A hypervariable STR polymorphism in the CFI gene: Southern origin of East Asian-specific group H alleles

Previous studies of four populations revealed that a hypervariable short tandem repeat (iSTR) in intron 7 of the human complement factor I (CFI) gene on chromosome 4q was unique, with 17 possible East Asian-specific group H alleles observed at relatively high frequencies. To develop a deeper anthropological and forensic understanding of iSTR, 1161 additional individuals from 11 Asian populations were investigated. Group H alleles of iSTR and c.1217A allele of a SNP in exon 11 of the CFI gene were associated with each other and were almost entirely confined to East Asian populations. Han Chinese in Changsha, southern China, showed the highest frequency for East Asian-specific group H alleles (0.201) among 15 populations. Group H alleles were observed to decrease gradually from south to north in 11 East Asian populations. This expansion of group H alleles provides evidence that southern China and Southeast Asia are a hotspot of Asian diversity and a genetic reservoir of Asians after they entered East Asia. The expected heterozygosity values of iSTR ranged from 0.927 in Thais to 0.874 in Oroqens, higher than those of an STR in the fibrinogen alpha chain (FGA) gene on chromosome 4q. Thus, iSTR is a useful marker for anthropological and forensic genetics.     

A hypervariable STR polymorphism in the CFI gene: Mutation rate and no linkage disequilibrium with FGA

A hypervariable short tandem repeat (STR) polymorphism in intron 7 of the human complement factor I gene (CFI) was investigated to estimate the mutation rate in Japanese samples and to test linkage disequilibrium (LD) with an STR in the fibrinogen alpha chain gene (FGA). The expected heterozygosity and the mutation rate of CFI were estimated to be 0.917 and 0.002, respectively. No LD was observed between CFI and FGA. CFI is a useful supplementary marker for forensic science.     

Short tandem repeat HumACTBP2 (SE33) and HumVWA: population genetic study on a north Italian population

Allele frequencies at the short tandem repeat (STR) loci HumACTBP2 and HumVWA were determined in 118 unrelated individuals from Northern Italy (Milan area). For locus HumACTBP2 (SE33) a total of 39 alleles was observed. Furthermore, two interalleles (N18m + N19m) and one allele (> N35) were found which were not observed in a wider German population survey (n = 560). For the STR system HumVWA, 7 alleles could be detected. Both systems showed no significant deviation from Hardy-Weinberg equilibrium. A comparison of Italian and German population data revealed no significant differences for locus HumVWA, while significant differences were observed for locus HumACTBP2.     

The effects of Asian population substructure on Y STR forensic analyses

A total of 3046 males of Chinese, Malay, Thai, Japanese, and Indian population affinity were previously typed for the Y STR loci DYS19, DYS385 (counted as two loci), DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS456, DYS458, DYS635, DYS448, and Y GATA H4 using the AmpFlSTR® Yfiler™ kit. These samples were assessed for population genetic parameters that impact forensic statistical calculations. All population samples were highly polymorphic for the 16 Y STR markers with the marker DYS385 being the most polymorphic, because it is comprised of two loci. Most (2677 out of a total of 2806 distinct haplotypes) of the 16 marker haplotypes observed in the sample populations were represented only once in the data set. Haplotype diversities were greater than 99.57% for the Chinese, Malay, Thai, Japanese, and Indian sample populations. For the Y STR markers, population substructure correction was considered when calculating the rarity of a Y STR profile. An F_ST value, rather than a R_ST value, is more appropriate under a forensic model. Because the F_ST values are very small within the Asian populations, the estimate of the rarity of a haplotype comprised of 10–16 markers does not need substructure correction. However haplotypes with fewer markers may require F_ST corrections when calculating the rarity of the profile.     

The polymorphisms of DYS388 and DYS392 on the Y chromosome in Japanese and German populations

The analysis of a genotype survey in Japanese and German populations at the loci DYS388 and DYS392 located on the Y chromosome is reported. The gene diversities of DYS388 were 0.34 and 0.30 in the Japanese and German males, respectively, and six alleles were found in both groups. The gene diversities of DYS392 were 0.65 and 0.64 and the number of alleles was 8 and 9, respectively in the two populations. The distribution of DYS388 alleles in the Japanese population was different from the German population. The allele distribution of DYS392 showed significant differences among Asian populations. Received: 5 January 1998 / Received in revised form: 27 April 1998     

Genetic analysis of the STR system D20S161 in Japanese and Bangladeshi

The allele distributions of the STR locus D20S161 have been investigated in Japanese and Bangladeshi people. No deviation from the Hardy-Weinberg equilibrium was observed in either population. D20S161 was found to be a polymorphic STR with seven alleles in Japanese and with six alleles in Bangladeshi. The distribution of allele frequencies in Japanese was very similar to that in Bangladeshi. The D20S161 system can be a potential marker for medicolegal individualization and paternity testing.     

Analysis of the short tandem repeat systems HumVWA and HumF13B in a population sample from northern Thailand

Two STR systems (HumVWA, HumF13B) were analysed in a northern Thailand population sample using PCR and gel electrophoresis. No deviations from Hardy-Weinberg equilibrium were observed. A rare VWA allele was detected, sequenced and the molecular structure is presented. Interpopulation comparisons revealed that the Thai allele frequencies were most similar to data from other Asian populations. Received: 1 January 1997 / Received in revised form: 20 February 1997     

The STR systems HumVWA and HumACTBP2 in a Hungarian population

Allele frequencies of the Short tandem repeat systems HumVWA and HumACTBP2 were determined from 105 unrelated individuals from the area of Szeged, Hungary. A total of 8 alleles was detected for VWA, and 23 alleles were found for ACTBP2. In both systems no deviations from Hardy-Weinberg equilibrium were observed. A comparison of the Hungarian and German frequency profiles revealed significant differences at both STR loci.     

DXS10011: a hypervariable tetranucleotide STR polymorphism on the X chromosome

The locus DXS10011 is a polymorphic system with a tetranucleotide repeat sequence located on the human X chromosome. The distribution of allele frequencies was examined in 334 Japanese and 171 German individuals and a total of 36 alleles was detected in the two population groups. This STR polymorphism will be a useful marker for linkage analysis. Received: 8 March 1999 / Received in revised form: 14 July 1999     

Population genetics of the hypervariable locus D12S391 in Koreans

The hypervariable short tandem repeat (STR) locus D12S391 was investigated in a Korean population and 34 fragments were sequenced to confirm the structure of alleles. From these sequenced fragments an allelic ladder containing 13 sequenced alleles was constructed. From 595 unrelated Koreans, 14 alleles were detected and one variant allele 19.3 was observed. The observed heterozygosity was 0.795 and no deviation from Hardy-Weinberg equilibrium was observed in the Korean population (p = 0.606). The allele frequency distribution in the Korean population was not similar to other racial or ethnic groups except for Egyptians, Yemenis, Japanese and Caucasoids from the Rhine area. No mutations were observed in the 702 meioses from 144 Korean families. This study demonstrates that the STR locus D12S391 is a useful tool for forensic identification and parentage testing. Received: 15 September 1999 / Accepted: 18 December 1999     

Frequency data for the STR loci HumFibra (FGA) and HumACTBP2 (SE33) in a population of Germans and Turks from South-West Germany

Population studies were carried out on German and Turkish individuals from South-West Germany using the short tandem repeat (STR) systems HumFibra (n = 138 Turkish and 1161 German individuals) and HumACTBP2 (n = 202 Turkish and 1338 German individuals). After electrophoresis 19 alleles could be identified for HumFibra and 55 for HumACTBP2. No significant deviations from Hardy-Weinberg equilibrium were observed. Received: 11 February 1998 / Received in revised form: 4 May 1998     

Tetrameric short tandem repeat (STR) system D15S233 (wg1d1): sequencing and frequency data in the japanese and Chinese populations

We evaluated the forensic usefulness of D15S233 (wg1d1), a tetrameric short tandem repeat (STR) locus, in the Japanese and Chinese populations. Typing was performed by denaturing polyacrylamide gel electrophoresis followed by silver staining. Nine different alleles were found in 472 Japanese chromosomes and seven in 186 Chinese chromosomes. 102 alleles sequenced were composed of two kinds of repeats (AGGA and GGGA). All alleles differed in size by one tetranucleotide repeat unit, and no insertion or deletion was found. The expected unbiased heterozygosities in Japanese and Chinese were 0.766 and 0.785, respectively. No significant deviations from the Hardy-Weinberg equilibrium were found in either population. We retyped all samples using an alternative pair of flanking primers in order to detect any spurious appearances of homozygotes due to sequence variation at the primer annealing site. One heterozygous sample had unbalanced density bands when the original primer set was used, but equal density bands when our newly designed primer set was used. Sequencing analysis revealed that the sparser allele had one nucleotide substitution near the 5' end of the annealing site of the original primer region. Thus, all apparently homo/heterozygous samples were thought to be truly homo/heterozygous. We also applied the D15S233 locus to paternity testing and forensic identification. Our results suggest that this locus should be a very useful STR locus for forensic practice in Japanese and Chinese.     

The STR loci HumTPO and HumLPL: population genetic data in eight populations

The two STR systems HumTPO and HumLPL were investigated in eight human populations (Moroccans, Ovambos, Papuans, Australian aborigines, Germans, Turks, Japanese and Chinese). After electrophoresis, seven and eight alleles were identified in the HumTPO and HumLPL systems, respectively. In each population, no deviations from Hardy-Weinberg equilibrium were observed, but considerable differences in phenotype frequencies of each system were found between major ethnic groups. Received: 10 June 1997 / Accepted: 10 July 1997     

Japanese population data for two STR loci,HumTPO and HumLPL

The two short tandem repeat (STR) systems, HumTPO and HumLPL, were investigated in blood samples obtained from approximately 800 unrelated Japanese individuals living in seven geographically different areas of Japan. Neither deviation from a Hardy-Weinberg equilibrium nor significant difference between the allele distributions was found among the seven Japanese populations in the two STR systems. These findings indicate that there is a general uniformity for both the STR loci in the Japanese population.     

Sequence analysis of alleles at a microsatellite locus D14S299 (wg1c5) and population genetic comparisons

In order to increase the discriminating power of DNA analysis in personal identification, we evaluated the forensic utility of the microsatellite locus D14S299 (wg1c5) in the Japanese population and also in the Chinese and Caucasian populations. Twelve different alleles were identified in length by gel electrophoresis with silver staining. The major alleles in Japanese were sequenced and designated as the numbers of the variable repeats (GGAT or GGAA). There were five variable regions and extensive homoplasy was found. However, the allele fragment lengths were in 4 bp increments and no “interalleles” were found. The estimated heterozygosity and the polymorphism information content (PIC) were 0.726 and 0.689, respectively in Japanese. Those in Chinese (0.743 and 0.704) were similar to those in Japanese, while those in Caucasians (0.812 and 0.781) were much higher. After adjacent alleles were combined to yield at least five entries, statistical analysis was performed. The power of discrimination (PD) was 0.887 in Japanese, 0.895 in Chinese and 0.935 in Caucasians and no significant deviations from the Hardy-Weinberg equilibrium were found in the three populations. We retyped all apparently homozygous samples using an alternative pair of flanking primers and found them to be true homozygotes. D14S299 appears to be a useful STR locus for forensic practice. Received: 28 September 1998 / Received in revised form: 4 January 1999 / Accepted: 8 February 1999     

Parentally imprinted allele typing at a short tandem repeat locus in intron 1a of imprinted gene KCNQ1

A short tandem repeat (STR) in the intron 1a of paternally imprinted gene, KCNQ1, is evaluated as a new probe for use in parentally imprinting allele (PIA) typing. This typing can determine the inheritance of one allele from father by the methylation difference. Allelic and genotypic frequencies of the STR were determined using samples from 175 unrelated Japanese and 170 unrelated Germans. The polymorphism information contents were 0.652 and 0.634 for the Japanese and the Germans, respectively, indicating usefulness in individual identification. This method was applied to five Japanese families consisting of 19 individuals. Genomic DNA was digested by methylation-sensitive restriction endonucleases, HhaI and HapII, followed by PCR amplification using two-step sandwich primer sets and the products were analyzed on polyacrylamide gel electrophoresis. For all of the families, each child's paternal allele given by PIA typing corresponded to one of the two alleles from father, not the two from mother, that were determined by the STR genotyping. The results demonstrate that this STR probe is feasible for use in PIA typing and that its typing method can contribute to paternity testing.     

Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems

Rare variants are widely observed in human genome and sequence variations at primer binding sites might impair the process of PCR amplification resulting in dropouts of alleles, named as null alleles. In this study, 5 cases from routine paternity testing using PowerPlex^®21 System for STR genotyping were considered to harbor null alleles at TH01, FGA, D5S818, D8S1179, and D16S539, respectively. The dropout of alleles was confirmed by using alternative commercial kits AGCU Expressmarker 22 PCR amplification kit and AmpFℓSTR^®. Identifiler^® Plus Kit, and sequencing results revealed a single base variation at the primer binding site of each STR locus. Results from the collection of previous reports show that null alleles at D5S818 were frequently observed in population detected by two PowerPlex^® typing systems and null alleles at D19S433 were mostly observed in Japanese population detected by two AmpFℓSTR™ typing systems. Furthermore, the most popular mutation type appeared the transition from C to T with G to A, which might have a potential relationship with DNA methylation. Altogether, these results can provide helpful information in forensic practice to the elimination of genotyping discrepancy and the development of primer sets.     

Validation studies and characterization of variant alleles at the short tandem repeat locus D12S391

Validation studies were carried out on the short tandem repeat (STR) locus D12S391 including the determination of the allele frequencies, forensic application and sequence analysis of variant alleles. A total of 16 alleles were found in a population survey of 158 unrelated individuals from the Rhine area, none of which exceeded the 0.20 frequency level. In 316 alleles analysed so far 18 alleles were found with an incomplete repeat unit in the 5′-end of the repeat region. The statistical values were similar to those of other European populations and no deviation from Hardy-Weinberg equilibrium (HWE) was observed. Received: 4 February 1998 / Received in revised form: 22 April 1998     

D20S161 data for three ethnic populations and forensic validation

In order to evaluate the forensic applicability of the STR locus D20S161 and construct a preliminary database, the genotype distributions and allele frequencies in five populations from three main ethnic groups were investigated, including Germans, Slovakians, African Americans, Japanese and Chinese. A total of 512 samples from unrelated individuals and 85 confirmed father/mother/¶child triplets were analyzed by PCR and allele determination was carried out by comparison with a sequenced human allelic ladder. The results showed that D20S161 typing was both precise and reliable. A total of 7 alleles was found in these populations and no evidence of deviation from Hardy-Weinberg equilibrium was observed. Pairwise comparisons between populations showed that there were significant differences in the distributions of the allele frequencies among the three main ethnic groups. No mutation events were observed from the confirmed father/mother/¶child triplets. With a maximum likelihood method, the mutation rate was indirectly estimated as 2.5 × 10^–5. These results suggest that D20S161 is a useful marker for forensic casework and paternity analysis.     

Automated analysis of sequence polymorphism in STR alleles by PCR and direct electrospray ionization mass spectrometry

Short tandem repeats (STRs) are the primary genetic markers used for the analysis of biological samples in forensic and human identity testing. The discrimination power of a combination of STRs is sufficient in many human identity testing comparisons unless the evidence is substantially compromised and/or there are insufficient relatives or a potential mutation may have arisen in kinship analyses. An automated STR assay system that is based on electrospray ionization mass spectrometry (ESI-MS) has been developed that can increase the discrimination power of some of the CODIS core STR loci and thus provide more information in typical and challenged samples and cases. Data from the ESI-MS STR system is fully backwards compatible with existing STR typing results generated by capillary electrophoresis. In contrast, however, the ESI-MS analytical system also reveals nucleotide polymorphisms residing within the STR alleles. The presence of these polymorphisms expands the number of alleles at a locus. Population studies were performed on the 13 core CODIS STR loci from African Americans, Caucasians and Hispanics capturing both the length of the allele, as well as nucleotide variations contained within repeat motifs or flanking regions. Such additional polymorphisms were identified in 11 of the 13 loci examined whereby several nominal length alleles were subdivided. A substantial increase in heterozygosity was observed, with close to or greater than 5% of samples analyzed being heterozygous with equal-length alleles in at least one of five of the core CODIS loci. This additional polymorphism increases discrimination power significantly, whereby the seven most polymorphic STR loci have a discrimination power equivalent to the 10 most discriminating of the CODIS core loci. An analysis of substructure among the three population groups revealed a higher θ than would be observed compared with using alleles designated by nominal length, i.e., repeats solely. Two loci, D3S1358 and vWA produced θ estimates of 0.0477 and 0.0234, respectively, when the expanded allele complement (i.e., nominal allele and SNPs) was considered compared to 0.0145 and 0.01266, respectively when only nominal repeat number was considered. These differences may indicate underlying population specific allele distributions exist within these populations. A system of nomenclature has been developed that facilitates the databasing, searching and analyses of these combined data forms.