犬17A STR 5色荧光检测试剂盒在警犬DNA鉴定中的应用研究

目的建立犬DNA检测方法。方法采用自主研发的多重PCR扩增体系和五色荧光（FAM、HEX、TAMRA、ROX和SIZ）自动化检测技术调查了犬DAmel和VWFX等16个STR基因座和1个性别决定基因座多态性,并计算该16个STR基因座的等位基因频率（P）、杂合度（H）、多态信息含量（PIC）和非父排除率（PE）。实验犬为11个品种231头犬。结果结果显示该16个STR位点的非父排除率（PE）和个体识别力（DP）分别为0.995026和0.999999992。结论显示研发的犬STR-DNA荧光检测试剂盒可作为犬DNA鉴定常规应用。     

犬11个STR基因座的遗传多态性

目的调查犬11个STR基因座的群体遗传多态性。方法应用自主构建的犬11个STR基因座（PEZ1、PEZ2、PEZ3、PEZ5、PEZ6、PEZ8、PEZ12、FH2010、FH2054、FH2132和FH2611）荧光复合扩增体系，扩增105只犬的样本，统计各基因座扩增结果，并分析其群体遗传参数。结果11个STR基因座的累积非父排除率和累积个体识别率分别为0．9330621和0．9999999．平均杂和度和平均多态信息含量分别为0．502和0．640。结论该11个犬STR基因座的遗传多态性较好，可以有效用于犬的个体识别和亲权鉴定。     

A proposal for standardization in forensic canine DNA typing: allele nomenclature of six canine-specific STR loci

In this study a proposal for the allele nomenclature of six polymorphic short tandem repeat (STR) loci (PEZ3, PEZ6, PEZ8, PEZ10, FHC2161, and FHC2328) for canine genotyping (Canis lupus familiaris) is presented. The nomenclature is based on the sequence data of the polymorphic region of the microsatellite markers as recommended by the DNA commission of the International Society of Forensic Haemogenetics (ISFH) in 1994 for human DNA typing. To cover commonly and rarely occurring alleles, a selection of homozygous and heterozygous animals were analyzed and subjected to sequence studies. The alleles consisted of simple tri- and tetra-nucleotide repeat patterns as well as compound and highly complex repeat patterns. Several alleles revealing the same fragment size but different repeat structures were found. The allele designation described here was adopted to the number of repeats, including all variable regions within the amplified fragment. In a second step the most commonly occurring alleles were added to an allelic ladder for each marker allowing a reliable typing of all alleles differing in size. A total number of 142 unrelated dogs from surrounding municipal animal homes, private households, and canines in police duty were analyzed. The data were added to a population database providing allele frequencies for each marker.     

The effect of linkage on the calculation of DNA match probabilities for siblings and half siblings

The loci in many forensic multiplexes are often selected to avoid linked loci. However as the multiplices used increase in the number of loci represented instances are occurring of loci that are loosely linked. As yet little attention has been paid to the likely consequence of this. We begin the process of developing formulae to give the match probability at two linked loci for full and half siblings. The methodology proceeds from the previously published joint IBD states for two linked loci [B.K. Suarez, J. Rice, T. Reich, The generalized sib pair IBD distribution: its use in the detection of linkage, Ann. Hum. Genet. Lond. 42 (1978) 87; J.K. Haseman, R.C. Elston, The investigation of linkage between a quantitative trait and a marker locus, Behav. Genet. 2 (1972) 3-19]. Our formulation has the drawback of assuming linkage equilibrium. This assumption may be tenable as a first order approximation. We hope to stimulate work on developing better treatments.     

The effect of linkage on the calculation of DNA match probabilities for siblings and half siblings

The loci in many forensic multiplexes are often selected to avoid linked loci. However as the multiplices used increase in the number of loci represented instances are occurring of loci that are loosely linked. As yet little attention has been paid to the likely consequence of this. We begin the process of developing formulae to give the match probability at two linked loci for full and half siblings. The methodology proceeds from the previously published joint IBD states for two linked loci [B.K. Suarez, J. Rice, T. Reich, The generalized sib pair IBD distribution: its use in the detection of linkage, Ann. Hum. Genet. Lond. 42 (1978) 87; J.K. Haseman, R.C. Elston, The investigation of linkage between a quantitative trait and a marker locus, Behav. Genet. 2 (1972) 3–19]. Our formulation has the drawback of assuming linkage equilibrium. This assumption may be tenable as a first order approximation. We hope to stimulate work on developing better treatments.     

Genetic polymorphism revealed by 13 tetrameric and 2 pentameric STR loci in four Mongoloid tribal population

The short tandem repeat allelic profiles at to 15 autosomal polymorphic loci were analyzed in four tribal populations of Mizoram (India). The analysis was performed on 354 unrelated healthy individuals belonging to Mongoloid races. All the samples were subjected to sex test (Amelogenin marker) besides the STR typing and in all instances; it has shown no deviation from expectation. The allele frequencies for all the analyzed loci in the studied populations are within expected range in comparison to the populations from same racial background. No significant deviation from the Hardy-Weinberg Equilibrium was observed for all the populations. In no cases the observed heterozygosity is less than that of expected values and it varied from 0.978 (Penta E) to as low as 0.425 (THO1). The discriminatory power and exclusion probability values for all the analyzed markers are significantly high and thus reveal high forensic significance. There is no evidence for association of alleles among the 15 studied loci. This allele frequency data will be useful for human identity testing in Mizo population.     

DNATyper^TM15基因座的研究与选择

目的为研发复合扩增荧光检测试剂盒,对现有的STR基因座进行分析研究并优选新的高鉴别力基因座。方法收集汉族、锡泊族、畲族、壮族、藏族等5个民族群体血样共1200份,提取DNA,应用复合扩增方法检测1200名5个民族群体无关个体的24个基因座的等位基因分布。结果TPOX和TH01基因座的等位基因在5个民族群体中分布不平衡;D2S1338、D6S1043和Penta E等3个STR基因座在5个民族群体中均具有高度遗传多态性,等位基因频率分布均匀,在各群体间无显著差异,而且等位基因传递遵循孟德尔遗传规律。结论确定出DNATyperTM15试剂盒中的14个适合中国人群体遗传学特征和法医学应用的STR基因座。     

A new 15 autosomal STRs multiplex for domestic horse genotyping

Horse genotyping has a wide range of applications such as identification, pedigree verification, parentage test, forensic investigation, population genetics, analysis of diversity, legitimate registration, among others. Following the recommendations of the International Society for Forensic Genetics (ISFG) regarding the use of non-human (animal) DNA in forensic genetic investigations we have developed a multiplex PCR system of 15 autosomal tetra-nucleotide STRs loci to Equus caballus. The system includes the newly described ECAC2, ECAC4, ECAC5, ECAC9, ECAC10, ECAC12, ECAC14, ECAC15, ECAC18, ECAC21, ECAC23, ECAC26, ECAC28, ECAC29 and ECAC30 loci (on chromosomes 2, 4, 5, 9, 10, 12, 14, 15, 18, 21, 23, 26, 28, 29 and 30, respectively). The polymorphism is in average 8 alleles per marker with a maximum of eleven and a minimum of five for the population studied. All markers were in Hardy–Weinberg equilibrium, except ECAC5 (p = 0.0007). The probabilities of paternity (W), exclusion (PE) and cumulative discrimination (PD) for all loci were greater than 0.9999. This work will contribute to the implementation of standardized horse genotyping systems in the forensic community and the horse industry.     

4个miniSTR基因座复合扩增体系及应用

目的构建D6S474、D20S482、D4S2408、D6S1017等4个miniSTR基因座复合扩增体系,评价其对腐败检材的应用价值,调查4个基因座在汉族人群中的遗传多态性。方法采用不同荧光标记4个miniSTR基因座上游引物,构建复合扩增体系。用分子克隆方法制备等位基因分型标准物。采用上述体系对135份汉族无关个体血样进行检测,并计算群体遗传学参数。比较该体系与ID试剂盒在降解检材分析中的成功率。结果采用本文复合扩增体系检测,汉族人群中4个基因座基因型频率分布均符合Hardy-Weinberg平衡定律,累积个人识别能力为0.999 666,累积非父排除率为0.914 902。本文体系较ID试剂盒对自然腐败检材的分型成功率更高。结论 4个miniSTR基因座复合扩增体系对法庭科学实践,特别是对腐败检材的检测有应用价值。     

Evaluation of the DNA stability of forensic markers used in betel-quid chewers' oral swab samples and oral cancerous specimens: implications for forensic application

Chewed betel-quid (BQ) residues are often considered vital biological evidence at crime scenes, since the human DNA extracted from the residues is actually from buccal epithelial cells and can be associated with suspects. BQ-chewing is also a risk factor for oral diseases and/or cancers. Archived medical oral-specimens can be used to identify specific individuals under adverse conditions, although STR markers are known to be unstable in various tumor tissues. This study evaluates the DNA stability of forensic marker systems in BQ-chewers' oral epithelial cells, and in archived clinical specimens of oral cancer patients. The genotypes of oral and paired peripheral blood samples in 200 subjects were compared, using the commercialized typing systems of HLA-DQA1, PM (including LDLR, GYPA, HBGG, D7S8, and GC loci), and AmpFlSTR markers (including 9 STR loci and the Amelogenin gene). The 100 healthy BQ-chewers had consistent oral swab and paired blood sample genotypes analyzed withboth DQA1/PM and STR marker systems. In the 100 oral cancer patients, one discordant result at D7S8 was found in the 600DQA1/PM-marker loci, and 25 allelic alterations with expansion or contraction were detected in the 900 STR loci. The findings herein suggest that when cancerous specimens were tested, the HLA-DQA1/PM system with point polymorphism appears more reliable than the STR system with length polymorphism. Our results also indicate that healthy BQ-chewers' oral cotton swabs containing buccal epithelial cells are useful for forensic purposes using the HLA-DQA1, PM, and STR marker systems.     

中国东部蒙古族人群15个STR基因座多态性研究

目的调查15个STR基因座在中国东部蒙古族人群中的基因频率分布。方法应用四色荧光标记引物复合扩增技术,对105名东部蒙古族无关个的血样15个STR基因座进行多态性研究。结果在东部蒙古族人群中15个STR基因座偶合率在0.0084～0.2169之间,个体识别概率(DP)在0.7831～0.9916之间,杂合度在0.5619～0.9231之间,三联非父排除率(PE)在0.4490～0.8444之间,多态性信息总量(PIC)在0.5438～0.9178之间,15个STR基因座总TDP值为0.9999999999998,所有基因座经χ2检验符合Hard-Weinberg平衡。结论上述15个STR基因座在东部蒙古族人群中等位基因分布较好,个体识别率高,适合法医个体识别和亲子鉴定。     

中国鄂温克族人群15个STR基因座多态性研究

目的调查15个STR基因座在中国鄂温克族人群中的基因频率分布。方法应用PowerPlex16System复合扩增系统,对99名鄂温克族无关个的血样DNA进行多态性研究。结果在鄂温克族人群中15个STR基因座偶合率(Pm)在0.0205～0.1733之间,个体识别概率(DP)在0.8267～0.9795之间,杂合度在0.6061～0.9091之间,三联非父排除率(PE)在0.4038～0.7690之间,多态性信息总量(PIC)在0.5985～0.8734之间,15个STR基因座总TDP值为0.9999999999998,所有基因座经χ2检验符合Hard-Weinberg平衡。结论上述15个STR基因座在鄂温克族人群中等位基因分布较好,个体识别率高,适合法医个体识别和亲子鉴定。     

共有基因数在同胞鉴定中应用的研究

目的　探索利用两个体间共有基因数目资料进行同胞关系鉴定的应用价值。方法　根据 80 7对同胞及无关个体的 13个STR基因座的分型结果 ,进行统计学计算。结果　同胞间及无关个体间共有基因数目均符合正态分布 ,分别得到同胞及无关个体关系的判别函数和后验概率 ,以及该方法的平均错判率。其中同胞组判别函数为 :L同胞 =-2 7 0 870 3 +3 2 0 2 3 2S (S为共有基因个数 ) ;无关个体组判别函数为 :L无关 =-7 495 63 +1 685 0 9S ,用上述判别函数进行同胞 /无关个体关系判别时的平均错判率为 0 0 2 65。结论　当共有基因数目大于 17或小于 8时 ,两个体为同胞或无关个体的后验概率分别大于 0 9980和 0 9994。此方法不失为同胞关系鉴定的可信度较高的方法。     

Selection of twenty-four highly informative SNP markers for human identification and paternity analysis in Koreans

A number of DNA marker types suitable for human identification and parentage testing have been developed, of which single nucleotide polymorphisms (SNPs) merit attention as they are abundant, genetically stable, and amenable to high-throughput automated analysis. In this regard, 24 highly informative SNP markers representing each 22 autosome and both sex chromosomes were selected, and the allele and genotype frequencies of these SNPs were determined in a group composed of 30 unrelated Koreans. Based on frequency data from this group, the estimated probability of identity (P(I)) and probability of paternity exclusion (P(E)) with 22 autosomal SNP loci were 1.905x10(-10) and 98.9%, respectively. The SNPs in this study offer a small but highly accurate database that will be an essential reference for SNP-based forensic application in the future.     

Genetic polymorphism of 14 non-CODIS STR loci for forensic use in southeast China population

We investigated 14 polymorphic STR loci (D1S2142, D2S1360, D3S1545, D7S1517, D10S2325, D12S391, D13S1492, D14S306, D15S659, D16S3253, D18S1270, D19S253, D20S470, D21S1437) which are not included in the standard sets of forensic loci (CODIS) in a sample of 216 unrelated healthy southeast Chinese individuals. The studied loci were highly informative and did not show departures from Hardy-Weinberg equilibrium. The accumulated powers of discrimination and power of exclusion for the 14 loci were 99.9999999999 and 99.999998%, respectively. No linkage was observed between the 14 loci and the traditional set of STR markers included in commercially available kits (the AmpFLSTR IdentifilerTM 15 System loci). We thus considered the studied 14 STRs are informative and when necessary, can be used as the candidate genetic markers in the study and application in genetics and forensic practice.     

A cautionary note on the evaluation of genetic evidence from uniparentally transmitted markers

The combination of the information obtained from lineage genetic markers, such as mitochondrial DNA (mtDNA) and the non-homologous region of Y-chromosome, with data resulting from meiotically recombining loci (diploid/autosomal or haplodiploid/X chromosome) into a single likelihood ratio has been recently proposed. In this work we challenge this proposal and demonstrate that while the genetic evidence obtained from loci which reshuffle at meiosis is appropriate for individual probability calculations, mtDNA and Y-chromosome data are not and, consequently, that joining the evidential value of the two types of markers is generally inconsistent and should be avoided. The assumption of non-involvement of relatives must be clearly and explicitly stated and its acceptance must be left to the court decision.     

Evaluation of gastrointestinal cancer tissues as a source of genetic information for forensic investigations by using STRs

Malignant tissue samples may sometimes be the only source of biological material for forensic investigations, including identification of individuals or paternity testing. However, in use of such samples, uncertainties due to microsatellite instability (MSI) and loss of heterozygosity (LOH) often associated with neoplasias may be encountered. In this study, we have analysed the applicability of autosomal tetranucleotide short tandem repeat (STR) markers, which are routinely used in forensic analysis, to gain genetic information. MSI and LOH were analysed in 41 surgically removed gastrointestinal cancer specimens and the adjascent non-cancerous tissue marginals. The cancer specimens showed great variability in their genetic phenotypes due to MSI or LOH, with only 32% being microsatellite-stable. Of the 15 autosomal STR loci analysed, only TH01 had no MSI-type alteration in these samples. The loci most frequently affected by MSI were D8S1179, D21S11, D18S51 and D19S433 (MSI in 15-17% of cases). LOH-type alterations were observed at all of the loci, including the amelogenin locus used for sex determination. The highest LOH frequency was found at locus D18S51 (27%). The genetic alterations at the marker loci may indicate false homozygosity or heterozygosity, and false gender may result from erroneous deduction of DNA profiles. Therefore, typing of autosomal STRs from malignant tissues in forensic settings warrants careful interpretation of MSI and LOH results together with microscopic analysis of a tissue specimen. Results by two commercially available and widely used forensic DNA profiling kits used here were comparable.     

Genetic Polymorphisms of four X-STR Loci: DXS6797, DXS6800, HPRTB and GATA172D05 in a Peruvian population sample

The X linked short tandem repeats (STR) markers have proven to be very useful tools for paternity testing when the disputed child is female. The purpose of this study was to describe the genetic polymorphism of four X-chromosomal STR loci (DXS6797, DXS6800, HPRTB and GATA172D05) in a Peruvian population sample and evaluate their efficiency in forensic practice and paternity testing.     

Forensic Identification Using a Multiplex Assay of 47 SNPs*

Abstract: As a powerful alternative to short tandem repeat (STR) profiling, we have developed a novel panel of 47 single nucleotide polymorphisms (SNPs) for DNA profiling and ABO genotyping. We selected 42 of the 47 SNPs from a panel of 86 markers that were previously validated as universal individual identification markers and identified five additional SNPs including one gender marker and four ABO loci. Match probability of the 42 validated SNPs was found to be 9.5 × 10^?18 in Han Chinese. SNP analysis correctly assessed a panel of historical cases, including both paternity identifications in trios and individual identifications. In addition, while STR profiling of degraded DNA provided information for 11 loci of 16 potential markers with low peak intensities, SNPstream^® genotyping was sufficient to identify all 47 SNPs. In summary, SNP analysis is equally effective as STR profiling, but appears more suited for individual identification than STR profiling in cases where DNA may be degraded.     

Informativeness of the CODIS STR loci for admixture analysis

Population admixture (or ancestry) is used as an approach to gene discovery in complex diseases, particularly when the disease prevalence varies widely across geographic populations. Admixture analysis could be useful for forensics because an indication of a perpetrator's ancestry would narrow the pool of suspects for a particular crime. The purpose of this study was to use Fisher's information to identify informative sets of markers for admixture analysis. Using published founding population allele frequencies we test three marker sets for efficacy for estimating admixture: the FBI CODIS Core STR loci, the HGDP-CEPH Human Genome Diversity Cell Line Panel and the set of 39 ancestry informative SNPS from the Shriver lab at Pennsylvania State University. We conclude that the FBI CODIS Core STR set is valid for admixture analysis, but not the most precise. We recommend using a combination of the most informative markers from the HGDP-CEPH and Shriver loci sets.