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.     

Genetic polymorphism analyses of three novel X chromosomal short tandem repeat loci in the Xp22.3 region

X chromosomal short tandem repeats (X-STRs) can be useful for haplotype analysis in DNA testing, particularly for complex kinship testing or when one parent is absent. We searched downstream of four previously detected loci in the Xp22.3 region (LC149476, LC149479, LC149480, and LC149484) and detected and analyzed three novel short tandem repeats (STRs), LC317283, LC317284, and LC317285, with the repeat sequences TATAA, TTTA, and TATC, respectively. The forensic statistical values in Japanese subjects were confirmed to be noninferior to existing loci, with values for polymorphism information content, the power of discrimination in males (PDm), and the power of discrimination in females (PDf) of 0.5606–0.7448, 0.6078–0.7774, and 0.7990–0.9178, respectively. Haplotype analysis also revealed linkage disequilibrium between LC317283 and the four known loci (LC149476, LC149479, LC149480, and LC149484) and between two other novel loci (LC317284 and LC317285). Analysis of three family samples suggested that these STRs could be useful in complex kinship testing, so we developed an X-STR multiplex polymerase chain reaction (PCR) system for the seven loci and confirmed its ability to provide favorable amplification. We anticipate that the identified loci and developed multiplex PCR system will be beneficial to the field of forensic medicine.     

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     

Genetic structure of a Cuban population based on nine short tandem repeat loci

Cuba is a multiethnic and multiracial society. Here we describe the genetic variation of a sample of the Cuban population, which include the three most common racial groups, Caucasians, Negroids and Mestizos, by means of a set of nine microsatellites (HUMTH01, HUMTPOX, HUMCFS1PO, HUMVWA, HUMFESFPS, HUMF13A, HUMF13B, HUMLPL and HUMHPRTB). The analysis presented here indicates that these STR loci are highly informative for forensic purposes. The genetic data on the major racial groups is in good agreement with current demographic tendencies and with historic events that took place during the formation of the Cuban population.     

Improvement of short tandem repeat analysis of samples highly contaminated by humic acid

We investigated several methods for obtaining successful short tandem repeat (STR) results from high-humic acid (HA)-content samples. DNA purification efficiency was tested for QIAquick^® PCR Purification, QIAamp^® DNA Investigator and Prepfiler? Forensic DNA Extraction kits. HA-removal capacity of Inhibitor Remover and InhibitEX^® Tablet was tested. Experiments on overcoming HA effects on STR amplification were conducted using an AmpliTaq Gold^® DNA Polymerase and a TaKaRa Ex Taq? Hot Start Version (Ex Taq HS) with BSA addition. QIAquick kit was most efficient in HA removal and Ex Taq HS showed high resistance to HA. Increasing the amounts of Taq polymerases and BSA addition were shown to be efficient in overcoming PCR inhibition, but BSA addition was superior to the former method. Inhibitor Remover and InhibitEX^® Tablet did not positively affect the STR results. This study will help achieve better STR results with high-HA-content samples.     

Population data on the seven short tandem repeat loci D4S2366, D6S474, D14S608, D19S246, D20S480, D21S226 and D22S689 in a German population

Allele frequencies for the autosomal tetranucleotide short tandem repeat loci D4S2366, D6S474, D14S608, D19S246, D20S480, D21S226 and D22S689 were investigated in a sample of 189 unrelated German individuals using a multiplex polymerase chain reaction approach. The loci showed no significant deviations from Hardy-Weinberg equilibrium except for D14S608. All genotyped alleles were cloned and sequenced, and an allelic nomenclature consistent with the ISFH recommendations was defined.     

Population genetic analysis of Xiamen Han population on 21 short tandem repeat loci

GlobalFiler™ Express amplification kit incorporates 21 commonly used autosomal short tandem repeat (STR) loci and three gender determination loci. In this study, we analyzed GlobalFiler STR loci on 1006 unrelated individuals sampled of the Han population from Xiamen city, Fujian province, China. No deviations from Hardy–Weinberg equilibrium were observed. The combined probability of exclusion (CPE) for all 21 STR loci were >0.99999999771. A comparison of the allele frequencies in the population under study has been performed with other published from East Asian population for the same loci. Multiple STR loci showed significant differences between Han population from Xiamen and Korea, as well as Japan.     

Thirteen X-chromosomal short tandem repeat loci multiplex data from Taiwanese

Study results of variations in the X chromosome are useful tools in researching the genetic diversity of human populations and individual identification. We developed a 13 X chromosomal short tandem repeat (STR) multiplex system (DXS6807, DXS8378, DSX9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7424, DXS101, GATA172D05, HPRTB, DXS8377, DXS7423) amplified in one single polymerase chain reaction. DNA samples of 113 male and 108 female Taiwanese Han subjects were successfully analyzed using this 13 X-STR multiplex system. The distributions of allele frequencies were examined for independence. DXS8377, DXS101, DXS6789, and DXS6809 were found to be the most polymorphic markers in this study. High values of discrimination power and mean exclusion chance without significant evidence of association between these markers were obtained. In conclusion, this 13 X chromosomal STR multiplex system offers considerable forensic efficiency and may be useful in forensic identification casework.     

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.     

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.     

Forensic and population genetic analysis of Xinjiang Uyghur population on 21 short tandem repeat loci of 6-dye GlobalFiler™ PCR Amplification kit

Estimating the allele frequencies and forensic statistical parameters of commonly used short tandem repeat (STR) loci of the Uyghur population, which is the fifth largest group in China, provides a more precise reference database for forensic investigation. The 6-dye GlobalFiler™ Express PCR Amplification kit incorporates 21 autosomal STRs, which have been proven that could provide reliable DNA typing results and enhance the power of discrimination. Here we analyzed the GlobalFiler STR loci on 1962 unrelated individuals from Chinese Uyghur population of Xinjiang, China. No significant deviations from Hardy–Weinberg equilibrium and linkage disequilibrium were detected within and between the GlobalFiler STR loci. SE33 showed the greatest power of discrimination in Uyghur population, whereas TPOX showed the lowest. The combined power of discrimination was 99.999999999999999999999998746%. No significant difference was observed between Uyghur and the other two Uyghur populations at all tested STRs, as well as Dai and Mongolian. Significant differences were only observed between Uyghur and other Chinese populations at TH01, as well as Central-South Asian at D13S317, East Asian at TH01 and VWA. The phylogenetic analysis showed that Uyghur is genetically close to Chinese populations, as well as East Asian and Central-South Asian.     

Frequency data on four tetrameric STR loci D18S1270, D14S608, D16S3253 and D21S1437 in a Korean population

We present the results of a population study in Korea for four new tetrameric short tandem repeat (STR) loci employing multiplex PCR amplification, polyacrylamide gel electrophoresis of the PCR products and silver staining, which allow single base pair resolution and rapid typing. The loci tested were D18S1270, D14S608, D16S3253 and D21S1437 and all loci showed no significant deviations from Hardy-Weinberg equilibrium in more than 100 unrelated Koreans. This allelic frequency data can be used in forensic analyses and paternity tests to estimate the frequency of a multiplex PCR based DNA profile in the Korean population. Received: 13 January 1999 / Received in revised form: 14 June 1999     

Allele frequencies for 15 STR loci in a population from the Republic of Macedonia

Allele frequencies of 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA) were determined in a sample of 163 unrelated individuals from the Republic of Macedonia. AmpFISTR Identifiler Kit (Applied Biosystems) was used for PCR amplification. For all 15 loci, the combined matching chance is 6.6×10¹⁸ and the power of exclusion is 99.999954%.     

Genetic variation and sequence studies of a highly variable short tandem repeat at the D17S976 locus

The STR locus D17S976 was investigated by PCR amplification and native polyacrylamide gel electrophoresis in 158 unrelated Austrian Caucasians. No deviations from Hardy-Weinberg expectations were observed. The mean exclusion chance was 0.792, the discriminating power was 0.980 and the observed heterozygosity rate was 0.873. Moreover two alternative denaturing electrophoretic protocols are proposed. An allelic ladder consisting of 14 sequenced alleles (236–288 bp) was constructed. Sequence analysis revealed that the locus contained three different repeat motifs: ATCA, ATCT and ACCT, all of which vary in number between alleles. The aggregate number of the three tetrameric repeat types was used for allele designation. As a repeat with a single base deletion (ATC) was found in both the smallest and the largest alleles, a “.3” was added to the allele designation in those cases. Therefore the smallest allele is designated 19.3, and the largest allele is designated 32.3. To evaluate the exact extent of sequence variation more extensive sequence studies are necessary.     

Differences of PCR efficiency between two-step PCR and standard three-step PCR protocols in short tandem repeat amplification

The effects on STR typing results, using a two-step PCR protocol that combines the annealing and extension steps, were determined using samples at various DNA concentrations. DNA samples ranging from 62.5 to 500 pg were amplified using the reagents contained within the AmpFlSTR Identifiler PCR Amplification Kit. At 250–500 pg of DNA template, the rates of detecting alleles were close to those found when using three-step PCR (the standard Identifiler protocol) and two-step PCR protocols. The two-step PCR increased by 8.1% and 64.2% the average number of amplified alleles compared with the three-step PCR at 125 pg and 62.5 pg of template DNA, respectively. At 62.5–500 pg of DNA, the average peak heights were 23.3–65.0% higher than heights using the three-step PCR protocol. When two different PCR protocols were applied to old bones, the average number of amplified loci was similar. These results suggested that the two-step PCR protocol can generate more STR alleles in low template DNA samples; however, the method may be limited with samples of very low-quality, i.e., degraded DNA, compared with the three-step protocol. A better understanding of the effects of the two-step PCR protocol on amplification conditions might help researchers improve STR typing.     

High sensitivity multiplex short tandem repeat loci analyses with massively parallel sequencing

STR typing in forensic genetics has been performed traditionally using capillary electrophoresis (CE). However, CE-based method has some limitations: a small number of STR loci can be used; stutter products, dye artifacts and low level alleles. Massively parallel sequencing (MPS) has been considered a viable technology in recent years allowing high-throughput coverage at a relatively affordable price. Some of the CE-based limitations may be overcome with the application of MPS. In this study, a prototype multiplex STR System (Promega) was amplified and prepared using the TruSeq DNA LT Sample Preparation Kit (Illumina) in 24 samples. Results showed that the MinElute PCR Purification Kit (Qiagen) was a better size selection method compared with recommended diluted bead mixtures. The library input sensitivity study showed that a wide range of amplicon product (6–200 ng) could be used for library preparation without apparent differences in the STR profile. PCR sensitivity study indicated that 62 pg may be minimum input amount for generating complete profiles. Reliability study results on 24 different individuals showed that high depth of coverage (DoC) and balanced heterozygote allele coverage ratios (ACRs) could be obtained with 250 pg of input DNA, and 62 pg could generate complete or nearly complete profiles. These studies indicate that this STR multiplex system and the Illumina MiSeq can generate reliable STR profiles at a sensitivity level that competes with current widely used CE-based method.     

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.     

Analysis of nine short tandem repeat (STR) loci in the Slovenian population

A polymerase chain reaction (PCR)-based short tandem repeat (STR) system consisting of nine loci has recently been introduced in Slovenia for use in routine forensic identity testing. Fluorescently labelled PCR products were analysed using an ABI PRISM 310 Genetic Analyzer. The STR loci analysed exibit between 6 and 14 observed alleles per locus and have a combined matching probability of 2.3 × 10^–10. Received: 28 November 1997 / Received in revised form: 30 January 1998