Genetic data on 10 autosomal STR loci in the Bangladeshi population

Allele frequencies of 10 autosomal short tandem repeat (STR) loci, D3S1358, vWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01 and FGA were determined in 211 unrelated Bangladeshi individual using AmpFLSTR SGM Plus PCR Amplification Kit. Statistical parameters of forensic importance, the power of discrimination (PD), observed and expected heterozygosity values (H), polymorphism information content (PIC), probability of match (PM), power of exclusion (PE) and typical paternity index (TPI) were calculated for the loci. These parameters indicated the usefulness of the loci in paternity testing and personal identification in the Bangladeshi population.     

Allele frequency data for 15 autosomal STR loci in eight Indonesian subpopulations

Evolutionary and cultural history can affect the genetic characteristics of a population and influences the frequency of different variants at a particular genetic marker (allele frequency). These characteristics directly influence the strength of forensic DNA evidence and make the availability of suitable allele frequency information for every discrete country or jurisdiction highly relevant. Population sub-structure within Indonesia has not been well characterised but should be expected given the complex geographical, linguistic and cultural architecture of the Indonesian population. Here we use forensic short tandem repeat (STR) markers to identify a number of distinct genetic subpopulations within Indonesia and calculate appropriate population sub-structure correction factors. This data represents the most comprehensive investigation of population sub-structure within Indonesia to date using these markers. The results demonstrate that significant sub-structure is present within the Indonesian population and must be accounted for using island specific allele frequencies and corresponding sub-structure correction factors in the calculation of forensic DNA match statistics.     

Population data for 12 STR loci in Hong Kong Chinese

The allele distributions at the 12 short tandem repeat (STR) loci D3S1358, HUMvWA, HUMFIBRA/FGA, HUMTHO1, HUMTPOX, HUMCSF1P0, D5S818, D13S317, D7S820, D8S1179, D21S11 and D18S51 have been determined for 284 unrelated Chinese in Hong Kong. The combined probability of identity for the 12 STR loci was about 4.1 × 10^–14 and the overall probability of excluding paternity 0.999978. None of the 12 loci were found to deviate from Hardy-Weinberg expectations according to the results of the exact test. There was also little evidence for association of alleles between loci. The results demonstrate that the loci are useful for forensic human identification and parentage testing for the Chinese population in Hong Kong. Received: 2 December 1999 / Accepted: 12 April 2000     

Comparing six commercial autosomal STR kits in a large Dutch population sample

Regularly, STR results obtained with different PCR amplification kits are compared, for instance with old cases, when revisiting cold cases or when addressing cross-border crimes. It is known that differences in primer design for the same loci in different kits may give rise to null alleles or shifted alleles. In this study, the genotyping results of 2085 Dutch male samples were compared for six autosomal STR kits (Promega's PowerPlex® 16, ESX-16 and ESI-17 Systems, Qiagen's Investigator® ESSplex Kit and Applied Biosystems’ AmpFlSTR® Identifiler and NGM PCR Amplification Kits). A total of 19 discordant autosomal genotyping results were obtained that were examined by sequence analysis using Roche-454 next generation sequencing and/or Sanger sequencing. A further 25 discordances were found and sequenced for the Amelogenin locus. The 24 samples showing the same primer binding site mutation at the Amelogenin locus were subjected to X-STR analysis in order to assess whether they could share a common origin, which appeared not to be the case. Based on the sequencing results, we set the final genotypes and determined the allele frequencies of 23 autosomal STRs for the Dutch reference database.     

Population genetic data of 22 autosomal STR loci for the Mong people in Vietnam

This study investigated 22 autosomal short tandem repeat (STR) loci in 156 unrelated individuals from the Mong ethnic minority in Ha Giang Province, Vietnam. Allele frequencies and forensic parameters were calculated, showing the combined Powers of Discrimination reaching 1.000000000000000000000000000000 and the combined Power of Exclusion greater than 0.999999986623. Phylogenetic analysis indicated that the Vietnamese Mong population has close genetic relationships with other Hmong-Mien populations.     

Massively parallel sequencing data of 31 autosomal STR loci obtained using the Precision ID GlobalFiler NGS STR Panel v2 for 82 Japanese population samples

Allele frequencies for 31 autosomal short tandem repeat (STR) loci (CSF1PO, D10S1248, D12ATA63, D12S391, D13S317, D14S1434, D16S539, D18S51, D19S433, D1S1656, D1S1677, D21S11, D22S1045, D2S1338, D2S1776, D2S441, D3S1358, D3S4529, D4S2408, D5S2800, D5S818, D6S1043, D6S474, D7S820, D8S1179, FGA, Penta D, Penta E, TH01, TPOX, and vWA) were obtained using Precision ID GlobalFiler NGS STR Panel v2 from 82 unrelated individuals sampled from the Japanese population. Autosomal STR alleles designated by NGS and conventional capillary electrophoresis were found to be concordant except at D2S441 allele 9.     

Population data and phylogenetic structure of 19 STR loci in Chinese Hui ethnic group residing in Yunnan province of China

Allele frequency distributions and statistical forensic parameters of 19 autosomal STR loci in a sample of 535 unrelated healthy Hui individuals from Yunnan province were estimated. A total of 236 alleles at these loci were identified and their corresponding allele frequencies ranged from 0.000935 to 0.527103. Penta E is the most informative in Hui population, whereas TPOX showed the lowest. All of the STR loci reached the Hardy–Weinberg equilibrium after Bonferroni correction. The combined discrimination power and probability of excluding paternity of the 19 STR loci were 0.999 999 999 999 999 999 999 984 47 16 and 0.999 999 988, respectively. Furthermore, the genetic relationship between the Yunnan Hui population and other 8 different Hui groups or 25 previously investigated groups residing in other areas of China were also estimated based on pairwise genetic distance. These results suggest that the 19 STR loci are highly polymorphic, which is suitable for forensic personal identification and paternity testing.     

Massively parallel sequence data of 31 autosomal STR loci from 496 Spanish individuals revealed concordance with CE-STR technology and enhanced discrimination power

This study reports Short Tandem Repeat (STR) sequence-based allele data from 496 Spanish individuals across 31 autosomal STR (auSTR) loci included in the Precision ID GlobalFiler™ NGS STR Panel v2: D12S391, D13S317, D8S1179, D21S11, D3S1358, D5S818, D1S1656, D2S1338, vWA, D2S441, D5S2800, D7S820, D16S539, D6S474, D12ATA63, D4S2408, D6S1043, D19S433, D14S1434, CSF1PO, D10S1248, D18S51, D1S1677, D22S1045, D2S1776, D3S4529, FGA, Penta D, Penta E, TH01 and TPOX. The sequence of each allele was aligned to the reference sequence GRCh37 (hg19) and formatted according to the guidance of the International Society for Forensic Genetics. A subset of 221 samples was evaluated for testing concordance with allele calls derived from CE-based analysis using PowerPlex Fusion 6C, and there was 99.95% allele concordance. Twenty-five out of 31 auSTR loci showed an increased number of alleles due to repeat region sequence variation and/or single nucleotide polymorphisms (SNP) residing in the flanking regions. A total of 18 loci showed increased observed heterozygosity due to sequence variation; the loci exhibiting the greatest increase were: D13S317 (12% points), D5S818 (10% points), D8S1179 (7% points), D3S1358 (7% points), and D21S11 (6% points). The combined match probability decreased from 2.022E-24 (length-based data) to 1.042E-27 (sequence-based data) for the 20 CODIS core STR loci. The combined match probability (sequence-based data) for the 31 STR loci studied was 4.777E-40. The combined typical paternity index increased from 1.118E + 12 to 8.179E + 13 using length and sequence-based data, respectively. This Spanish population study performed in the framework of the EU-funded DNASEQEX project is expected to provide STR sequence-based allele frequencies for forensic casework and support implementation of massively parallel sequencing (MPS) technology in forensic laboratories.     

Allele frequencies for 22 autosomal short tandem repeat loci obtained by PowerPlex Fusion in a sample of 1501 individuals from the Japanese population

Allele frequencies for 22 autosomal short tandem repeat loci (D3S1358, D1S1656, D2S441, D10S1248, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433, FGA, and D22S1045) were obtained from 1501 unrelated individuals sampled from the Japanese population.     

Population genetics of STR loci in Caucasians

STR loci are becoming increasingly important in forensic casework. In order to be used fairly and efficiently, the population genetics of these loci must be investigated and the implications for forensic inference assessed. A key population genetics parameter is the “coancestry coefficient”, orF _ST, which is the correlation between two genes sampled from distinct individuals within a subpopulation. We present analyses of STR data, at geographic scales which range from national to regional, from the UK and other European sources. We implement a likelihood-based method of estimating F_ST, which has important advantages over alternative methods: it allows a range of plausible values to be assessed, rather than presenting a single point estimate, and it allows a subpopulation to be compared with a larger population from which a database has been drawn, which is the relevant comparison in forensic work. Our results suggest that values ofF _ST appropriate to forensic applications in Europe are too large to be ignored. With appropriate allowance, however, it is possible to make use of STR evidence in a way which is efficient yet avoids overstatement of evidential strength.     

Genetic analysis of 20 autosomal STR loci in the Miao ethnic group from Yunnan Province,Southwest China

The genetic polymorphisms of 20 autosomal short tandem repeat (STR) loci included in the PowerPlex^® 21 kit were evaluated from 748 unrelated healthy individuals of the Miao ethnic minority living in the Yunnan province in southwestern China. All of the loci reached Hardy–Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. The genetic relationship between the Miao population and other Chinese populations were also estimated. The combined discrimination power and probability of excluding paternity of the 20 STR loci were 0.999 999 999 999 999 999 999 991 26 and 0.999 999 975, respectively. The results suggested that the 20 STR loci were highly polymorphic, which makes them suitable for forensic personal identification and paternity testing.     

Phylogenic analysis and forensic genetic characterization of Guizhou Miao tribes from 58 microareas via autosomal STR

Genetic polymorphism of 17 autosomal short tandem repeat (STR) loci, included in the PowerPlex®18D amplification kit, were analyzed in Miao tribes from 58 different sampling microareas (N = 5255) of Guizhou as well as two cities (N = 151) of Hunan, China. Allele frequencies and forensic efficiency parameters were calculated. Moreover, comprehensive population genetic comparisons among 91 nationwide populations and 174 Asian populations were conducted based on raw genotype data and allele frequency data, respectively. Our results of forensic efficiency parameters showed that the panel was a robust tool in forensic individual identification and paternity cases for this population. Genetic affinities were observed among most of the Miao tribes revealed by multidimensional scaling plot, principal component analysis, and neighboring-joining tree. The genetic distance between Miao tribes and Han nationalities were varies by different geographical positions. Some of the Miao tribes were genetically closer to the Hmong-Mien populations living in southeastern contiguous regions and even the Indochina. The result coincided with the migration or reverse migration routes for Miao nationality in modern history. This study of the Miao tribes from plenty of microareas in Guizhou would be useful in reconstructing the population history and establishing a more comprehensive forensic reference database.     

Genetic variation of 20 autosomal STR loci in the Han nationality in Central Yunnan,Southwest China

A total of 20 autosomal short tandem repeat (STR) loci from 2220 unrelated healthy individuals of Han population living in the central area of Yunnan province, Southwest China were amplified with the PowerPlex® 21 System. After Hardy-Weinberg equilibrium examination, the allele frequencies and forensic statistical parameters of 20 STR loci were evaluated. A total of 298 alleles and 1225 genotypes were observed for all the 20 loci. The allele frequencies varied from 0.0002 to 0.5130. The combined power of discrimination and the combined probability of exclusion of all 20 STR loci were 0.99999999521565 and 0.999999999999999999999999637, respectively. Meanwhile, genetic distances between Central Yunnan Han and 17 previously published populations were compared and a neighbor-joining (NJ) phylogenetic tree was developed and visualized by using MEGA 7 based on Nei’s standard genetic distance. The results demonstrated that these loci were highly polymorphic in the Han nationality in Central Yunnan, Southwest China and could be applied in forensic medicine and population genetics.     

Quadruplex amplification of polymorphic STR loci in a Korean population

Multiplex PCR amplification has been useful for gene mapping with polymorphic short tandem repeat (STR) loci. We have tested the four loci D20S470, D13S325, HumFOLP23 and D10S2325 for the simultaneous typing of more than 100 unrelated Koreans. This analysis allows a single base pair resolution and rapid typing with silver staining. The allele and genotype distributions are in accordance with Hardy – Weinberg expectations. These STR loci have proven useful for forensic analysis and paternity tests in which the variable number of tandem repeat (VNTR) loci have some limitations. Received: 25 November 1997 / Received in revised form: 25 February 1998     

FST estimates of 94 populations in China based on STR markers

The proper assessment of DNA evidence in cases of personal identification is a recurring theme in forensics. It is common practice to evaluate the strength of DNA evidence using the likelihood ratio (LR). The accurate use of population allele frequencies is a crucial problem in LR calculation. Allele frequency differences among different populations could be estimated by the F_ST values. Thus, F_ST would also affect LR values by correcting the allele frequencies. In this study, Chinese population allele frequency data were selected from population reports published in Chinese and English journals. The population-specific F_ST values of each population, the overall F_ST values of each province, each region, and the whole country, and the locus-specific F_ST values of different loci were calculated. The LRs using different allele frequencies and different F_ST values were compared based on the combination of simulated genotypes. As a result, the F_ST values of 94 populations, 19 provinces, 7 regions, and the whole country were obtained. The LR was overestimated using allele frequencies of the combined population containing multiple populations rather than using allele frequencies of a population, and the LRs after F_ST correction were lower than those without correction. Conclusively, the correction in conjunction with corresponding F_ST values can make the LRs more accurate and reasonable.     

Characterization of copy number variation in genomic regions containing STR loci using array comparative genomic hybridization

Short tandem repeat (STR) loci are commonly used in forensic casework, familial analysis for human identification, and for monitoring hematopoietic cell engraftment after bone marrow transplant. Unexpected genetic variation leading to sequence and length differences in STR loci can complicate STR typing, and presents challenges in casework interpretation. Copy number variation (CNV) is a relatively recently identified form of genetic variation consisting of genomic regions present at variable copy numbers within an individual compared to a reference genome. Large scale population studies have demonstrated that likely all individuals carry multiple regions with CNV of 1 kb in size or greater in their genome. To date, no study correlating genomic regions containing STR loci with CNV has been conducted. In this study, we analyzed results from 32,850 samples sent for clinical array comparative genomic hybridization (CGH) analysis for the presence of CNV at regions containing the 13 CODIS (Combined DNA Index System) STR, and the Amelogenin X (AMELX) and Amelogenin Y (AMELY) loci. Thirty-two individuals with CNV involving STR loci on chromosomes 2, 4, 7, 11, 12, 13, 16, and 21, and twelve with CNV involving the AMELX/AMELY loci were identified. These results were correlated with data from publicly available databases housing information on CNV identified in normal populations and additional clinical cases. These collective results demonstrate the presence of CNV in regions containing 9 of the 13 CODIS STR and AMELX/Y loci. Further characterization of STR profiles within regions of CNV, additional cataloging of these variants in multiple populations, and contributing such examples to the public domain will provide valuable information for reliable use of these loci.     

Estimating number of contributors in massively parallel sequencing data of STR loci

In recent years a number of computer-based algorithms have been developed for the deconvolution of complex DNA mixtures in forensic science. These procedures utilize likelihood ratios that quantify the evidence for a hypothesis for the presence of a person of interest in a DNA profile compared to an alternative hypothesis. Proper operation of these software systems requires an assumption regarding the total number of contributors present in the mixture. Unfortunately, estimates based on counting the number of alleles at a locus can be inaccurate due to the sharing and masking of alleles at individual loci. The effects of allele masking become increasingly severe as the number of contributors increases, rendering estimates about high-order mixtures uncertain. The accuracy of these estimates can be improved by increasing the number of STR markers in panels, and by using highly polymorphic markers. Increasing the number of STR markers from 13 to 20 (expanded CODIS panel) improves the accuracy of allele count-based estimation methods for low-order mixtures, but accuracy for high-order mixtures (> 3 contributors) remains poor due to allele masking. An alternative technique, massively parallel sequencing, holds great potential to improve the accuracy of the estimate of number of contributors due to its ability to detect sequence polymorphisms within alleles. This process results in an expansion of the number of alleles when compared to that obtained using capillary electrophoresis. Here, we show that the detection of these additional sequence-defined alleles in 22-marker panels improves number of contributor estimates in conceptual mixtures of 4 and 5 contributors.     

Genetic variation of 17 autosomal STR loci in the Lahu population from Yunnan and phylogenetic structure exploration among 28 populations

This study evaluated the genetic variation of 17 autosomal short tandem repeat (STR) loci included in the PowerPlex® 18D Kit. Samples of 562 unrelated healthy Lahu individuals living in Yunnan Province in southwestern China were investigated. The data were analyzed to provide information on allele frequencies and other statistical parameters relevant to the forensic population. Of the 17 loci, 16 reached the Hardy–Weinberg equilibrium after Bonferroni correction. A total of 176 alleles were identified in 17 STR loci, and allele frequencies ranged from 0.000 890 to 0.578 292. The combined discrimination power (CPD) and probability of excluding paternity (CPE) of the 17 STR loci were 0.999 999 999 999 999 999 489 and 0.999 998 301 753 122. The genetic relationships among 28 populations were also estimated.     

Allele frequencies of 37 short tandem repeat loci in a Japanese population

Allele frequencies for 37 STR autosomal loci (D1S1656, D2S1338, D2S1360, D2S441, D3S1358, D3S1744, D4S2366, D5S2500, D5S818, D6S474, D7S1517, D7S820, D8S1132, D8S1179, D10S1248, D10S2325, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, D21S2055, D22S1045, CSF1PO, F13A01, F13B, FESFPS, FGA, LPL, Penta C, Penta D, Penta E, SE33, TH01, TPOX, vWA) were obtained from a sample of 175 unrelated individuals in a Japanese population.