Amelogenin等位基因丢失的研究现状

Amelogenin基因座作为性别标记包含于常用的商品化STR分型试剂盒中,被应用于法医亲子鉴定、个体识别和DNA数据库等。大量报道显示Amelogenin基因可发生变异,导致X染色体或Y染色体特异性产物扩增失败,即AMELX或AMELY丢失。AMELY丢失可导致性别判断错误,性别错判可误导侦查方向。下面对近年来国内外Amelogenin基因座等位基因丢失现象的研究现状进行综述,探讨Amelogenin基因座的变异频率、变异类型、变异机制及其对性别鉴定的影响和应对方法,为准确地进行法医物证性别鉴定提供帮助。     

疑似Amelogenin等位基因丢失的检测与分析12例

目的观察并分析亲权鉴定案件中Amelogenin等位基因丢失的案例,探讨Amelogenin等位基因丢失的类型、机制以及对性别鉴定的影响和应对方法。方法选择经Si Fa STRTM 23plex DNA身份鉴定系统检测,女性出现Amelogenin X的峰面积与相邻杂合子峰面积一致或低于相邻纯合子峰面积的1/2,男性出现Amelogenin X丢失的样本,进行X-STR分型及Amelogenin X测序,同时对出现Amelogenin Y丢失的男性样本,检测Y-STR分型及Y染色体性别决定区(sex-determining region of Y,SRY)进行验证。统计Amelogenin等位基因丢失的类型及丢失率,分析出现变异的机制及影响。结果 1例男性Amelogenin X等位基因丢失,经测序证实为引物结合区突变;4例女性疑似Amelogenin X等位基因丢失,经测序证实出现引物结合区突变的仅为1例。7例男性出现Amelogenin Y丢失,其中SRY阳性5例,SRY阴性2例。5例SRY阳性案件中4例可检出部分Y-STR分型,1例未检出Y-STR分型,2例SRY阴性案件均未检出Y-STR分型。Amelogenin等位基因丢失率约为0.029%。结论 Amelogenin X丢失不影响性别判定,Amelogenin Y丢失可能对性别造成误判,需要检测Y-STR或SRY来明确性别,对于未检出Y-STR分型且SRY检测为阴性的"男性",建议进行染色体核型分析及性别分化相关基因检测以进一步明确性别。     

27例Amelogenin基因等位基因Y丢失分析

牙釉质蛋白基因(Amelogenin,以下简称Amel)DNA技术是目前普遍采用的性别鉴定技术手段。在X-Y染色体同源引物扩增检测Amel基因图谱上,男性显示为双峰,获得X和Y染色体扩增产物;女性显示为单峰,获得X染色体扩增产物[1]。但Amel-Y缺失或异常都可导致无法获得Y染色体扩增产物,从而导致性别的错判,使侦查走向歧途[2]。     

男性个体Amelogenin基因座Y片段缺失1例

在法医学实践中．扩增Amelogenin基因是进行生物样本的性别鉴定的主要方法，并为大多数的商品化法医鉴定试剂盒如AmpFlSTR IdentifierTM（ABI）、PowerPlex（Promega）等所采用。但个体的Amelogenin基因如果发生突变，致X或Y特异片段扩增失败，则可能导致错误的性别判定。     

Amelogenin基因遗传变异及其法医学应用研究进展

人类牙釉质蛋白基因(Amelogenin, AMEL)为X、Y染色体同源基因,分别称为AMEL-X和AMEL-Y。根据二者在扩增序列大小的不同可以确定性别,在法医学实践和临床医学等应用中具有重要意义。但是,AMEL基因在不同个体和人群中的遗传变异而导致性别决定并不是100%准确;通常由于特异性产物扩增异常,有可能导致性别错判。本文重点从AMEL基因的遗传变异、分型技术、以及引起性别误判的应对策略方面进行综述。     

一种用于降解DNA样本的性别鉴定方法

目的 建立一种采用PCR技术对降解DNA样本进行性别鉴定的新方法。方法 采用针对amelogenin基因X染色体外显子3bp缺失设计的引物AMELU1及AMELD1,对在室温环境下放置5－15年的男、女血痕标本各50例、毛发各20例、骨骼各20例以及现场提取5－－20天的男、女腐败肌肉各10例标本中提取的降解DNA样本进行扩增。用PGA（9％T,3％C）电泳、银染显带检测扩增产物。结果 所有样本均得到正确结果,男性检材表现为83bp的Y特异性及80bp的X特异性2条谱带,而女性检材仅有1条80bp的X特异性谱带。结论 用针对amelogenin基因X染色体外显子3bp缺失设计的引物AMELU1及AMELD1鉴定性别的方法灵敏、可靠、方便,是降解DNA检材性别鉴定十分理想的方法。     

一种用于降解DNA样本的性别鉴定方法

目的　建立一种采用PCR技术对降解DNA样本进行性别鉴定的新方法。　方法　采用针对amelogenin基因X染色体外显子 3bp缺失设计的引物AMELU1及AMELD1,对在室温环境下放置 5～ 15年的男、女血痕标本各 5 0例、毛发各 2 0例、骨骼各 2 0例以及现场提取 5 - - 2 0天的男、女腐败肌肉各 10例标本中提取的降解DNA样本进行扩增。用PAG( 9%T ,3 %C)电泳、银染显带检测扩增产物。　结果　所有样本均得到正确结果 ,男性检材表现为 83bp的Y特异性及 80bp的X特异性 2条谱带 ,而女性检材仅有 1条 80bp的X特异性谱带。　结论　用针对amelogenin基因X染色体外显子 3bp缺失设计的引物AMELU1及AMELD1鉴定性别的方法灵敏、可靠、方便 ,是降解DNA检材性别鉴定十分理想的方法。     

扩增X—Y同源Amelogenin基因内含子在性别鉴定中的应用研究

本文用一对针对X－Y同源的Amelogenin基因第一内含子的引物，于同一试管中分别扩增出针对于x和Y染色体的特异性DNA片段：106bp及112bp的PCR产物，经聚丙烯酰胺凝胶电泳后用银染法观察扩增结果，取得了满意的效果．对50pgDNA模板室温放置16年的血痕及单根毛发、烟头等检材均可得到明确的性别鉴定结果．本实验证明该方法简便、灵敏、可靠、特别适用于腐败降解检材的法医学性别鉴定．     

1例Turner患者Amelogenin和STR基因座分型及核型分析

应用Amelogenin基因座和染色体核型分型技术,对一名10岁,社会性别为女性、Amelogenin基因座为＂X,Y＂的儿童进行亲子鉴定,结果否定女童的亲子关系并判断女童是Turner综合征患者,现报道如下。     

考古样品中Amelogenin同源基因的提取和检测

目的利用人类性染色体Amelogenin同源基因在X、Y染色体上序列长度的差异,选择设计引物,对考古样本进行古DNA性别信息研究。方法采用苯酚/氯仿-二氧化硅-超滤离心方法提取东岭墓葬群殉人骨骼、牙齿古DNA,PCR扩增,非变性聚丙烯酰胺凝胶电泳(PAGE)分离和检测古DNA扩增片段。结果8个墓葬16个样品中有7个样品出现阳性扩增检测,目标基因片段清楚,男性为二条带(X、Y),女性为一条带(X),牙齿样品检测成功率优于骨骼样品。结论改进的苯酚/氯仿—二氧化硅—超滤分离法是较好的古DNA提取方法,具有降低PCR抑制剂、消耗成本低和提取成功率高等特点。基于人类X、Y染色体Amelogenin同源基因的古DNA性别分析方法可成为分子考古重要的技术方法。     

Higher failures of amelogenin sex test in an Indian population group

The human sex test in forensic multiplexes is based on the amelogenin gene on both the X and Y chromosomes commonly used in sex genotyping. In this study of 338 male individuals in a Malaysian population comprising Malays, Chinese and Indians, using the AmpFlSTR Profiler Plus kit, the amelogenin test gave a significant proportion of null alleles in the Indian ethnic group (3.6% frequency) and 0.88% frequency in the Malay ethnic group due to a deletion of the gene on the Y chromosome. This sex test also failed in a forensic casework sample. Failure of the amelogenin test highlights the need for more reliable sex determination than is offered by the amelogenin locus in the Malay and Indian populations. The gender of the Indian-Malay amelogenin nulls was confirmed by the presence of three Y-STR alleles (DYS438, DYS390 and DYS439). For the Indian ethnic group, one of the Y-STR forms a stable haplotype with the amelogenin null. The amelogenin-deletion individuals also showed a null with a male-specific minisatellite MSY1, indicating that a very large deletion was involved that included the amelogenin and the MSY1 loci on the short arm of the Y chromosomes (Yp).     

A distinct Y-STR haplotype for Amelogenin negative males characterized by a large Y(p)11.2 (DYS458-MSY1-AMEL-Y) deletion

The use of STR multiplexes with the incorporated gender marker Amelogenin is common practice in forensic DNA analysis. However, when a known male sample shows a dropout of the Amelogenin Y-allele, the STR system falsely genotypes it as a female. To date, our laboratory has observed 18 such cases: 12 from our Y-STR database and six from casework. A study on 980 male individuals in the Malaysian population using the AmpFlSTR Y-filer has revealed a distinct Y-chromosome haplotype associated with the Amelogenin nulls. Our results showed that whilst the Amelogenin nulls were noticeably absent among the Chinese, both the Indians and Malays exhibited such mutations at 3.2 and 0.6%, respectively. It was also found that the Amelogenin negative individuals predominantly belonged to the J2e lineage, suggesting the possibility of a common ancestor for at least some of these chromosomes. The null frequencies showed concordance with the data published in Chang et al. [Higher failures of Amelogenin sex test in an Indian population group, J. Forensic Sci. 48 (2003) 1309-1313] on a smaller Malaysian population of 338 males which used a Y-STR triplex. In the current study, apart from the absence of the Amelogenin Y-locus, a complete absence of the DYS458 locus in all the nulls was also observed. This study together with the 2003 study has indicated a similar deletion region exists on the Y(p)11.2 band in all the 18 Y-chromosomes. Using bioinformatics, this deletion has been mapped to a region of at least 1.13 Mb on the Y(p)11.2 encompassing the Amelogenin, MSY1 minisatellite and DYS458 locus. Further, the Y-filer haplotypes revealed an additional null at Y-GATA H4 in two of the Indian males presented here.     

A Y‐Chromosomal Haplotype with Two Short Tandem Repeat Mutations*

Abstract:  The male‐specific Y‐chromosomal short tandem repeat (STR) is a useful tool in forensic casework. The Y haplotype comprised of 16 loci, which is amplified simultaneously by AmpFlSTR^® Yfiler^TM PCR kit and provides strong exculpatory evidence in individual identification. We reported a rare Y‐STR profile with a null allele at the DYS448 locus and an off‐ladder allele at the DYS456 locus, when genotyping material from a vaginal swab in an alleged rape case. Sequence analysis revealed that the DYS448 null allele was a true type of null allele because of a total deletion of 11 upstream repeats and 9 bp of the N₄₂ region, and there were numerous primer binding site mutations as well. The amplicon of the DYS456 locus was a small 92‐bp fragment that was off‐ladder, and sequencing analysis showed that there were only 10 repeats (AGAT)₁₀. This Y chromosome haplotype that was comprised of two variations provided helpful evidence for personal identification.     

Male amelogenin dropouts: phylogenetic context, origins and implications

Several commercial PCR multiplex kits incorporate the amelogenin locus for the purpose of human gender identification. Consequently, erroneous results in the electropherogram profile of this locus can carry important forensic implications. In this study, dropout of the amelogenin Y allele was detected in 5 out of 77 phenotypically normal Kathmandu males using the AmpFlSTR Identifiler kit. A battery of male-specific markers including SNPs, STRs, STSs, and a minisatellite were amplified for the five amelogenin null samples in order to delineate the breakpoints of the deletions as well as assess the overall integrity of the Y-chromosome. This study represents the first to examine the haplogroup affiliation of the AMGY deletions. The analyses performed suggest a single origin for the five deletions as indicated by their allocation to a specific Y-haplogroup (J2b2-M241), related Y-STR haplotypes and identical regional localization of breakpoints. The age estimated from the microsatellite variation for the amelogenin deletions (if they are associated by descent) is approximately 6.5+/-3.3 ky, younger than the previously reported related age of the M241 haplogroup representatives (13-14 ky). Our data in combination with previous publications suggest a concentration of afflicted individuals in the Indian subcontinent, possibly as a result of common ancestry. The elevated incidence of the amelogenin dropout in these populations accentuates the need to utilize other loci for gender determination in order to obtain an accurate set of inclusion criteria in forensic casework.     

Alternative primers for DYS391 typing: advantages of their application to forensic genetics

The amplification of the STR DYS391, using the primers described in the Genome Data Base (GDB: G00-365-251), shows not only an additional band to the Y-specific one in males with a size range of 26 bp less than those of DYS391 locus alleles, but also a polymorphic pattern in females in the same size range as the additional band observed in males. The DYS391 pattern in families reflects a Y-specific linked locus and also a polymorphic X locus with an X-linked pattern of inheritance. A first screening in the X homologous locus allowed the identification of five different alleles. Allele frequencies were explored in different population groups for both the Y locus and the homologous locus in the X chromosome showing a similar allele distribution pattern in the X and Y homologous loci. An alternative reverse primer was designed to amplify the Y-chromosome specific STR in order to improve the specificity and applicability of this system to forensic genetics. Comparative results of the amplification with the new and the previously described primers proved that with this new primer there is a substantial increase in the specificity of the amplification. Moreover, a smaller fragment is amplified with a size out of the range of the alleles of the other Y-STRs usually used in forensic applications, therefore simplifying its inclusion in multiplex systems.     

中国汉族人群17个Y-STR基因座突变情况分析

目的 调查分析17个Y-STR基因座等位基因突变的情况.方法 收集中国汉族人群867对父子共1 649份男性血样本.采用YfilerTM复合扩增试剂盒进行17个Y-STR基因座分型,共检测出14 739次等位基因传递,统计各基因座发生等位基因突变的频率.结果 在17个基因座中发现涉及13个基因座共41次突变,其中一步突变40次(97.6％),两步突变1次(2.4％);突变共涉及40对父子,其中39对仅1个基因座发生突变(97.5％),1对同时有2个基因座发生突变(2.5％);平均突变率为2.8×10-3(95％CI 2.0～3.8×10-3).等位基因突变时获得重复单位数19次,丢失重复单位数22次,两者比例接近.结论 中国汉族人群Y-STR基因座突变可涉及多数基因座,突变率在2.8×10-3左右,在数据库的建立与应用中应重视,注意采用相关方法进行甄别.     

中国人群亲权鉴定常用STR基因座平均突变率的估计

目的对亲权鉴定中常用STR基因座在中国人群中的平均突变率进行估计,并与美国人群中的相应数据进行比较。方法突变数据来自按拟定标准筛选获得的15篇国内文献及本中心数据。对中国不同地区同一STR基因座突变率无显著差异的突变数据进行合并,计算中国人群该STR基因座的平均突变率,并采用Poisson分布的近似正态分布法计算该STR基因座平均突变率的95%可信区间。对中国人群和美国人群中常用STR基因座平均突变率的95%可信区间进行比较。结果 Identifiler和PowerPlex 16两个系统所包含的17个亲权鉴定常用STR基因座在中国不同地区人群中的突变率无显著差异,合并计算其平均突变率介于0.0120%～0.2078%,不同STR基因座的平均突变率差异显著（P〈0.0001）。这17个亲权鉴定常用STR基因座在中国人群中的累积突变率达到1.9836%。结论本研究通过文献分析获得中国大样本人群的FGA等17个STR基因座突变率数据,对于疑似突变案例的累积亲权指数计算具有借鉴价值。     

联合应用STR和SRY基因分型技术分析性分化异常者

目的对Amelogenin分型结果为“X,X”的一名“男孩”进行性别确认。方法采用STR检测和SRY基因检测技术进行分析。结果孩子STR、X-STR的检验结果符合女性性别特征,SRY基因检测结果为阴性。结论应用STR、X-STR检测和SRY基因检测技术可以确证“男孩”Amelogenin基因座结果为“X,X”,推断其患有“46,XX”男性性反转综合症。     

Sex identification of forensic specimens by polymerase chain reaction (PCR): two alternative methods

Sex identification of forensic samples (bloodstains and decomposed tissue) by polymerase chain reaction (PCR) was investigated. Amplification of a segment of the amelogenin gene using a pair of primers revealed both Y- and X-specific bands at the same time. The gene has counterparts in both the X and Y chromosomes and a small deletion in the former made it possible to distinguish them. Analysis of the X-specific band is the most reliable method for sex identification. THe locus includes a single copy gene so a sample of 250 ng/tube of deoxyribonucleic acid (DNA) is required for identification. Amplification of part of the DYZ1 locus was attempted as an alternative method for analysis of infinitesimal amounts of sample. Even DNA from putrefied tissue could be analyzed by PCR because the locus consists of thousands of copies of repeating units pHY10.     

Sequence characterization of microvariant alleles at DYS627 and DYS458

Y chromosome short tandem repeats (Y-STRs) have been widely used in genetic applications and forensic casework. Recently, we found two intermediate alleles, the DYS627 allele 24.1 and the DYS458 allele 15.3, from Chinese Han population. The two allelic variants have not been recorded by the YHRD database. We have examined the molecular structure of these allelic variants by Sanger sequencing. The results showed that this intermediate allele at DYS627 was confirmed as 24.1, the sequence of which showed a base “A” insertion in the 13th repeat unit, and the intermediate allele at DYS458 was confirmed as 15.3, the sequence of which showed a base “G” deletion in the 12th repeat unit. This may be important for individual identification and paternal kinship testing. Besides, more allelic variants detected can be enriched in the Y-STR database.