Use of polymerase chain reaction of the HLA-DQ alpha system in forensic trace analysis]

The polymerase chain reaction (PCR) can be used for genetic typing of minute amounts of biological stains. This is achieved by in vitro amplification of a well-defined and genetically polymorphic human genomic DNA sequence. Using the HLA-DQ alpha system, a population study was carried out among 212 unrelated individuals of German origin. The usefulness of this system is discussed by presenting examples of its application in forensic casework, i.e. the analysis of mixed (male/female) body fluids as well as segregation studies on embryonic and paraffin-embedded tissue samples.     

PCR-based detection of HLA-DQ alpha and polymarker loci and their application in forensic science

Studies were conducted to evaluate the forensic applicability of multiplex amplification of HLA-DQ alpha and PM loci. These loci could be simultaneously typed by reverse dot blot approach where allele specific oligonucleotide probes were immobilized on a nylon membrane strip. Allele and genotype frequencies for HLA-DQ alpha and PM loci were determined in Chinese Han population. The frequency data can be used in individual identification and paternity test.     

D6S1043和D12S391基因座在亲权鉴定中的应用

目的研究D6S1043和D12S391基因座在亲权关系鉴定案件中的应用价值。方法应用荧光标记复合扩增系统对日常检案中所收集的192名汉族无关个体血样DNA进行PCR扩增,用ABI3100-Avant遗传分析仪对扩增产物进行毛细管电泳,用GeneMapperv3.2软件进行基因分型,统计分析D6S1043和D12S391基因座的多态信息。结果在D6S1043和D12S391基因座分别发现12个等位基因,它们在中国汉族人群中的个体识别能力分别为0.9656和0.9510,二联体非父排除率分别为0.573和0.510,三联体非父排除率分别为0.731和0.679。结论D6S1043和D12S391基因座具有高度多态性,在亲权鉴定中具有重要应用价值。     

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.     

Simultaneous detection of multiple STR loci on sex chromosomes for forensic testing of sex and identity.

The forensic usefulness of X and Y chromosomal STR loci has recently been demonstrated. One quadruplex-PCR, using 2 X- and 2 Y-STRs (STRX1/HPRTB and DYS390/ DYS393), and 2 duplex-PCRs, each using an X- and a Y-STR (ARA/DYS390 and ARA/DYS393), and detection of PCR products by using an automated DNA sequencer are reported herein. This approach allows us to determine not only the sex of the donor of a sample, but also the X- and/or Y-STR genotypes of the sample. A male biological specimen yields 4 amplified products in quadruplex-PCR and 2 amplified fragments in duplex-PCRs, whereas a female biological specimen yields only 2 amplified fragments of X-STR in quadruplex-PCR and one fragment, also of X-STR, in duplex-PCRs. Our study thus provides useful information for many activities in forensic practice, such as identity testing, paternity testing, especially of deficiency cases, compilation of population data, and sex determination of a biological sample from a single PCR.     

D1S80等位点在法医物证鉴定中应用价值评估

比较D1S80 ,DQA1+PM和CTT等位点在法医物证鉴定中应用情况 ,经研究发现 ,D1S80位点识别能力较强 ,基因遗传稳定 ,其电泳检测操作简单 ,易推广 ;DQA1+PM位点扩增片段较短 ,反向斑点杂交法灵敏度高 ,特别适用于陈旧、降解和微量生物检材的鉴定 ;CTT位点的荧光检测法稳定、可靠 ,实验结果便于保存和管理。总之 ,D1S80、DQA1+PM和CTT位点的遗传符合孟德尔定律 ,分型简便、可靠 ,在亲子鉴定和个人识别中发挥重要作用。     

复合扩增D16S539、D7S820、D13S317基因座的DNA分型及法医学应用

通过对3个位于不同染色体上的STR基因座（D165539,D7S820,D13S317）所组成的复合扩增体系的DNA分型研究,以期在实际法医物证检验中增加检验基因座,以提高总的个体识别率。笔者运用复合扩增技术,经4％变性聚丙烯酸胺凝胶电泳分离扩增产物和银染检测,首次对108个无关中国人个体的D16S539,D7S820,D13S317基因座进行研究,检测出中国人群中3个基因座的等位基因数均为7个;偶合率P（m）分别为0．0847、0．0740、0．0741;个体识别率DP值分别为0．9153、0．9260、0．9259;杂合度分别为77．7％、79.1％、79．3％;各基因座亲子关系指数PItypical分别为2．24、2．39、2．42。3个STR基因座总的个体识别率很高,达0．9995;总的亲子关系指数PItypical达12．96;所有基因座经卡方检验符合Hardy－Weinberg平衡。通过以上数据可以看出,D165539,D7S820,D13S317基因座所组成的复合扩增体系在中国人群中等位基因分布较好,个体识别率很高,适合用于法医个体识别及亲子鉴定。     

Rapid and sensitive quantitation of cyanide in blood and its application to fire victims.

We developed a head-space method for the determination of blood cyanide by gas chromatography with electron-capture detection. In this technique, a reaction precolumn packed with chloramine-T was used for the conversion of hydrogen cyanide into cyanogen chloride. Since the reaction precolumn eliminated the necessity of trapping hydrogen cyanide from biological samples, blood cyanide could be analyzed quickly by acidification only. Using this method, blood cyanide levels of fire victims were determined at autopsy. The serum values of cyanide ranged from 0.11 micrograms/ml to 18.12 micrograms/ml. However, a significantly higher cyanide content was detected in the left ventricular blood than in the right. This indicates that death was caused by the fire and suggests that the collecting point of the blood sample is an important factor in the determination of inhaled cyanide. There was a positive correlation between blood cyanide and carboxyhemoglobin contents.     

上海地区D1S80位点基因频率分布及其在亲子鉴定中的应用

目的：将D1S80位点的DNA多态性分析应用于亲子鉴定。方法;PCR、聚丙烯酰胺凝胶电泳及溴已锭染色。结果：获得D1S80位点的DNA多态性分布数据。结论：D1S80位点的PCR检测方法可成功地用于亲权纠纷案的鉴定。     

The Slovenian population data on the PCR based loci HLA-DQA1, LDLR, GYPA, HBGG, D7S8, GC, and D1S80

Allele frequencies for the loci HLA-DQA1, LDLR, GYPA, HBGG, D7S8, GC, and D1S80 were determined for a sample population of unrelated individuals from Slovenia. All loci meet Hardy-Weinberg expectations, except the loci GYPA (p = 0.041) and D1S80 (p = 0.009). There is little evidence for association of alleles among the seven loci. Only one out of 21 pairwise comparisons demonstrated departures from independence (HLA-DQA1/HBGG, p = 0.008). The allelic frequency data generally are similar to that of U.S. Caucasians.     

Polymorphism of LDLR, GYPA, HBGG, D7S8, GC, HLA-DQA1, Ig-JH, D17S30, ApoB and D1S80 loci in northwestern Russians

Allele frequencies for polymarker, HLA-DQA1, Ig-JH, D17S30, ApoB and D1S80 loci and population genetic parameters were obtained from a sample of 501 unrelated individuals born in the northwestern Federal Region of Russia.     

Analysis of genotype frequencies and interlocus association for the PM, DQA1, and D1S80 loci in four populations

Allele frequencies of the LDLR, HBGG, GYPA, D7S8, GC, DQA1, and D1S80 loci are presented and genotypes are analyzed for each of four ethnic groups: African Americans (n = 200), US Caucasians (n = 200), US Hispanics (n = 200), and Japanese (n = 89). Hardy-Weinberg genotypic proportions were observed in all but two of the 28 population-locus tests undertaken. Those two instances are attributable to type I statistical error. Gametic equilibrium among loci is an assumption invoked for application of the product rule to utilize the discriminatory power from two or more loci simultaneously. Two statistical methods, a genotype matching statistic and log-linear modeling, were used to evaluate gametic disequilibrium. The match statistic, comparing observed to expected likelihood of genotypic identity for seven loci among pairs of individuals within the database, revealed only one statistically significant deviation among 20 tests. As expected, the probability of match was generally lowest in the test on all ethnic groups combined, indicating that allele frequencies differ among ethnic groups for some of the loci. This was confirmed with the statistic theta to measure ethnic stratification, in which about 0.10 of the genetic variation is apportioned among the four ethnic groups for four of the structural loci (LDLR, HBGG, GC, and DQA1), while for GYPA, D7S8, and D1S80, variation is more uniformly distributed among ethnic groups. Log-linear modeling was also applied to the five PM loci. The most parsimonious log-linear model included only three higher order terms: the two-way interactions of three of the PM loci with ethnic group. These three instances (LDLR, HBGG, and GC) indicated differences in allele frequencies between ethnic groups. No two or higher way interaction (disequilibrium) was observed among loci. In summary, the assumptions of Hardy-Weinberg and gametic equilibrium that facilitate the use of the five PM loci, DQA1 and D1S80 in forensic applications are consistent with the allele and genotype frequencies observed in these populations.     

Amplification of a variable number of tandem repeats (VNTR) locus (pMCT118) by the polymerase chain reaction (PCR) and its application to forensic science

A genetic locus (D1S58, defined by DNA probe pMCT118) that contains a variable number of tandem repeats (VNTR) has been successfully amplified from a very small amount of genomic deoxyribonucleic acid (DNA) by the polymerase chain reaction (PCR). The DNA sequence of the locus was determined and was found to consist of a 16-base consensus sequence and flanking sequences. Oligonucleotide primers complementary to the flanking sequences were synthesized to serve as primers for amplification of MCT118 by the PCR method. Human genomic DNA isolated from blood (2 ng from each sample) was successfully amplified at the MCT118 locus, and polymorphic bands were detectable by ethidium bromide staining after electrophoresis on polyacrylamide gels. Determination of genotypes at this VNTR locus can now be routinely achieved within 24 h, without the need for Southern blots or radioactive materials. Furthermore, the small size (387 to 723 base pairs) of the DNA fragments produced in the PCR amplification permits good resolution of individual alleles that differ by only one repeat unit. The precise specification of the number of tandem repeats present in each allelic fragment is reproducible from one analysis to another.     

World population data for the HLA-DQA1, PM and D1S80 loci with least and most common profile frequencies for combinations of loci estimated following NRC II guidelines

All published and unpublished gene frequency data for the PCR-based loci HLA-DQA1, LDLR, GYPA, HBGG, D7S8, GC, and D1S80 that could be located are presented in summary tables. These gene frequencies provide the data necessary for estimating probabilities of chance match according to NRC II guidelines for any DNA profile that includes any combination of these loci for any of the populations. To illustrate the range of polymorphism for combined locus profiles, least and most common profile frequencies were estimated following NRC II guidelines for: the PM loci for all populations for which PM data were available; and for combinations of HLA-DQA1/PM, HLA-DQA1/D1S80, PM/D1S80, and HLA-DQA1/ PM/D1S80 for populations for which data were available for the relevant combinations. The profile frequencies were calculated at theta values of zero and 0.01. Minimum allele frequencies (MAF) were calculated, and are shown, for each data set for which the MAF was greater than the lowest observed allele frequency. Least common profile frequencies were calculated using MAF in those cases to illustrate a conservative estimate. The effect of using MAF versus lowest observed allele frequency in estimating least common profile frequencies is briefly illustrated as well. We finally show that aggregate U.S. gene frequency data for the classical MN and GC polymorphisms for both Caucasian and African-American populations is fully in accord with the DNA-based gene frequency data obtained from PM reverse dot-blot strips for GYPA and GC, respectively.     

The effect of luminol on presumptive tests and DNA analysis using the polymerase chain reaction.

This study was designed to test the following factors involved with processing luminol treated bloodstained evidence: 1) The reactivity of other presumptive chemical color tests, phenolphthalin (PT) and tetramethylbenzidine (TMB), following the application of the light emitting luminol presumptive test. 2) The effect of different cleanings of various bloody substrates on the luminol test. 3) The effect of different cleanings of various bloody substrates on the ability to obtain DNA suitable for PCR testing. 4) The ability to extract DNA from luminol treated bloodstained substrates using three extraction techniques. 5) The effect of spraying washed and unwashed bloodstains on various substrates with luminol on the ability to correctly type the DNA using PCR. Our findings indicated that luminol did not adversely effect the PCR testing and did not interfere with the PT and TMB presumptive tests for blood. It was determined that the substrate and the method of cleaning were the major factors affecting DNA yield and the ability to type the bloodstains using PCR based technologies.     

The structure, frequency, and forensic application of the STR locus D16S543 in the Japanese population

D16S543 is a complex STR locus consisting of five types of repeat units. The frequency distribution and genetic characteristics of this locus in Japanese were investigated using blood samples from 124 unrelated Japanese and 15 families. Alleles were detected using denatured polyacrylamide gels followed by automated analysis on an ABI 373 sequencer using Genescan software 672. Twenty-one alleles were identified, ranging in size from 281 to 489 bp. An allelic ladder containing the 21 alleles was constructed and used as a typing standard. The repeat unit arrays allowed the 21 alleles to be classified into three distinct groups, including alleles 1 to 7 in group I, alleles 8 to 14 in group II, and alleles 15 to 22 in group III. The alleles in group II were characterized by the insertion of one repeat unit of CAGG, one of AAAG, and three of AAGG, while the group III alleles differed from those of groups I and II by the insertion of a total of 32 repeat units ranging in 5 types. Within each group, the alleles differed from each other only in one 5' side tetranucleotide AAGG. The power of discrimination (Pd) and the estimated heterozygosity were calculated to be 0.989 and 0.934, respectively. Typing of this locus was successfully applied in four old forensic materials. The study presented herein demonstrates that D16S543 is a highly polymorphic and applicable locus in Japanese.     

Analysis of the co-amplified STR loci D1S1656, D12S391 and D18S51: population data and validation study for a highly discriminating triplex-PCR

A multiplex-PCR composed of the three highly variable STR loci D1S1656, D12S391 and D18S51 has been established. The non-overlapping fragment sizes allow allele detection using a monochrome automated laser fluorescent sequencer (A.L.F. express, Pharmacia Biotech). The typing results of the triplex-PCR showed no difference to those of singleplex-PCR. Allele frequencies were determined in a Western German population of 228 individuals from Cologne. The heterozygosities and exclusion chances (D1S1656, 0.982; D12S391, 0.979; D18S51, 0.97) are very high compared to other short tandem repeats used for forensic applications. No deviations from the Hardy-Weinberg equilibrium were found. Successful typing of DNA amounts down to 50-100 pg is possible. Mixtures of up to 1:10 can be identified. In conclusion, the high combined exclusion chance due to the well-balanced allelic distribution and its high sensitivity make this triplex-PCR a valuable tool for forensic casework.