A novel fluorescent quadruplex STR typing system and the allele frequency distributions in a Thai population

We have previously reported a new triplex amplification and typing system by silver staining for three short tandem repeat (STR) loci, 9q2h2 (D2S3020), D15S233, and D14S299 without "microvariant" alleles such as .1, .2, and, .3 alleles in the Japanese population. In the present study, we established a new quadruplex system with an additional locus D7S809 using primer sets labeled with fluorescent multi-color dyes. Using this system, we genotyped 183 Thai people, found only one "microvariant" allele (allele 20.2) at D7S809, and calculated allele frequencies and some statistical properties at these four STR loci. From these allele frequencies at four STR loci, we performed three statistical analyses including a homozygosity test, a likelihood ratio test, and an exact test for Hardy-Weinberg equilibrium (HWE). Deviations from HWE (p < 0.05) were observed only in the two tests at the locus D7S809. In the present study, we compared the allele frequencies at these four loci in the Thai population to those in the Japanese population described previously. Consequently, all observed heterozygosities and power of discrimination (PD) at those loci in the Thai population were higher than 0.8 and 0.9, respectively, and all statistical values for discriminating power in the Thai population were slightly higher than those in the Japanese population. The combined paternity exclusion rate (combined PE) in the Thai population (0.978) was almost the same as that in the Japanese population (0.971). Therefore, this novel PCR amplification and typing system for four STR loci would be a convenient and informative DNA profiling system in the forensic field.     

Consideration of the probative value of single donor 15-plex STR profiles in UK populations and its presentation in UK courts

The adoption of new 15 locus STR multiplex systems into UK forensic science would be facilitated by agreed guidelines for reporting the strength of DNA evidence using likelihood ratios. To facilitate such an agreement, we present an analysis of previously published UK allele frequencies for white Caucasian, Afro-Caribbean and Indo-Pakistani populations and investigate their effect on likelihood ratios for single donor profiles. We consider the implication of the five additional loci and suggest a procedure for reporting likelihood ratios for 15-plex STR profiles.     

Haplotype frequencies and population data of nine Y-chromosomal STR polymorphisms in a German and a Chinese population

Y-chromosomal STR loci are of increasing interest in paternity testing, forensic casework, anthropological and evolutionary studies. We participate in a cooperation to establish an international reference database of at least nine Y-chromosomal STR loci to be used for biostatistic calculations. We present frequency distributions of nine Y-chromosome specific STR polymorphisms and frequencies of compound haplotypes in two populations. We chose the loci DYS393, DYS19, DYS392, DYS385I, DYS385II, DYS390, DYS391 and DYS389I and II. Blood samples were taken from 136 unrelated male individuals from Cologne (Germany) and of 63 unrelated males from Chengdu (Sichuan Province, PR China). DNA was extracted by a salting out procedure or chelex extraction. PCR was carried out in two multiplex reactions. Fragment analysis was conducted on an ALF- or ALF-express sequencer. Frequency profiles of the German men showed no significant differences compared to most European populations. Mean exclusion chances were between 0.44 for DYS393 and 0.94 for DYS385. Haplotype diversity for the complete haplotype was 86.66% in Germans and 98% in Chinese. The Chinese men showed for all analysed loci except for DYS389I and DYS390 remarkably different allele distributions.     

Population frequency distribution of HumF13A01, HumFXIIIB, and HumLIPOL loci in the Basque Country (Northern Spain)

A population study of unrelated individuals from the Basque Country (Northern Spain) was carried out using the GenePrint STR System. The PCR products were separated on denaturing polyacrylamide gels and visualized by silver staining. Three tetrameric loci were evaluated: HumF13A01, HumFXIIIB, and HumLIPOL. All loci fit Hardy-Weinberg expectations, and independence of alleles was found between these STR loci. A comparison with other population groups indicated allele frequencies are well conserved in Caucasians, but differ from other racial groups. The calculated parameters a priori probability of exclusion (Pex) and "power of discrimination" (PD) show how informative these loci are for the determination of identity and relatedness of individuals.     

The application of minisatellite variant repeat mapping by PCR (MVR-PCR) in a paternity case showing false exclusion due to STR mutation

A boy and a girl with their mother brought a paternity suit against an alleged but deceased father. We tested six conventional genetic markers, the AmpliType PM+ DQA1 and twelve STR loci the children and mother together with the alleged paternal grandparents. We also DNA typed the bloodstain found later in the alleged father's medical record. Only the result at D3S1358 in a nineplex STR system excluded the alleged father from parentage of the boy, whereas all markers were inclusive for the girl. Accordingly, we performed sequence analysis at D3S1358 to confirm the presence of a paternal exclusion or mutation. The sequence analysis indicated that the boy's allele 17 could have originated from either of the alleged father's allele 16 or 18 by a single-step mutation associated with slippage mutation in STR loci. We carried out minisatellite variant repeat mapping by PCR (MVR-PCR) at loci D1S8 (MS32) and D7S21 (MS31A) and mapped allele haplotypes of all individuals except the deceased alleged father. The MVR-PCR analysis showed that the boy has no inconsistency with the relationship between the alleged grandparents, and was very effective at increasing the paternity index (PI) value. We conclude that there is biological relationship between not only the girl but also the boy and the alleged father.     

Allele frequencies for nine STR loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) in the Italian population

Genotype and allele frequencies for STR loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820 were investigated in 289 unrelated Italian Caucasian individuals from the North and South regions. After co-amplification by polymerase chain reaction, automatic DNA profiling of these nine STR loci was performed by ABI PRISM((R)) 310 DNA Genetic Analyzer. For each locus, statistical parameters for forensic and paternity purposes were then calculated; the combined power of discrimination and the combined power of exclusion of all nine loci were 0.9999999999917 and 0.99992 for the Northern population and 0.9999999999921 and 0.99991 for the Southern population.     

A Peruvian population study of eight Y-chromosome STR loci

We have analyzed the distribution of the allele frequencies and haplotypes at eight Y-chromosomal short tandem repeat (STR) loci (DYS437, DYS438, DYS439, DYS460, DYS461, GATA A10, GATA C4 and GATA H4) in a sample population of 87 unrelated individuals from Perú.     

Evaluation of sensitivity and specificity of sibship determination in the Caucasian population of the Russian Federation using the 23 STR loci VeriFiler panel

We performed a simulation study to evaluate sensitivity and specificity of sibship determination in the Caucasian population of the Russian Federation using 23 autosomal STR loci included in the VeriFiler Express (Applied Biosystems) kit. Population genetic data were obtained from 1609 unrelated Caucasian individuals from different regions of the Russian Federation. Several scenarios were analyzed: half siblings duo vs unrelated; half siblings vs unrelated (mother(s) will be genotyped); full siblings duo vs half siblings; full siblings vs half siblings (mother will be genotyped); full siblings duo vs unrelated.     

Practical applications of genotypic surveys for forensic STR testing

Legitimate genotype frequency estimation for multiallelic loci relies on component allele frequencies, as population surveys represent only a fraction of possible DNA profiles. Multilocus genotypes from two ethnic human populations, African American (n=195) and U.S. Caucasian (n=200), were compiled at 13 STR loci that are used worldwide in forensic investigation (D3S1358, vWA, FGA, D16S539, TH01, TPOX, CSF1PO, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820). Sex-specific AmpFlSTR multiplexes provided stringent PCR-based STR typing specifically optimized for multicolor fluorescence detection. Heterozygosity at each STR locus ranged from 0.57 to 0.89 and encompassed from seven (TH01) to twenty-one (D21S11) alleles. Homozygosity tests, tests based on the distinct numbers of observed homozygous and heterozygous classes, log likelihood ratio tests, and exact tests assessed that the degree of divergence from theoretical Hardy-Weinberg proportions for all 13 STRs does not have practical consequence in genotype frequency estimation. Departures from linkage equilibrium, between loci, that imposed significance to forensic calculations were not indicated by observed variance of the number of heterozygous loci or Karlin interclass correlation tests. For forensic casework, reliable multilocus profile estimates may be obtained from the product of component genotype frequencies, each calculated through application of the Hardy-Weinberg equation to population database allele frequency estimates reported here. The average probability that two randomly selected, unrelated individuals possess an identical thirteen-locus DNA profile was one in 1.8x10(15) African Americans and one in 3.8x10(14) U.S. Caucasians.     

Matching and partially-matching DNA profiles

The DNA profiles of two individuals can have 0, 1, or 2 pairs of alleles that are the same at each locus. These events may be called mismatches, partial matches or matches, respectively, and they have probabilities that depend on the population proportions of alleles as well as the population structure parameter theta. The observed and expected numbers of pairs of individuals with various numbers of matching or partially matching loci in FBI and Australian databases are found to be in good agreement provided theta is set equal to some small value greater than zero. The likelihood ratios for two individuals having a specified degree of relationship versus being unrelated also depend on the numbers of matching and partially matching loci, but even unrelated pairs of individuals can have likelihood ratios that support hypotheses of relatedness. Matching probabilities allow predictions to be made for the sizes of databases that are expected to contain a pair of individuals with high numbers of matching loci. It is very likely that two individuals with at least 9 matching loci among the 13 CODIS loci have already been typed.     

Concordance Between the AmpFℓSTR® MiniFiler™ and AmpFℓSTR® Identifiler® PCR Amplification Kits in the Kuwaiti Population

Abstract:  The AmpFℓSTR^® MiniFiler™ polymerase chain reaction amplification kit, developed and supplied by Applied Biosystems, complements the AmpFℓSTR^® Identifiler^® polymerase chain reaction amplification kit (Applied Biosystems, Warrington, U.K.) by improving the success rate when profiling DNA that is degraded or contains inhibitors. Before applying the MiniFiler™ kit to casework, the profiles from 200 unrelated Kuwaitis were compared to Identifiler^® profiles. Concordance was observed for 99.875% (1598 of 1600) of the compared STR loci. The two discordant profiles displayed allelic dropout: one at the D13S317 locus due to nonamplification of allele 10 in the MiniFiler™ profile, and one at the D18S51 locus due to nonamplification of allele 18 in the Identifiler^® profile.     

Population genetic data of eight tetrameric short tandem repeats (STRs) in Casablanca resident population to use in forensic casework

The allele frequencies for eight short tandem repeat (STR) loci HUMvWA, HUMFES/FPS, HUMF13A, HUMF13B, HUMTHO1, HUMTPOX, HUMCSF1P0, HUMLPL included in Geneprint STR kits were obtained from 234 unrelated individuals in Casablanca.     

Investigation of 74 microhaplotypes for kinship testing in US populations

Microhaplotypes are markers that consist of haplotype blocks of SNPs, which can be analyzed by massively parallel sequencing technologies. These allow determining the haplotype phase at every locus by clonal sequencing each DNA strand. MHs are polymorphic loci with same size alleles, no stutter, and lower mutation rate than STRs. They can provide the same power of discrimination of STR-kits, thus useful for mixture deconvolution, but more accurate ancestry prediction than STRs. In this study we investigated the potential of a recently developed 74plex-MH panel for kinship testing using the Familias software.Samples from families of four major US population groups were collected and genotyped using the 74plex-MH panel. MH allele frequency data from 347 individuals were imported into Familias software along with STR allele frequency data of 29 loci (NIST dataset) from 1036 individuals. Different family scenarios were tested and these included unrelated vs parent-child, unrelated vs full siblings, unrelated vs half siblings, unrelated vs cousin pairs. The prediction of the kinship relation for the four populations of interest was reported as Log10 of the likelihood ratio (LR).Overall, the panel of 74MHs and 29STRs showed similar performance in predicting the correct kinship scenarios tested. Correct prediction was reported for parent-child, full siblings, and half sibling scenarios, but not for the cousin pairs scenario. The panel of 74 MHs showed larger Log10LR values than the 29 STR-assay, thus demonstrating the effectiveness of this biomarker as a tool for kinship testing in addition to mixture deconvolution and ancestry prediction.     

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.     

福尔马林固定组织SNP与STR检测的比较

目的检测经长期福尔马林固定的组织降解情况,并比较组织中SNP与STR的检出率。方法本文对24例经福尔马林固定、-20℃保存5年的组织样本,采用Quantifiler?Trio DNA定量试剂盒检测样本DNA的降解系数及浓度,运用55-SNPs SNa Pshot复合分型体系和Power Plex?21试剂盒分别进行SNP与STR检测。结果大部分样本降解系数在1~8,发生不同程度的降解。与未降解样本相比,SNP分型完全一致,检出率为100%;其中8例样本STR分型存在33个等位基因丢失,降解系数均大于2.6,且75.8%的等位基因片段长度大于300bp。当样本检测出16个STR基因座时,似然率与54个SNP相当。当样本检出大于17个STR时,似然率大于54个SNP。STR基因座片段长度与等位基因检出率之间呈负相关。除2例样本降解系数较小却发生等位基因丢失外,其余样本降解系数与等位基因检出率之间呈负相关。结论经福尔马林长期固定的组织DNA易降解,检测SNP明显优于STR,但需要更多的SNP以提高个体识别能力。     

Genetic Data Analysis of Nine STRs in Two Caribbean Colombian Populations: César and Guajira

POPULATION:  We have analyzed the distribution of the allele frequencies and parameters of forensic interest at nine short tandem repeat (STR) loci (CSF1PO, D3S1358, D5S818, D7S820, D13S317, FGA, TH01, TPOX, and vWA) in a sample population of 165 unrelated individuals from César and Guajira, Caribbean populations of Colombia.     

Analysis of STR polymorphisms in the northeast Chinese population

The distribution of allele frequencies for 12 short tandem repeats (STR) loci were determined in 300 unrelated healthy Chinese individuals living in northeast of China, using AmpFlSTR Profiler Plus kit and AmpFlSTR Green I kit (PE, Applied Biosystems). In these samples, 123 alleles and 399 genotypes were observed for 12 STR loci. The distribution of these observed genotypes were not significantly different from the expected distribution according to Hardy-Weinberg equilibrium.     

Belgian population data for 15 STR loci (AmpFlSTR SGM Plus and AmpFlSTR profiler PCR amplification kit)

The allele and genotype distributions for 15 STR loci included in the AmpFlSTR SGM Plus and AmpFlSTR Profiler kits (Applied Biosystems, Foster City, USA) were determined in a sample of 222 unrelated individuals of Belgian origin.     

Genetic data analysis of nine STRs in two Caribbean Colombian populations: César and Guajira.

POPULATION: We have analyzed the distribution of the allele frequencies and parameters of forensic interest at nine short tandem repeat (STR) loci (CSF1PO, D3S1358, D5S818, D7S820, D13S317, FGA, TH01, TPOX, and vWA) in a sample population of 165 unrelated individuals from César and Guajira, Caribbean populations of Colombia.     

Forensic and population genetic analysis of Serbian population using 21 STR loci of GlobalFiler™ PCR amplification kit

Autosomal short tandem repeats (STRs) have been widely used in forensic investigations. Prior to the application of any DNA based identification method, it is essential to estimate the allele frequencies and forensic statistical parameters of targeted STR loci in each population in order to provide a more precise reference database for forensic investigation. The GlobalFiler™ Kit is a multiplex assay that combines the 13 original CODIS loci with 7 non-overlapping loci from the expanded European Standard Set (ESS), as well as the highly discriminating SE33 locus, two Y-based loci and the sex determining maker, Amelogenin. The full complement of loci in the GlobalFiler™ Kit are: D13S317, D7S820, D5S818, CSF1PO, D1S1656, D12S391, D2S441, D10S1248, D18S51, FGA, D21S11, D8S1179, vWA, D16S539, TH01, D3S1358, AMEL, D2S1338, D19S433, DYS391, TPOX, D22S1045, SE33 and a Y-specific insertion/deletion locus (Yindel). The 6-dye GlobalFiler™ PCR Amplification kit (ThermoFisher Scientific) comprises 21 autosomal STRs have already been proven to be able to provide reliable DNA profiling results and enhance the power of discrimination between individuals. In this study, we are presenting an analysis of GlobalFiler STR loci on 209 unrelated individuals from Serbia.