Population data for 17 Y-chromosome STRs in a sample from Apulia (Southern Italy)

The 17 Y-STR loci included in the AmpFLSTR Yfiler PCR Amplification Kit were analyzed in 98 unrelated healthy males from Apulia (Southern Italy). A total of 97 different haplotypes were identified, of which 96 haplotypes were unique and 1 occurred twice. Allele frequencies for each Y-STR locus in pooled sample and estimated value of gene diversity (GD) were evaluated. The lowest value of GD was observed for DYS392 (0.126) and the highest one (0.936) for DYS385. The HD (haplotype diversity) for the studied Y-STR set showed a value of 0.9994, with an HMP (haplotype match probability) value of 0.0006, while the overall DC was 98.98%. Microvariant alleles were found for the DYS458 and DYS385 markers and sequenced.Furthermore, Φ_st-based genetic distance computation and pair-wise analysis of molecular variance (AMOVA) test were carried out. When comparing our population with the Apulia sample previously investigated, the AMOVA analysis detected no evidence for significant differentiation. The comparison with all Italian populations submitted to the YHRD website showed no relevant differences with all Southern Italian populations (San Giorgio La Molara, Belvedere, Trapani and Catania) and significant genetic deviation with all Northern Italian populations (Udine, Biella, La Spezia, Modena, Ravenna, Marche and North Sardinia). Moreover, the other populations and meta-populations belonging to the whole Mediterranean area (Croatia, Macedonia, Albania, Greece, Turkey, Israel, Libya, Tunisia, Algeria, Morocco and Spain) were different from our Apulia sample. The data were submitted to YHRD.     

Evaluation of an extended set of 15 candidate STR loci for paternity and kinship analysis in an Austrian population sample

We investigated 15 polymorphic short tandem repeat (STR) loci (D1S1656, D7S1517, D8S306, D8S639, D9S304, D10S2325, D11S488, D12S391, D14S608, D16S3253, D17S976, D18S1270, D19S253, D20S161, and D21S1437) which are not included in the standard sets of forensic loci. The markers were selected according to the complexity of the polymorphic region: Of the 15 investigated loci, 7 loci showed a simple repeat structure (D9S304, D10S2325, D14S608, D16S3253, D18S1270, D19S253, and D21S1437), 3 loci (D7S1517, D12S391, and D20S161) consisted of compound repeat units, and 5 loci (D1S1656, D8S306, D8S639, D11S488, and D17S976) showed a more complex polymorphic region partly including different repeat blocks and incomplete repeat units, which resulted in a relatively high proportion of intermediate alleles. A population study on a sample of 270 unrelated persons from Austria was carried out. We did not observe significant deviations from Hardy–Weinberg expectations. The combined probability of exclusion for the 15 loci was 0.99999998. In combination with the conventional set of STR markers included in commercially available kits (no linkage was observed between these 15 loci and the Powerplex 16 System loci), these markers are approved as highly discriminating forensic tools, also suitable for the analysis of difficult paternity and kinship constellations. Electronic Supplementary Material Supplementary material is available for this article at     

Genetic variation of 15 autosomal STR loci in a population sample from Poland

Fifteen autosomal STR loci included in AmpF?STR® NGM? kit were analyzed in 154 unrelated individuals from Poland. This multiplex kit enables simultaneous amplification of 10 standard STR loci included in AmpF?STR® SGM Plus® kit (D3S1358, vWA, D16S539, D2S1338, D8S1179, D19S433, TH01, FGA, D21S11 and D18S51) and five new mini- and midi-STR loci (D10S1248, D22S1045, D2S441, D1S1656 and D12S391). Population study was conducted to evaluate usefulness of the loci (especially the five new microsatellite systems) in forensic genetic identification examinations. All 15 markers were found to be in Hardy–Weinberg equilibrium. The combined probability of match for the 15 studied STR loci was 3.998 × 10^?19. The same parameter calculated for five new microsatellite loci equaled 8.83 × 10^?7. Discrimination power was particularly high in case of D1S1656 (0.975) and D12S391 (0.972) STR loci.     

产前亲子鉴定方法研究(附23例报告)

目的对23个产前案例进行亲子鉴定。方法超声监视下行羊膜穿刺术,抽取羊水30~40ml。离心收集羊水沉渣后提取其基因组DNA,同时抽取其父母双方外周血基因组DNA。应用毛细管电泳技术和五色荧光复合扩增的方法,检测所有DNA样本的16个STR基因座基因型。结果所有羊水基因组DNA均来自独立个体,无母体DNA的污染。三联体分析显示23个案例中17例为肯定亲权关系,亲子关系概率均大于0.9999,6例确定为排除亲权关系,平均排除(位点数)指标为7.67个。二联体分析显示23个案例中17例肯定父权的平均亲子关系概率为0.9997以上,6例排除亲权关系的平均排除(位点数)指标为5个,但其中1例的排除位点只有1个。结论16个STR位点的多重荧光扩增方法在对羊水中母体DNA的污染程度进行评估的同时,可以准确、可靠的应用于产前亲子鉴定。在检测单亲鉴定案例时,若排除(位点数)指标小于2时必须补充母亲样本或增加检测的STR位点指标数,直至得出明确结论。     

New alleles and mutational events at 14 STR loci from different German populations

The molecular origin of DNA mutations and the mutation rates were analyzed at 14 short tandem repeat (STR) loci with samples from trio cases derived from 10 different German population samples. STR loci comprised of D2S1360, D3S1744, D4S2366, D5S2500, D6S474, D7S1517, D8S1132, D10S2325, D12S391, D18S51, D19S246, D20S480, D21S226, and D22S689. In a total of 488 meioses, 16 isolated genetic inconsistencies in 8 different STRs were observed, whereas no mutations were found at the other loci. The data of five mutations suggested the presence of silent or null alleles due to sequence variation in primer binding site. This could be confirmed for four suspected cases by the use of alternative primer sets and by DNA sequence analyses. Furthermore, this study revealed nine new allelic variants at five different loci.     

Casework application of a stand-alone pentaplex assay of extended-ESS STRs

Using a stand-alone pentaplex comprising two standard-length short tandem repeats (STRs): D12S391 and D1S1656 plus three mini-STRs: D2S441, D10S1248 and D22S1045, all recently adopted to extend the European Standard Set (ESS) STRs, we have examined the genotyping performance of the new markers in 111 challenging casework samples. Although commercial kits now combine the five new STRs with existing core loci, we found the ESS-pentaplex we developed in-house performed better than both MiniFiler (comprising eight miniaturized STRs) and the NGM kit that includes the new STRs in a 15-marker multiplex. Our findings suggest at least part of the improved sensitivity of recently available ESS STRs can be attributed to the loci themselves as well as applying long-standing, robust primer designs that were first designed for the extended ESS markers by the laboratories that originally developed them. Therefore the ESS-pentaplex provides an ideal adjunct to Identifiler or MiniFiler to allow laboratories to assess the new STRs alongside existing standard loci, measure performance with challenging material and generate population frequency data ahead of a final decision on which additional STRs will extend the reconfigured CODIS core set.     

Genetic data obtained for two Chinese Han populations with a quadruplex fluorescent STR typing system (HUMVWA, HUMTH01, D21S11 and HPRT)

DNA typing of four tetrameric repeat loci (HUMVWA, HUMTH01, D21S11 and HPRT) was carried out in a Chinese Han population from Shanghai (East China) and one from Guangzhou (South-East China) using a quadruplex PCR amplification and detection of the fluorescent-labeled alleles on the ALF DNA sequencer. All loci were in accordance with Hardy-Weinberg equilibrium except for D21S11 in the Guangzhou population. A test for population differentiation showed no statistical difference in the allele frequency distribution between the two populations. Comparison of the allele frequency data with other Chinese Han populations from North and South-West China for the STR loci HUMVWA and HUMTH01 revealed heterogeneity between Northern Chinese Han and Southern Chinese Han, which is in accordance with previous studies on the basis of protein markers. Received: 22 December 1997 / Accepted: 23 April 1998     

Genetic analyzing of 15 STR loci in a Han population of Jinan (northern China)

This study reports the genetic polymorphic data of 15 autosomal STRs D3S1358, TH01, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, D2S1338, D19S433, and FGA observed in Han ethnic group living in Jinan, Shandong, China. The combined match probability and exclusion probability for 15 loci was 3.89 × 10⁻¹⁷ and 0.99997, respectively. No mutations at these loci were found in 78 pedigrees, and Chi-test of allelic frequencies in 420 unrelated samples showed no departure from Hardy-Weinberg equilibrium at these loci. The pairwise comparisons between Jinan and 41 reference populations were performed.     

Allele frequencies of the six miniSTR loci in a population from Japan

Allele frequencies and forensic parameters for the six miniSTR loci D1S1677, D2S441, D4S2364, D10S1248, D14S1434, and D22S1045 were investigated in a sample of 142 unrelated healthy Japanese individuals. The polymerase chain reaction (PCR) products contained within the six loci were less than 119 bp in size. The frequency distributions in the six short tandem repeat (STR) loci showed no deviations from Hardy–Weinberg equilibrium expectations. The accumulated powers of discrimination and power of exclusion for the six loci were 0.999998 and 0.98, respectively. It was thus considered that due to the small PCR products and the moderate degree of polymorphism, analysis with use of the six miniSTR loci was highly beneficial for the forensic analysis of degraded DNA.     

Genetic diversity at 15 microsatellite loci among the Adi Pasi population of Adi tribal cluster in Arunachal Pradesh, India

Genetic polymorphisms at 15 tetrameric short tandem repeat (STR) loci were studied in 203 healthy individuals of Adi Pasi population from Arunachal Pradesh, India. All the loci analyzed were highly polymorphic and there was no significant deviation from the Hardy-Weinberg equilibrium (HWE) excepting D8S1179 and D18S51. Other forensic useful statistical parameters were also calculated and the 15 microsatellite markers selected for this study were found to be suitable for human identification and population genetic studies.     

Forensic STR profile of two endogamous populations of Madhya Pradesh, India

Genotypic polymorphism studies at 15 highly polymorphic short tandem repeat (STR) loci were carried out in two populations belonging to one caste and one tribal group of Madhya Pradesh, in central region of India. These include 110 individuals from Brahmin caste (Kanyakubj) and 89 from Gond tribe (Ojha). The 15 loci studied are: 13 CODIS STR core markers, i.e., D8S1179, D3S1358, D21S11, D7S820, CSF1PO, vWA, TPOX, D18S51, THO1, D13S317, D16S539, D5S818, FGA and 2 other loci D19S433 and D2S1338. The results show departure from the Hardy-Weinberg equilibrium with respect to two loci, viz., D3S1358 and FGA in Gond tribe and at seven loci, viz., D21S11, D19S433, TPOX, D18S51, THO1, D5S818, and FGA in Brahmin caste. Population differentiation tests between the two studied populations and with seven neighboring populations (4 tribes and 3 castes - two middle castes and one Deshasth Brahmin) revealed significant differences at several loci. The power of discrimination of the microsatellite markers used was found to be high for both the populations. The data thereof is of immense significance for forensic result interpretation and is an addition to the existing autosomal STR database on Indian population.     

Forensic evaluation of STR typing reliability in lung cancer

Short tandem repeats (STR) analysis is the gold standard method in the forensics field for personal identification and paternity testing. In cancerous tissues, STR markers are gaining attention, with some studies showing increased instability. Lung cancer, which is one of the most common malignancies, has become the most lethal among all cancers. In certain situations, lung cancer tissues may be the only resource available for forensic analysis. Therefore, evaluating the reliability of STR markers in lung cancer tissues is required to avoid false exclusions. In this study, 75 lung cancer tissue samples were examined to evaluate the reliability of various STR markers. Out of the 75 examined samples, 24 of the cancerous samples (32%) showed genetic alterations on at least one STR loci, totaling 55 times. The most common type of STR variation was a partial loss of heterozygosity, with the D5S818 loci having the highest variation frequency and no alterations detected on the D2S441 and Penta E loci. Moreover, STR variation frequencies were shown to increase with an increased patient age and increased clinical and pathological characteristics, thus an older patient with an advanced stage of progression exhibited a higher variation frequency. Overall, this study provides forensic scientists with further insight into STR analysis relating to lung cancer tissue.     

Population genetic data of 15 STR loci in Han population of Henan province (central China)

Allele frequencies of the 15 STR loci were determined in 208 unrelated individuals from Han population living in Henan, China (central China). All loci except D5S818 were found no deviation from Hardy-Weinberg equilibrium. The combined power of discrimination (PD) and the combined chance of exclusion (CE) for the 15 studied loci were >0.9999999 and 0.999996119, respectively. Our data were statistically compared with the previously reported data from other Chinese population groups, and significant difference was found between central Han Chinese (n=208) and eastern Chinese (n=100) at vWA, or between central Han Chinese (n=208) and southeast Chinese (n=122) at D13S317.     

Allele frequencies for the new European Standard Set (ESS) loci and D1S1677 in the Belgian population

The nine Belgian laboratories, officially recognized by the Belgian Minister of Justice for performing DNA analysis in criminal cases, have jointly decided to use a common local population database for statistical calculations. A first database has been set up for the loci covered in AmpFlSTR^® Identifiler? and PowerPlex^® 16 [1], [2]. With the decision of ENFSI and EDNAP to extend the current ESS loci (D3S1358, vWA, D8S1179, D21S11, D18S51, THO1 and FGA) with new loci (D1S1656, D2S441, D10S1248, D12S391 and D22S1045), there was a need to obtain also data for these loci within the Belgian population [3], [4]. Here, we present the allele frequencies and forensic efficiency data for the new ESS loci and one additional miniSTR, D1S1677.     

Corrigendum to “Linkage disequilibrium analysis of D12S391 and vWA in U.S. population and paternity samples” [Forensic Sci. Int.: Genet. (in press), doi:10.1016/j.fsigen.2010.09.003]

Recently, the European Network of Forensic Science Institutes voted to adopt five additional STR loci (D12S391, D1S1656, D2S441, D10S1248, and D22S1045) to their existing European Standard Set of seven STRs (TH01, vWA, FGA, D8S1179, D18S51, D21S11, and D3S1358). The D12S391 and vWA loci are located 6.3 megabases (Mb) apart on chromosome 12. Ideally for use in forensic analyses, genetic markers on the same chromosome should be more than 50 Mb in physical distance in order to ensure full recombination and thus independent inheritance. The purpose of this study was to evaluate if the closely located D12S391 and vWA loci are independent and, consequently, if these loci can be included in the product rule calculation for forensic and kinship analyses. Departures from Hardy–Weinberg equilibrium and linkage disequilibrium between the D12S391 and vWA loci were tested using n = 654 unrelated U.S. African American, Caucasian, and Hispanic samples, and n = 764 father/son paternity samples. In the unrelated U.S. population samples, no significant departures from HWE were detected for D12S391 or vWA. No significant evidence of linkage disequilibrium was observed between the loci in the population samples. However, significant linkage disequilibrium was detected in U.S. African American, Caucasian, and Asian father/son samples with phased genotypes. No significant linkage disequilibrium was detected for U.S. Hispanic paternity samples. The use of phased father/son pairs allowed for robust detection of linkage disequilibrium between D12S391 and vWA. In unrelated population samples, linkage disequilibrium is present but more difficult to detect due to the large number of possible haplotype combinations and unknown allelic phase. For casework analyses that involve unrelated or related individuals, the single-locus genotype probabilities for D12S391 and vWA should not be multiplied to determine the match probability of an autosomal STR profile. Since the D12S391 and vWA loci are not independent, it is recommended that the observed combination of alleles at D12S391 and vWA should be treated as a non-independent diplotype for profile probability calculations. The observed haplotype frequencies for U.S. African American, Caucasian, Hispanic, and Asian populations are provided for match probability calculations.     

Forensic genetic analysis of nine miniSTR loci in the Korean population

Nine miniSTR loci were analyzed in 191 unrelated individuals from Korea using three multiplex PCR systems (multiplex I: D1S1677, D2S441 and D4S2364; multiplex II: D10S1248, D14S1434 and D22S1045; multiplex III: D12S391, D16S3253 and D20S161). Due to the short PCR amplicons (<145 bp), miniSTR systems can effectively be used in forensic analysis with highly degraded DNAs. Allele frequencies and forensic parameters were calculated to evaluate their usefulness in forensic casework. The Exact Test demonstrated that all loci surveyed here were found to be no deviation from Hardy–Weinberg equilibrium, except two miniSTR markers (D4S2364 and D16S3253). When we compared the distribution of genetic variation of six miniSTR markers (D1S1677, D2S441, D4S2364, D10S1248, D14S1434 and D22S1045), the Exact Test revealed significant differences (P < 0.05) between the Korean sample studied here and almost all of other samples of East Asian and European populations. The combined probability of match calculated from nine miniSTR loci was 1.28 × 10⁻⁸, which is high degree of polymorphism. Thus, the miniSTR system, combined with other valuable miniSTR markers, may be suitable for recovering useful information in analyzing degraded DNA samples.     

Development and population study of the 12 X-STR loci multiplexes PCR systems

To develop a multiplex polymerase chain reaction (PCR) system with 12 X-chromosomal short-tandem repeat (X-STR) loci and to investigate their polymorphism and linkage and/or independence, the 12 loci (DXS6807, DXS8378, DXS9902, DXS6800, DXS6803, DXS6799, DXS6804, GATA172D05, DXS6854, HPRTB, DXS8377, and DXS7423) were simultaneously analyzed in 1,005 unrelated individuals (574 males and 431 females) from Guangdong Han individuals and Kazakh populations living in China. The allele frequencies and mutation rates were investigated. Allele frequency distribution among different populations was compared. Haplotypes of linkage disequilibrium markers (DXS6807-DXS8378-DXS9902) and linked markers (DXS6804-GATA172D05 and DXS8377-DXS7423) were also reported. A total of 117 alleles, ranging from five to 20 for each locus, were observed in our selected populations. Eight cases with mutation of the selected loci were detected in 9,480 meioses. Pairwise comparisons of allele frequencies distribution showed statistically significant differences at most loci among different populations. Haplotype diversity of linked markers was 0.9404-0.9694. The results indicated that this multiplex system is very useful for forensic analysis and may be complementarities for X-12 kits or X-8 kits in forensic case.     

Linkage disequilibrium analysis of D12S391 and vWA in U.S. population and paternity samples

Recently, the European Network of Forensic Science Institutes voted to adopt five additional STR loci (D12S391, D1S1656, D2S441, D10S1248, and D22S1045) to their existing European Standard Set of seven STRs (TH01, vWA, FGA, D8S1179, D18S51, D21S11, and D3S1358). The D12S391 and vWA loci are located 6.3megabases (Mb) apart on chromosome 12. Ideally for use in forensic analyses, genetic markers on the same chromosome should be more than 50Mb in physical distance in order to ensure full recombination and thus independent inheritance. The purpose of this study was to evaluate if the closely located D12S391 and vWA loci are independent and, consequently, if these loci can be included in the product rule calculation for forensic and kinship analyses. Departures from Hardy-Weinberg equilibrium and linkage disequilibrium between the D12S391 and vWA loci were tested using n=654 unrelated U.S. African American, Caucasian, and Hispanic samples, and n=764 father/son paternity samples. In the unrelated U.S. population samples, no significant departures from HWE were detected for D12S391 or vWA. No significant evidence of linkage disequilibrium was observed between the loci in the population samples. However, significant linkage disequilibrium was detected in U.S. African American, Caucasian, and Asian father/son samples with phased genotypes. No significant linkage disequilibrium was detected for U.S. Hispanic paternity samples. The use of phased father/son pairs allowed for robust detection of linkage disequilibrium between D12S391 and vWA. In unrelated population samples, linkage disequilibrium is present but more difficult to detect due to the large number of possible haplotype combinations and unknown allelic phase. For casework analyses that involve unrelated or related individuals, the single-locus genotype probabilities for D12S391 and vWA should not be multiplied to determine the match probability of an autosomal STR profile. Since the D12S391 and vWA loci are not independent, it is recommended that the observed combination of alleles at D12S391 and vWA should be treated as a non-independent diplotype for profile probability calculations. The observed haplotype frequencies for U.S. African American, Caucasian, Hispanic, and Asian populations are provided for match probability calculations.     

Population genetic analyses of the AmpFlSTR® NGM™ in Brazil

Population data of 15 short tandem repeat loci of the AmpFlSTR? next generation multiplex (NGM)? were obtained from a sample of 835 individuals. The loci are the ten short tandem repeats (STRs) in the SGM Plus? Kit plus the EDNAP- and ENSFI-recommended STRs D10S1248, D22S1045, D2S441, D1S1656, and D12S391. Allele frequency and other forensically relevant statistics data were generated for the NGM loci into five current country macroregions of Brazil (North, Northeast, Central West, Southeast, and South). All the analyzed loci meet Hardy-Weinberg equilibrium expectations and no linkage disequilibrium in all pairs of loci. The observed and expected heterozygosity, power of discrimination, polymorphic information content, and the other population-genetic indices were calculated. The overall power of discrimination was greater than 0.99999999999999999996 and the combined power of exclusion was greater than 0.9999998 in all Brazilian populations. Comparative analysis between populations from different Brazilian macroregions as well as between Brazil and Caucasian, African Americans, and Hispanic US populations are presented.     

Population genetics of nine short tandem repeat (STR) loci – DNA typing using the AmpFlSTR Profiler PCR amplification kit

Frequency data for nine short tandem repeat (STR) loci were collected from 130 unrelated Caucasians from North Bavaria using the AmpFlSTR Profiler multiplex system. The loci D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, D7S820 and the sex test amelogenin were investigated. Allele frequencies, rates of heterozygosity and the discrimination power of the combined systems were calculated by statistical analysis. Except for D5S818 all loci met Hardy-Weinberg expectations. Received: 27 August 1998 / Received in revised form: 28 December 1998