Mutation analysis of 24 short tandem repeats in Chinese Han population

Germline mutations of 24 short tandem repeat (STR) loci (TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, Penta E, D16S539, D18S51, Penta D, D21S11, D2S1772, D6S1043, D7S3048, D8S1132, D11S2368, D12S391, D13S325, D18S1364, and GATA198B05) were studied for 6,441 parent–child meioses taken from the paternity testing cases in Chinese Han population. In total, 195 mutations were identified at 22 of the 24 loci. Among them, 189 (96.92%) mutations were one step, five mutations (2.56%) were two step, and one mutation (0.51%) was three step. No mutation was found at the TH01 and TPOX loci. The overall mutation rate estimated was 0.0013 (95% CI 0.0011–0.0015), and the locus-specific mutation rate estimated ranged from 0 to 0.0034. There was a bias in the STR mutations that repeat gains were more common than losses (∼1.7:1). Mutation events in the male germline were more frequent than in the female germline (∼4.3:1). Furthermore, loci with a larger heterozygosity tended to have a higher mutation rate. Mutation in short alleles was biased towards expansion, whereas mutation in long alleles favored contraction. The long alleles have a higher allelic mutational probability than short alleles.     

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.     

Bosnian population data for the 15 STR loci in the Power Plex 16 kit

The PowerPlex 16 amplification kit was used for the analysis of 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) in unrelated, autochthonous healthy adults from Bosnia (n=123 for TH01, Penta E, D16S539, CSF1PO, Penta D and TPOX, n=210 for D3S1358, D21S11, D18S51, D5S818, D13S317, D7S820, VWA, D8S1179 and FGA). The agreement with HWE was confirmed for all loci with the exception of Penta D (based on the ²-test only). The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 15 studied loci were 0.999999999999999997 and 0.999999, respectively.     

STR loci Penta D and Penta E: data from a Northern Thai population sample

We designed new primers that give shorter amplicons for Penta D and Penta E for easy separation on native polyacrylamide gels. 112 unrelated Northern Thai men were typed. A total of nine and eight-teen alleles was found for Penta D and Penta E, respectively. Both loci showed a high power of discrimination (Penta D: 0.927; Penta E: 0.966; both loci combined: 0.9975) as reported in other populations. Penta D met Hardy-Weinberg expectations, whereas Penta E did not, maybe because of the small sample size in relation to the large number of alleles of this locus.     

STR allele sequence variation: Current knowledge and future issues

This article reviews what is currently known about short tandem repeat (STR) allelic sequence variation in and around the twenty-four loci most commonly used throughout the world to perform forensic DNA investigations. These STR loci include D1S1656, TPOX, D2S441, D2S1338, D3S1358, FGA, CSF1PO, D5S818, SE33, D6S1043, D7S820, D8S1179, D10S1248, TH01, vWA, D12S391, D13S317, Penta E, D16S539, D18S51, D19S433, D21S11, Penta D, and D22S1045. All known reported variant alleles are compiled along with genomic information available from GenBank, dbSNP, and the 1000 Genomes Project. Supplementary files are included which provide annotated reference sequences for each STR locus, characterize genomic variation around the STR repeat region, and compare alleles present in currently available STR kit allelic ladders. Looking to the future, STR allele nomenclature options are discussed as they relate to next generation sequencing efforts underway.     

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.     

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.     

Genetic polymorphisms of 20 STR loci in a Chaoshan group from Jieyang,China

We obtained allelic frequencies and forensic parameters of 20 short tandem repeat (STR) loci (D3S1358, FGA, D5S818, D7S820, CSF1PO, D16S539, D19S433, vWA, D8S1179, D18S51, D13S317, TPOX, TH01, D2S1338, D12S391, D1S1656, D21S11, D6S1043, Penta D, Penta E) from 529 unrelated individuals in Jieyang Han population using PowerPlex® 21 (Promega, Madison, Wi, USA). The relationship between the Jieyang Han group and other Han populations was studied and the results showed that the Jieyang Han population had the closest genetic relationship with the Fujian Han population.     

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.     

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.     

联合应用D21S11,IFNAR位点定量PCR快速诊断先天愚型

为了探讨定量ＰＣＲ方法在分子水平对先天愚型基因诊断意义，本实验以ＳＴＲ（Ｄ２１Ｓ１１ＩＦＮＡＲ）做为遗传标记，合成特异引物对１１例正常人（６例外周血，５例羊水）及２８例先天愚型患者外周血进行同位素标记ＰＣＲ扩增后定量分析，结果显示在Ｄ２１Ｓ１１位点１１例正常人中１０人呈ＤＮＡ含量为１∶１关系的两条带，１人为１条带。２８例患者中２４人呈ＤＮＡ含量为２∶１的两条带，３人为ＤＮＡ含量为１∶１∶１关系的三条带，１人为１条带。在ＩＦＮＡＲ位点５例为纯合子，其余均为杂合子。实验表明Ｄ２１Ｓ１１和ＩＦ ＮＡＲ位点多态是对先天愚型基因诊断很有应用价值的遗传标记，应用定量ＰＣＲ的方法可在２４ｈ内对先天愚型做出快速、准确的产前及临床基因诊断。     

Population genetic study for 24 STR loci and Y indel (GlobalFiler™ PCR Amplification kit and PowerPlex® Fusion system) in 1000 Korean individuals

Allele frequencies for 23 autosomal short tandem repeat loci (D3S1358, vWA, D16S539, CSF1PO, TPOX, D8S1179, D21S11, D18S51, TH01, FGA, D5S818, D13S317, D7S820, D2S441, D19S433, D22S1045, D10S1248, D1S1656, D12S391, D2S1338, SE33, Penta D, Penta E), 1 Y-chromosome short tandem repeat locus (DYS391) and Y indel were obtained from 1000 unrelated individuals of the Korean population.     

Updated Brazilian STR allele frequency data using over 100,000 individuals: an analysis of CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, Penta D, Penta E, TH01, TPOX and vWA loci

The Brazilian population is one of the most heterogeneous populations of the world, formed mainly by an admixture of European, African and Native American populations. Brazil is the fifth largest country in the world (8,511,960 km²), being divided into five geographical regions. This study provides population genetic data of up to 137,161 unrelated individuals representing the entire Brazilian territory. Allelic frequencies and other population data analysis are reported for the 15 autosomal STR loci included in the PowerPlex^®16 kit (Promega Corporation, Madison, WI, USA). In order to guarantee that individuals were not related, we have considered only F1 data from couples undergoing paternity testing. The number of individuals genotyped for each locus was: CSF1PO (113,526); D3S1358 (135,133); D5S818 (135,181); D7S820 (137,136); D8S1179 (134,211); D13S317 (137,161); D16S539 (136,942); D18S51 (136,739); D21S11 (130,014); FGA (135,839); Penta D (110,333); Penta E (128,055); TH01 (112,695); TPOX (123,102); vWA (127,415). Allele sizes ranged from 1 to 48.2. Statistic parameters (PD, PIC and Ho; considering values ≥0.75) suggest that markers D13S317, D16S539, D18S51, D21S11, D7S820, D8S1179, Penta D, Penta E, TH01, FGA and vWA were more informative for genetic identification purposes in the Brazilian population.     

Analysis of 15 short tandem repeats reveals significant differences between the Arabian populations from Morocco and Syria

The short tandem repeat (STR) systems D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX and FGA were studied in Arabian population samples from Morocco and Syria. No significant deviation from Hardy-Weinberg equilibrium could be observed in either preparation. Comparing the Moroccan and Syrian populations using the program RxC, no similarity could be observed at all 15 loci. In the Moroccan and Syrian populations the matching probability is 1 in 1.4 x 10(17) and 1 in 2.6 x 10(17), respectively. Thus, the combination of these 15 STR loci is powerful tool for forensic identification in Arabian populations.     

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.     

Genetic variation of 15 autosomal short tandem repeat (STR) loci in the Palestinian population of Gaza Strip

Fifteen autosomal STR loci included in the PowerPlex^®16 System were typed in a population sample of 125 unrelated individuals from Palestinian population of Gaza Strip. Allele frequencies, Hardy–Weinberg equilibrium and forensic parameters were determined for the following loci: Penta E, D18S51, D21S11, TH01, D3S1358, FGA, TPOX, D8S1179, vWA, Penta D, CSF1PO, D16S539, D7S820, D13S317 and D5S818.     

Allele frequency data for 16 STR loci in the Vietnamese population

The short tandem repeat systems ACTBP2, D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, VWA, D8S1179, TPOX and FGA were studied in a population sample from Vietnam (178 individuals, mainly from the Hanoi area). The 16 loci met Hardy-Weinberg expectations and possess a combined power of discrimination greater than 0.9999999999999999998 and a combined power of exclusion greater than 0.99999994 in this Vietnamese population.     

Genetic variability of 15 autosomal STR loci in Russian populations

Allele frequencies for 15 STRs (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, Penta D, Penta E, THO1, TPOX, and vWA) in the PowerPlex 16 System (Promega Corporation) were assessed in 386 individuals from five Russian urban populations. No significant between-population differences in frequencies and molecular variance of 15 microsatellites were revealed. For all 15 loci, the combined matching probability is 3.19 × 10^?18 and the power of exclusion is 99.99989%.     

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 analysis of 15 autosomal and 12 Y-STR loci in the Espirito Santo State population, Brazil

This study provides population genetic data for individuals of Vitoria, Espirito Santo, Brazil, a location not yet characterized for STR frequencies used for genetic identification studies. Allelic frequencies and other population data analysis are reported for the 15 autosomal-STR loci included in the PowerPlex(?)16 kit (CSF1PO, D13S317, D16S539, D18S51, D21S11, D3S1358, D5S818, D7S820, D8S1179, FGA, Penta D, Penta E, TPOX, TH01 and vWA). Allele and haplotype frequencies, gene diversity and discrimination capacity were also estimated for the PowerPlex(?) Y System (DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439). Blood samples were obtained from 226 unrelated volunteers (135 males and 91 females) residents in the city of Vitoria, representing a typical sample of the mixed ethnicity present in the Espirito Santo State, Brazil. Within the tested population, the total number of individuals typed for specific markers is: 226 for D13S317, D21S11, D3S1358, D7S820, D8S1179 and FGA; 225 for D16S539 and D5S818; 224 for D18S51; 223 for CSF1PO; 222 for Penta D and vWA; 220 for Penta E; 207 for TPOX and 142 for TH01. Y-STR haplotypes were analyzed for 102 unrelated males, being 71 of them present in the 135 autosomal-STR sample, and 31 new males tested only for Y-STR markers. All autosomal markers were in Hardy-Weinberg Equilibrium. Y-STR analysis identified 101 haplotypes, being 100 of them unique.