹配概率等方法对检测的19份毛干样本进行人群来源推断.结果显示,通过检测毛干蛋白质组中的ns SNP可以实现东亚、欧洲、非洲三大洲际人群的区分.
Hair shaft is one kind of important biological evidence and is widely collected in the crime scene.However, it is very difficult to obtain full STR profiles as the nuclear DNA of hair shaft has degraded seriously.Mitochondrial DNA examination is the routine method for hair shaft, but it can not be used to identify individuals.Therefore, it is important to explore more genetic information of hair shaft in order to offer more clues for crime investigation. Protein is chemically more robust than DNA and can persist for a longer period. Proteins also contains genetic variation in the form of single amino acid polymorphisms(SAPs), which can be used to infer the status of non-synonymous single nucleotide polymorphisms(nsSNPs) for forensic ancestry analysis. Here, we used mass spectrometry-based shotgun proteomics to characterize hair shaft proteins in 104 Chinese Han subjects.A total of 552 nsSNPs were imputed from 703 SAPs in 460 proteins. 88 nsSNPs were selected according to a call rate of 15%, then validated using Sanger sequencing. Finally, clustering analysis and population random match probability calculation were performed to infer the ancestry of 19 Han Chinese individuals, and individual genotypes of 1 000 genome populations were employed as reference data. The results demonstrated that nsSNPs imputed from hair shaft can be used to distinguish East Asian, European and African population.
Hair shaft is one kind of important biological evidence and is widely collected in the crime scene.However, it is very difficult to obtain full STR profiles as the nuclear DNA of hair shaft has degraded seriously.Mitochondrial DNA examination is the routine method for hair shaft, but it can not be used to identify individuals.Therefore, it is important to explore more genetic information of hair shaft in order to offer more clues for crime investigation. Protein is chemically more robust than DNA and can persist for a longer period. Proteins also contains genetic variation in the form of single amino acid polymorphisms(SAPs), which can be used to infer the status of non-synonymous single nucleotide polymorphisms(nsSNPs) for forensic ancestry analysis. Here, we used mass spectrometry-based shotgun proteomics to characterize hair shaft proteins in 104 Chinese Han subjects.A total of 552 nsSNPs were imputed from 703 SAPs in 460 proteins. 88 nsSNPs were selected according to a call rate of 15%, then validated using Sanger sequencing. Finally, clustering analysis and population random match probability calculation were performed to infer the ancestry of 19 Han Chinese individuals, and individual genotypes of 1 000 genome populations were employed as reference data. The results demonstrated that nsSNPs imputed from hair shaft can be used to distinguish East Asian, European and African population.
引文
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[17]Liu F,Hamer M A,Heilmann S,et al.Prediction of male-pattern baldness from genotypes.Eur J Hum Genet,2016,24(6):895-902
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[19]Walsh S,Liu F,Wollstein A,et al.The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA.Forensic Sci Int Genet,2013,7(1):98-115
[2]Wadsworth C,Buckley M.Proteome degradation in fossils:investigating the longevity of protein survival in ancient bone.Rapid Commun Mass Spectrom,2014,28(6):605-615
[3]Sheynkman G M,Shortreed M R,Frey B L,et al.Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences.J Proteome Res,2014,13(1):228-240
[4]Frudakis T,Venkateswarlu K,Thomas M J,et al.Aclassifier for the SNP-based inference of ancestry.J Forensic Sci,2003,48(4):771-782
[5]Kidd K K,Speed W C,Pakstis A J,et al.Progress toward an efficient panel of SNPs for ancestry inference.Forensic Sci Int Genet,2014,10:23-32
[6]Pakstis A J,Haigh E,Cherni L,et al.52 additional reference population samples for the 55 AISNP panel.Forensic Sci Int Genet,2015,19:269-271
[7]Tennessen J A,Bigham A W,O'Connor T D,et al.Evolution and functional impact of rare coding variation from deep sequencing of human exomes.Science,2012,337(6090):64-69
[8]Parker G J,Leppert T,Anex D S,et al.Demonstration of proteinbased human identification using the hair shaft proteome.Plos One,2016,11(9):e0160653
[9]Wu J,Mao X,Cai T,et al.KOBAS server:a web-based platform for automated annotation and pathway identification.Nucleic Acids Res,2006,34(Web Server issue):W720-724
[10]Yoo J,Lee Y,Kim Y,et al.SNPAnalyzer 2.0:a web-based integrated workbench for linkage disequilibrium analysis and association analysis.BMC Bioinformatics,2008,9:290
[11]Pritchard J K,Stephens M,Donnelly P.Inference of population structure using multilocus genotype data.Genetics,2000,155(2):945-959
[12]Wei Y L,Wei L,Zhao L,et al.A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents.Int J Legal Med,2016,130(1):27-37
[13]杨小林,席焕久,温有锋,等.人类毛发的形态学研究及法医学意义.解剖科学进展,2011,17(1):86-89Yang X L,Xi H J,Wen Y F,et al.Progress of Anatomical Sciences,2011,17(1):86-89
[14]刘丹,李上勋,周鑫,等.毛发分析的临床及法医学应用研究.中外医疗,2010,29(18):178-179Liu D,Li S X,Zhou X,et al.China Foreign Medical Treatment,2010,29(18):178-179
[15]Medland S E,Nyholt D R,Painter J N,et al.Common variants in the trichohyalin gene are associated with straight hair in Europeans.Am J Hum Genet,2009,85(5):750-755
[16]Medland S E,Zhu G,Martin N G.Estimating the heritability of hair curliness in twins of European ancestry.Twin Res Hum Genet,2009,12(5):514-518
[17]Liu F,Hamer M A,Heilmann S,et al.Prediction of male-pattern baldness from genotypes.Eur J Hum Genet,2016,24(6):895-902
[18]Wu S,Tan J,Yang Y,et al.Genome-wide scans reveal variants at EDAR predominantly affecting hair straightness in Han Chinese and Uyghur populations.Hum Genet,2016,135(11):1279-1286
[19]Walsh S,Liu F,Wollstein A,et al.The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA.Forensic Sci Int Genet,2013,7(1):98-115