Allele frequency distributions of four variable number tandem repeat (VNTR) loci in the London area.

Allele frequency distributions of four hypervariable minisatellite loci were obtained from a large sample of individuals in the London area. The sample is subdivided into three major ethnic groups; Caucasian, Afro-Caribbean and Asian, and histograms for these groups are displayed for comparison. The distributions are discussed in relation to mutation rates, heterozygosity and the computer analysis and processing of results.     

Performance evaluation of two multiplexes used in fluorescent short tandem repeat DNA analysis

The performance of two commercial multiplex kits that together amplify the 13 core short tandem repeat (STR) loci currently in use by forensic laboratories and the U.S. national Combined DNA Indexing System (CODIS) were evaluated. The typing systems examined were AmpFlSTR Profiler Plus and AmpFlSTR COfiler (PE Applied Biosystems, Foster City, CA). Electrophoretic separation and detection of the fluorescent PCR products was achieved by capillary electrophoresis (CE) using an ABI Prism 310 Genetic Analyzer. The studies addressed the on-site validation of the instrument, the software, and each typing system. These studies included instrument sensitivity, resolution, precision, binning, peak height ratios, mixtures, stutter, and the amplification of non-probative and simulated forensic samples. Other additional developmental-type work is also reported herein, such as species specificity testing and amplification of environmentally insulted samples. Amplification conditions were found to be robust and the primer sets shown to be specific to human DNA. Stutter and peak height ratios fell within limits published by the manufacturer and other laboratories. The data demonstrate that the CE instrument can consistently resolve fragments differing in length by one base and that the +/-0.5 base bin used by the Genotyper software is acceptable for making accurate allele calls. Correct typing results were obtained from non-probative and simulated case samples, as well as samples exposed to outdoor environmental conditions. The results support the conclusion that DNA extracted from biological samples routinely encountered in the forensic laboratory can be reliably analyzed with AmpFlSTR Profiler Plus and COfiler using CE.     

Short tandem repeat (STR) DNA markers are hypervariable and informative in Cannabis sativa: implications for forensic investigations

Short tandem repeat (STR) markers are the DNA marker of choice in forensic analysis of human DNA. Here we extend the application of STR markers to Cannabis sativa and demonstrate their potential for forensic investigations. Ninety-three individual cannabis plants, representing drug and fibre accessions of widespread origin were profiled with five STR makers. A total of 79 alleles were detected across the five loci. All but four individuals from a single drug-type accession had a unique multilocus genotype. An analysis of molecular variance (AMOVA) revealed significant genetic variation among accessions, with an average of 25% genetic differentiation. By contrast, only 6% genetic difference was detected between drug and fibre crop accessions and it was not possible to unequivocally assign plants as either drug or fibre type. However, our results suggest that drug strains may typically possess lower genetic diversity than fibre strains, which may ultimately provide a means of genetic delineation. Our findings demonstrate the promise of cannabis STR markers to provide information on: (1) agronomic type, (2) the geographical origin of drug seizures, and (3) evidence of conspiracy in production of clonally propagated drug crops.     

Response of short tandem repeat systems to temperature and sizing methods

In capillary gel electrophoresis (CE), changing run conditions such as temperature can result in minor variations in the size determination of an allele. These effects are caused by secondary structure differences that can occur between the amplified sample and the internal standard. The type of method chosen to generate the sizing curve in STR analysis can influence the relationship between estimated allele size and temperature. To better understand the effects of temperature and sizing method on the reproducibility of DNA migration, two fluorescently labeled allelic ladders, CTTv and Y-PLEX 6 were analyzed using the ABI Prism 310 Genetic Analyzer. The default method on the Genetic Analyzer utilizes an electrophoretic temperature of 60 degrees C and a Local Southern method to generate a sizing curve from the fragment migration times of the internal lane standard. In this work, electrophoresis was conducted at 35-70 degrees C using the commercially available POP 4 buffer at pH 8 and two sizing methods, Global Southern and Local Southern, were compared. The slopes of the regression line between estimated allele size and temperature, using either sizing method, were measured in order to demonstrate the temperature sensitivity of migration time and the importance of the operator-chosen method. Our results indicate that the Global Southern method is a better choice in situations where temperature fluctuations can occur. In addition, the temperature dependence of the DNA size estimates using the POP 4 system were compared to results obtained using an experimental buffer consisting of 3% hydroxyethylcellulose at pH 11. These results demonstrate that secondary structure effects are minimized at an elevated pH, increasing the precision of size estimates obtained.     

Analysis of forensically used autosomal short tandem repeat markers in Polish and neighboring populations

The purpose of this study was to evaluate the homogeneity of Polish populations with respect to STRs chosen as core markers of the Polish Forensic National DNA Intelligence Database, and to provide reference allele frequencies and to explore the genetic interrelationship between Poland and neighboring countries. The allele frequency distribution of 10 STRs included in the SGMplus kit was analyzed among 2176 unrelated individuals from 6 regional Polish populations and among 4321 individuals from Germany (three samples), Austria, The Netherlands, Sweden, Czech Republic, Slovakia, Belarus, Ukraine and the Russian Federation (six samples). The statistical approach consisted of AMOVA, calculation of pairwise Rst values and analysis by multidimensional scaling. We found homogeneity of present day Poland and consistent differences between Polish and German populations which contrasted with relative similarities between Russian and German populations. These discrepancies between genetic and geographic distances were confirmed by analysis of an independent data set on Y chromosome STRs. Migrations of Goths, Viking influences, German settlements in the region of Volga river and/or forced population resettlements and other events related to World War II are the historic events which might have caused these finding.     

15个STR基因座的突变观察和分析

目的调查15个STR基因座的突变情况。方法采集817例亲子鉴定的2722份血样本,采用Identi—filerTM系统扩增15个STR基因座分型,共有33060次等位基因传递,统计各基因座发生突变的频率。结果在15个基因座中发现涉及11个基因座共25次突变,平均突变率为0．8×101（95％C10．5—1．1×10-3）,其中一步突变20次,两步突变3次,三步突变2次;父、母来源突变比率为2．6：1,不能确定来源突变7次。结论STR基因座等位基因在IdentifilerTM复合扩增系统突变现象较为常见,亲子鉴定时应引起注意。     

Genetics and genomics of core short tandem repeat loci used in human identity testing

Over the past decade, the human identity testing community has settled on a set of core short tandem repeat (STR) loci that are widely used for DNA typing applications. A variety of commercial kits enable robust amplification of these core STR loci. A brief history is presented regarding the selection of core autosomal and Y-chromosomal STR markers. The physical location of each STR locus in the human genome is delineated and allele ranges and variants observed in human populations are summarized as are mutation rates observed from parentage testing. Internet resources for additional information on core STR loci are reviewed. Additional topics are also discussed, including potential linkage of STR loci to genetic disease-causing genes, probabilistic predictions of sample ethnicity, and desirable characteristics for additional STR loci that may be added in the future to the current core loci. These core STR loci, which form the basis for DNA databases worldwide, will continue to play an important role in forensic science for many years to come.     

A study on ten short tandem repeat systems: African immigrant and Spanish population data

This work presents the results obtained from a genetic-population study for the D1S1656 system in the population of Southwest Spain (Huelva, Cádiz and Sevilla), Spaniards of Caucasian origin from North Africa (Ceuta), as well as in the black Central West African and Moroccan immigrant populations in Spain. The results of a study of the autochtonous population of the Canary Islands (n=138), and immigrant Central West African populations in Spain (n=132), obtained for nine short tandem repeat (STR) loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820), as well as the amelogenin locus, all contained in Profiler Plus (Perkin-Elmer) PCR amplification kits, are also presented. Except for the FGA and VWA data on immigrant Central West African populations in Spain, no deviations from the Hardy-Weinberg equilibrium were detected.     

DNA short tandem repeat profiling of three North Indian populations.

Population: Fifty healthy unrelated individuals were randomly chosen from each of the three populations viz., Bhargavas, Chaturvedies, and Brahmins. Three generation pedigree charts were prepared to ensure sirname endogamy in Bhargavas Chaturvedies and group endogamy in Brahmins subjects were chosen from several parts of Uttar Pradesh, a northern state of the Indian republic.     

A study on ten short tandem repeat systems: African immigrant and Spanish population data

This work presents the results obtained from a genetic–population study for the D1S1656 system in the population of Southwest Spain (Huelva, Cádiz and Sevilla), Spaniards of Caucasian origin from North Africa (Ceuta), as well as in the black Central West African and Moroccan immigrant populations in Spain. The results of a study of the autochtonous population of the Canary Islands (n=138), and immigrant Central West African populations in Spain (n=132), obtained for nine short tandem repeat (STR) loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820), as well as the amelogenin locus, all contained in Profiler Plus™ (Perkin-Elmer) PCR amplification kits, are also presented. Except for the FGA and VWA data on immigrant Central West African populations in Spain, no deviations from the Hardy–Weinberg equilibrium were detected.     

Fingerprint enhancement revisited and the effects of blood enhancement chemicals on subsequent profiler Plus fluorescent short tandem repeat DNA analysis of fresh and aged bloody fingerprints

This study was aimed at determining the effect of seven blood enhancement reagents on the subsequent Profiler Plus fluorescent STR DNA analysis of fresh or aged bloody fingerprints deposited on various porous and nonporous surfaces. Amido Black, Crowle's Double Stain. 1,8-diazafluoren-9-one (DFO), Hungarian Red, leucomalachite green, luminol and ninhydrin were tested on linoleum, glass, metal, wood (pine, painted white), clothing (85% polyester/15% cotton, 65% polyester/35% cotton, and blue denim) and paper (Scott 2-ply and Xerox-grade). Preliminary experiments were designed to determine the optimal blood dilutions to use to ensure a DNA typing result following chemical enhancement. A 1:200 blood dilution deposited on linoleum and enhanced with Crowle's Double Stain generated enough DNA for one to two rounds of Profiler Plus PCR amplification. A comparative study of the DNA yields before and after treatment indicated that the quantity of DNA recovered from bloody fingerprints following enhancement was reduced by a factor of 2 to 12. Such a reduction in the DNA yields could potentially compromise DNA typing analysis in the case of small stains. The blood enhancement chemicals selected were also evaluated for their capability to reveal bloodmarks on the various porous and nonporous surfaces chosen in this study. Luminol. Amido Black and Crowle's Double Stain showed the highest sensitivity of all seven chemicals tested and revealed highly diluted (1:200) bloody fingerprints. Both luminol and Amido Black produced excellent results on both porous and nonporous surfaces, but Crowle's Double Stain failed to produce any results on porous substrates. Hungarian Red, DFO, leucomalachite green and ninhydrin showed lower sensitivities. Enhancement of bloodmarks using any of the chemicals selected, and short-term exposure to these same chemicals (i.e., less than 54 days), had no adverse effects on the PCR amplification of the nine STR systems surveyed (D3S 1358, HumvWA, HumFGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) or of the gender determination marker Amelogenin. The intensity of the fluorescent signals was very similar and the allele size measurements remained constant and identical to those of untreated bloody fingerprints. No additional background fluorescence was noted. Continuous exposure (for 54 days) to two of the seven enhancement chemicals selected (i.e., Crowle's Double Stain and Hungarian Red) slightly reduced the amplification efficiency of the longer STR loci in profiles of fresh and 7 to 14-day-old bloodprints. This suggests that long-term exposure to these chemicals possibly affects the integrity of the DNA molecules. This study indicates that significant evidence can be obtained from fresh or aged bloody fingerprints applied to a variety of absorbent and nonabsorbent surfaces which are exposed to different enhancement chemicals for short or long periods of time. It also reaffirms that PCR STR DNA typing procedures are robust and provide excellent results when used in concert with fluorescence-based detection assays after fingerprint identification has taken place.     

常染色体STR分型鉴定半同胞关系的亲缘关系指数计算

目的获得双方生母均参与情形下计算两个或三个孩子间半同胞关系指数(half-sib index, HSI)的简化公式。方法在给定的前提假设下,根据HSI值的定义,首先推导出单基因座上HSI值的统一表达式,再获得不同基因型组合下的计算公式,最后归纳出两种鉴定情形下的简化公式。将简化公式应用于1例典型的半同胞关系鉴定,根据39个常染色体STR位点的分型计算不同鉴定情形下的累积HSI值。结果成功地推导和归纳出双方生母均参与情形下计算两个或三个孩子间HSI值的简化公式。实际案例的计算结果显示,当双方生母均参与时,任意两个孩子间的累积HSI值与生母均不参与时相比均发生了数量级的改变,即在半同胞关系情形下大约为10~4～10~6倍,在无关个体情形下大约为10~(-4)～10~(-3)倍。结论所推导出的简化公式可用于计算双方生母均参与情形下两个或三个孩子间的HSI值。     

经耳郭软骨DNA检验认定亲缘关系1例

1案情 某年9月16日凌晨4时左右，某烟花厂发生爆炸．爆炸现场中心有南北两处炸坑。两炸坑坑沿间距离7．5m。南侧炸坑呈东西走向，长34．5m，宽30．5m，坑内有东西两处炸点，炸点坑深分别为3．9m和2．58m。北侧炸坑呈东南、西北走向，长32．3m，宽18．89m，坑内有两个炸点，炸点坑深分别为3．3m和3．42m。爆炸现场外发现尸体一具（尸体已被附近村民认领）。9月20日刘某报称其丈夫在该厂工作，现已失踪。     

Combining autosomal and Y-chromosomal short tandem repeat data in paternity testing with male child: methods and application

Paternity testing is being increasingly requested with the aim of challenging presumptive fatherhood. The ability to establish the biological father is usually based on the genotyping of autosomal short tandem repeat (STR) in alleged father, mother and child, but the use of Y-chromosomal STR has gained interest in the last few years. In this work, we propose a new probabilistic approach that combines autosomal and Y-chromosomal STR data in paternity testing with father/son pairs taking into account mutation events. We also suggest a new two-stage approach where we first type Y-STRs and possibly autosomal STR for the putative father and son, conditional on Y-STR results. We applied this approach to 22 cases. Our results show that Y-STRs can identify nonpaternity cases with high accuracy but need to be validated with autosomal STR to establish paternity. Moreover, the two-stage approach is less costly than the standard approach and is very useful in motherless cases.     

DNA typing of short tandem repeat loci on Y-chromosome of Greek population

Haplotype, allele frequencies and population data of nine Y-chromosome STR loci, DYS385I, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, were determined from a sample of 69 unrelated Greek male individuals.     

Simulated approach to estimate the number and combination of known/unknown contributors in mixed DNA samples using 15 short tandem repeat loci

The calculation of likelihood ratios (LRs) for DNA mixture analysis is necessary to establish an appropriate hypothesis based on the estimated number of contributors and known contributor genotypes. In this paper, we recommend a relevant analytical method from the 15 short tandem repeat typing system (the Identifiler multiplex), which is used as a standard in Japanese forensic practice and incorporates a flowchart that facilitates hypothesis formulation. We postulate that: (1) all detected alleles need to be above the analytical threshold (e.g., 150 relative fluorescence unit (RFU)); (2) alleles of all known contributors should be detected in the mixture profile; (3) there should be no contribution from close relatives. Furthermore, we deduce that mixtures of four or more persons should not be interpreted by Identifiler as the LR values of 100,000 simulated cases have a lower expectation of exceeding our temporal LR threshold (10,000) which strongly supports the prosecution hypothesis. We validated the method using various computer-based simulations. The estimated number of contributors is most likely equal to the actual number if all alleles detected in the mixture can be assigned to those from the known contributors. By contrast, if an unknown contributor(s) needs to be designated, LRs should be calculated from both two-person and three-person contributions. We also consider some cases in which the unknown contributor(s) is genetically related to the known contributor(s).     

5个STR基因座的遗传多态性及其法医学应用

目的获得D11S4951、D11S4957、GATA193H05、D2S2951、D6S2421基因座的群体遗传学数据,并分析其在法医学中的应用价值。方法随机抽取成都地区汉族群体无血缘关系个体的静脉血,EDTA抗凝,用Chelex-100法提取DNA,应用PCR技术,扩增上述5个短串联重复序列基因座,聚丙烯酰胺凝胶垂直板电泳分型。结果5个基因座在中国成都汉族人群中分别发现了7、10、8、6、8个等位基因,5个基因座的基因型分布符合Hardy-Weinberg平衡(P>0.05)。各基因座的杂合度分别为0.743、0.772、0.833、0.650和0.800;非父排除概率分别为0.497、0.549、0.662、0.356和0.599;个人识别几率分别为0.863、0.912、0.947、0.829和0.931。结论5个基因座在中国汉族群体中具有法医学应用价值。     

中国成都地区汉族群体5个STR基因座的遗传多态性

采用PCR扩增,聚丙烯酰胺凝胶电泳分析技术,调查中国成都汉族群体DIS1656、D851179、D9S302、D185535及D195253等5个STR基因座的等位基因频率分布。D1S1656检出11个等位基因,35种基因型;DSS1179检出9个等位基因,32种基因型;D95302检出12个等位基因,50种基因型;D185535检出7个等位基因,20种基因型;D195253检出8个等位基因,28种基因型。5个STR基因座基因型频率分布符合Hardy-weinberg平衡（P＞0．05）。个人识别机率（DP）为0．92～0．98。分析了二代3口之家的遗传模式,证明5个STR基因座均符合孟德尔遗传规律。5个STR基因座PCR扩增采用同一条件,方法简单、快速、灵敏、重复性好,可用于法科学亲子鉴定和个人识别。