Fourteen non-CODIS autosomal short tandem repeat loci multiplex data from Taiwanese

Interest in the development of polymorphic short tandem repeat (STR) markers unlinked to the CODIS loci is growing among forensic practitioners. We developed a multiplex system in which14 autosomal STR (D3S1744, D4S2366, D8S1110, D12S1090, D13S765, D14S608, Penta E, D17S1294, D18S536, D18S1270, D20S470, D21S1437, Penta D, and D22S683) could be amplified in one single polymerase chain reaction. DNA samples from 572 unrelated Taiwanese Han subjects were analyzed using this 14 STR multiplex system. Thirty parent–child pairs of parentage testing cases with a combined paternity index (CPI) below 1,000 and 32 parent–child pairs with single-step mutations found in AmpFℓSTR Identifiler loci were also recruited for validation of the newly developed system. DNA sequencing was performed for novel STRs and novel alleles found in these subjects. The distributions of allelic frequencies for these autosomal STRs and sequence data, allele nomenclature for the STRs, and forensic parameters are presented. The discrimination power in our multiplex loci ranged from 0.6858 (D18S536) to 0.9168 (Penta E), with a combined discrimination power of 0.999999999. It provides additional power to distinguish the possible single-step mutations in parent–child pairs and improves the ability to prove parentage by increasing the CPI. The combined power of exclusion of these 14 loci in Taiwanese Han in this study was 0.9999995913. In conclusion, this 14-autosomal STRs multiplex system provides highly informative STR data and appears useful in forensic casework and parentage testing.     

Population data of 15 STR loci of Chinese Yi ethnic minority group

Allele frequency data and statistical parameters for D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA loci were determined in a sample of 120 healthy unrelated individuals of Chinese Yi ethnic minority group living in Yunnan province, China. We observed 132 alleles with allelic frequencies ranging from 0.0042 to 0.5333. The forensic statistical parameters from the data of all the loci showed high values. All loci were in accordance with Hardy-Weinberg equilibrium (p>0.05). The obtained frequency distributions were compared with previously published other population data, and significant differences were found between Yi population and Korean, Chinese Tibetan, Uigur, Ewenki, Han, Hui population at some STR loci. Our results of present study were valuable for forensic application and Chinese population genetic studies. These population data enriched Chinese genetic informational resources.     

Allele frequency data for 17 short tandem repeats in a Czech population sample

Allele frequencies for 17 short tandem repeats (STRs) autosomal loci (D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, CSF1PO, FGA, PentaD, PentaE, TH01, TPOX, vWA) were studied in an extensive sample (max. N = 1411) of unrelated individuals originating from the Czech Republic. Population and forensic parameters were estimated. Except for FGA and Penta E loci, no deviations from the Hardy–Weinberg equilibrium were detected. A comparative analysis with published data revealed significant differences in allele frequencies for some loci from the Polish population and three Hungarian populations (Ashkenazim population and Romany populations from Debrecen and Baranya County, respectively). A combination of these 17 STR loci provides a powerful tool for forensic identification in the native Czech population.     

Population genetics of six miniSTR loci (D1S1677, D2S441, D4S2364, D10S1248, D14S1434, D22S1045) in a Polish population

Allele frequency data and forensic efficiency parameters for six miniSTR loci: D1S1677, D2S441, D4S2364 (NC01), D10S1248, D14S1434, D22S1045 (NC02) were estimated from a sample of 116 unrelated individuals from Poland. No significant deviations from Hardy–Weinberg equilibrium expectations were detected. The combined power of discrimination for the six studied loci was 0.999995383.     

15 STR loci frequencies in the population from Paraná, Southern Brazil

Allele frequencies for 15 short tandem repeats (STR) loci were obtained from a sample of 4076 unrelated individuals undergoing paternity testing. The population is from Paraná, Southern Brazil. The loci are the most commonly used in forensic and paternity testing, being analyzed by the AmpFlSTR^® Identifiler™ (Applied Biosystems) commercial kit. The most polymorphic loci were D2S1338 and D18S51. Excepting the D13S317, all loci were in Hardy–Weinberg equilibrium. Comparative analyses between our population data and other populations are presented.     

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.     

Autosomal STR variations in three endogamous populations of West Bengal, India

The allele frequency distribution of 15 autosomal STR loci was determined using AmpFlSTR Identifiler kit in three endogamous caste populations namely, Rajbanshi, Paliya and Dhimal from northern regions of West Bengal, India. The study includes 13 CODIS STR core markers, i.e., D8S1179, D3S1358, D21S11, D7S820, CSF1PO, vWA, TPOX, D18S51, THO1, D13S317, D16S539, D5S818, FGA and two other loci D19S433 and D2S1338. All the loci followed Hardy-Weinberg equilibrium, except loci D8S1179, vWA and FGA in Rajbanshi population, D13S317 in Paliya population and D16S539 and TPOX in Dhimal population. The allele 12 in CSF1PO in Rajbanshi population and allele nine in THO1 in Paliya as well as in Dhimal population were found to be most frequent. All the 15 STR loci studied were found to be highly polymorphic with respect to observed heterozygosity values. Population differentiation tests revealed highly significant differences at several loci suggesting the endogamous nature of studied populations. STR allele frequency data on Dhimal population presented here is a unique contribution to the existing DNA data base on Indian population. To the best of our present knowledge, hitherto Dhimal Population has not been explored genetically for generating forensic data on STR markers.     

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.     

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.     

Fluorescence-based amplification of the STR loci D18S535, D1S1656 and D12S391 in a population sample from Aragon (North Spain)

Population data were generated for the STR loci D18S535, D1S1656 and D12S391 in a population sample of unrelated healthy individuals born and living in Aragon (North Spain). The three loci were amplified using a fluorescence-based PCR method and were typed automatically. No deviation from Hardy-Weinberg expectations were observed. The three loci proved to be highly discriminating and valuable polymorphisms for forensic analyses. Received: 28 January 1999 / Received in revised form: 15 March 1999     

Allele frequencies of the 15 AmpF<Emphasis Type="Italic">l</Emphasis>STR Identifiler loci in the population of Vojvodina Province,Serbia and Montenegro

The 15 AmpFlSTR Identifiler loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818 and FGA) were analyzed in the sample of 100 unrelated, autochthonous healthy adult Serbians from Novi Sad (Vojvodina Province, Serbia and Montenegro). The agreement with HWE was confirmed for all loci with the exception of D7S820 (based on the ²-test only). The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 15 tested STR loci were 0.99999999999999995 and 0.9999990, respectively. According to the presented data, D2S1338 and D18S51 are the most informative markers. Based on allelic frequencies and statistical parameters for forensic testing, it may be suggested that the AmpFlSTR Identifiler detection system represents a powerful strategy for individual identification and parentage analysis in the Serbian population.     

Tibetan population data on the PCR-typed loci D16S539, D7S820, D13S317, HUMF13A01, FESFPS, vWA, HUMTH01, TPOX and CSF1PO

Frequency data for nine tetrameric short tandem repeat loci (D16S539, D7S820, D13S317, HUMF13A01, FESFPS, vWA, HUMTH01, TPOX and CSF1PO) were investigated in a population sample of 107 unrelated Tibetan individuals by using a multiplex polymerase chain reaction (PCR), followed by 4% polyacrylamide gel electrophoresis (PAGE) and silver staining. All loci met the Hardy-Weinberg expectations. The forensically relevant parameters were calculated. This is the first time that Chinese Tibetan population data on DNA loci have been reported that are of forensic importance. Received: 8 February 2000 / Accepted: 7 November 2000     

Genetic polymorphism data on 15 autosomal STR markers in a Western Romanian population sample

The allelic frequency distribution and statistical genetic parameters of forensic relevance for 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, Penta E, Penta D, vWA, TPOX, D18S51, D5S818 and FGA) in a population sample of 336 non-related individuals residing in the Western part of Romania are presented.     

Population genetic data on 15 autosomal STRs in a Pakistani population sample

Allele frequencies for the 15 STR loci (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, VWA, D8S1179, TPOX and FGA) were investigated using PowerPlex^®16 amplification kit in a sample of 328 unrelated individuals from Islamic Republic of Pakistan. The allelic distributions were in Hardy Weinberg equilibrium for all loci except for the loci FGA, TPX and THO1. Various forensic indices were calculated and a comparison was made with geographically nearby populations.     

Genetic polymorphisms of 15 STR loci of Chinese Dongxiang and Salar ethnic minority living in Qinghai Province of China

Fifteen autosomal STRs loci were analyzed from two samples of 178 healthy unrelated autochthonous individuals of Chinese Dongxiang and Salar ethnic minority groups using a multiplex PCR system. Allele frequencies distribution and statistical parameters for all STR loci, D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA, were determined by the AmpFISTR Identifiler Kit. The observed genotype frequencies and expected of genotype frequencies were evaluated by chi(2)-test and the Fisher exact tests. chi(2)-test showed that the agreement with Hardy-Weinberg equilibrium (p>0.05) was for all studied STR loci of two populations. The data in the present study can be used greatly for routine forensic application in the region, and enrich Chinese ethnical genetic informational resources.     

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     

Forensic evaluation of 11 non-standard STR loci in Bangladeshi population

Allele frequencies and forensic efficiency parameters of 11 non-standard autosomal STR loci, D21S1437, D22S683, D8S1110, D10S2325, D12S1090, D17S1294, D3S1744, D14S608, D20S470, D18S536 and D13S765 were evaluated in a sample of 102 unrelated Bangladeshi individuals. No significant deviation from Hardy–Weinberg equilibrium was observed in any of the loci studied. Statistical parameters of forensic importance, the power of discrimination (PD), observed and expected heterozygosity (H), polymorphism information content (PIC), matching probability (MP), power of exclusion (PE) and typical paternity index (TPI) were calculated for the loci. The most informative locus among the 11 STR loci was D10S2325 (PD = 0.958), while the least informative was D17S129 (PD = 0.876). The combined PD (1-PM) and MP was calculated to be 0.9999999999997 and 2.23 × 10^?23, respectively. These parameters indicated the usefulness of the loci in forensic personal identification and parentage testing among Bangladeshi population.     

Allele frequency distribution for 15 autosomal STR loci in Afridi Pathan population of Uttar Pradesh,India

Allele frequencies of the 15 autosomal short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO D19S433, vWA, TPOX, D18S51, D3S1358, THO1, D13S317, D16S539, D2S1338, D5S818 and FGA were determined in Afridi Pathan population of Uttar Pradesh, India. All the 15 STR loci studied were found to be highly polymorphic with respect to observed heterozygosity values. Adherence to the expectations of the Hardy–Weinberg equilibrium (HWE) was confirmed for all the loci with an exception of TPOX and FGA. The allele 12 in CSF1PO was found to be most frequent. The power of discrimination was found to be high ranging from a minimum of 0.858 for the locus CSFIPO to maximum of 0.962 for the locus FGA, thereby facilitating the validation and efficiency of these STR markers in human identification. Population differentiation test between the studied and neighboring populations revealed significant differences at several loci suggesting the endogamous nature of the studied population. To the best of our knowledge, Afridi Pathan population has not been explored genetically for generating forensic data on STR markers. Therefore, STR allele frequency data of this unique population is a valuable contribution to the existing DNA database on Indian populations.     

Applying massively parallel sequencing to paternity testing on the Ion Torrent Personal Genome Machine

Massively parallel sequencing (MPS) is a promising supplementary method for forensic genetics and has gradually been applied to forensic casework. In this study, we applied MPS to forensic casework on an Ion Torrent Personal Genome Machine to evaluate its performance in paternity testing with mismatched STR loci. A total of 15 samples from seven cases containing one mismatched locus by capillary electrophoresis typing were analyzed. Combined paternity index (CPI) and relative chance of paternity were calculated according to the International Society for Forensic Genetics guidelines and the Chinese national standards recommended for paternity testing. With simultaneous analysis of enough STR loci, the results support the certainty of paternity, and the mismatched alleles were considered to be mutations (CPI > 10,000). With the detection of allele sequence structures, the origins of the mutations were inferred in some cases. Meanwhile, nine STRs (CSF1PO, D1S1656, D2S441, D2S1338, D3S1358, D8S1179, D12S391, D21S11 and D4S2408) were found in an increased number of unique alleles and three new alleles in three STRs (D2S441, D21S11, and FGA) that have not been reported before were detected. Therefore, MPS can provide valuable information for forensic genetics research and play a promising role in paternity testing.     

Population data and mutation rates of 19 STR loci in seven provinces from China based on Goldeneye™ DNA ID System 20A

Short tandem repeat (STR) analysis is a primary tool in forensic casework. Population data and mutation rates of STRs are very important for paternity testing and forensic genetics. However, the population data and mutation rates of STRs in Han nationality based on large samples have still not been fully described in China. In this study, the allelic frequencies, forensic parameters, and mutation rate of 19 STR loci (D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSFIPO, PentaD, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, and FGA) based on the Goldeneye™ DNA ID System 20A in Southern China Han nationality among seven provinces were investigated. Furthermore, population stratification of Southern China Han nationality among seven provinces was established. The multidimensional scaling (MDS) plot based on genetic distances (Fst) showed that the studied populations can be clustered into two major groups. However, relationships among populations were weak (Fst < 0.0043). A total of 376 cases of mutation were detected from the 19 selected loci in 15,396 meioses. The average mutation rate for the 19 loci was estimated to be 1.3 × 10⁻³ per meiosis. The mutation was mainly single step; the paternal mutation rate was higher than the maternal; and paternal mutation rate increases with paternal age.