Catalonian population study of the tetranucleotide repeat loci D3S1358, D8S1179, D18S51 and D19S253

Allele frequencies for four short tandem repeat loci were determined in a population sample from Catalonia (NE Spain). After denaturing PAGE electrophoresis, 8 alleles were identified for D3S1358 (n = 201), 10 alleles for D8S1179 (n = 198), 13 alleles for D18S51 (n = 197) and 11 alleles for D19S253 (n = 201). No deviation from Hardy-Weinberg equilibrium was found. Complete and relative uniformity in Caucasoid populations has been observed for D18S51 and D8S1179 respectively. Pronounced differences were found between different ethnic groups for both systems. Catalonia and Portugal do not differ for D3S1358 locus. Multiplex PCR amplifications of three loci (D3S1358, D18S51 and D19S253) without overlapping fragment size ranges could be interesting for monochrome automated laser fluorescence devices. Received: 15 January 1998 / Received in revised form: 20 April 1998     

AMPFLP analysis of the VNTR loci D1S80 and ApoB in Hungary

Population data studies for D1S80 and ApoB were carried out on a caucasian population sample from Hungary of 229 and 222 unrelated individuals, respectively. We observed 26 different alleles for D1S80 and 13 for ApoB. The allele frequencies found are similar to those reported in the literature for European caucasians. No evidence of significant deviations from Hardy-Weinberg equilibrium were observed for both AMPFLP systems.     

Population genetics of the D12S391, CSF1PO and TPOX loci in Catalonia (Northeast Spain)

Allele and genotype frequencies for three short tandem repeat loci were determined in a population sample from Catalonia (NE Spain). After denaturing PAGE electrophoresis, 11 alleles were identified for D12S391 (n = 167), 9 alleles for CSF1pO (n = 282) and 6 alleles for TPOX (n = 283). No deviation from Hardy-Weinberg equilibrium was found. The allele frequencies observed are similar to those of other compared European populations. Received: 28 April 1997 / Received in revised form: 10 July 1997     

D1S80 allele frequencies in a Chinese population

Allele frequencies for the VNTR locus D1S80 were determined in a Chinese population sample using the polymerase chain reaction and subsequent analysis of the amplified products by polyacrylamide gel electrophoresis and silver staining. A total of 18 nominal D1S80 alleles were observed in 105 unrelated Chinese. The data demonstrate that D1S80 is highly polymorphic in Chinese with a heterozygosity of 90.5%. The D1S80 frequency distribution meets Hardy-Weinberg expectations. This D1S80 data can be used in forensic analyses and paternity tests to estimate the frequency of a DNA profile in a Chinese population.     

Analysis of eight STR loci in two Hungarian populations

A multiplex reaction for the eight STR loci D3S1358, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820 was used to generate allele frequency databases for two Hungarian population samples, Caucasians from the Budapest area and Romanies from Baranya county. During the analysis two intermediate-sized alleles and a sequence variant allele were observed at the D7S820 locus. All three types of allelic variants were found to have modifications in the same block of a (T)₉ stretch located within the 3′ flanking region of each allele, which may indicate a possible higher mutation rate of this (T)₉ block. For the loci D3S1358 and D7S820 the Romany population database showed departures from Hardy-Weinberg equilibrium. The forensic efficiency values for the Romany population were slightly different from those found in the Hungarian Caucasian population. Comparing the allele frequency values by G-statistic, calculating the F_ST indices and with the pair-wise comparisons of inter-population variance, the two Hungarian populations could be distinguished using data from the eight STR loci. Received: 18 May 1999 / Received in revised form: 26 August 1999     

Population genetics and forensic efficiency data of 4 AMPFLP's

Summary Family studies were carried out in a population sample from north west Germany using 4 amplifiable VNTR polymorphic systems D1S80 (MCT118), ApoB, D17S30 (YNZ22) and COL2A1. Separation was carried out in polyacrylamide gels and visualised using silver staining. In family studies (n = 30) no evidence of new mutations was found. The population study of unrelated individuals (mothers and putative fathers) showed that all 4 systems were highly polymorphic and similar to other population studies. The combined exclusion chance was calculated to be approximately 99% and the combined discrimination index 1.5 · 10^–4. The HardyWeinberg equilibrium was checked by forming groups of alleles and no significant deviations could be found in all systems.     

pMCT 118 (D1S80): a new allelic ladder and an improved electrophoretic separation lead to the demonstration of 28 alleles

Summary Population data studies carried out on caucasians from Northwest Germany (n = 218) using the AMPFLP system pMCT 118 (D1S80). The method used in a previous study (Rand et al. 1992) for pMCT 118 could be improved by increasing the electrophoretic separation length from 10 to 20 cm and by using an extended allelic ladder which allowed the distinction of 8 additional alleles (a total of 28 alleles). Out of the 8 additional alleles 5 could be differentiated which differed within the 16 by repeat sequence. The allele frequencies found were compared to population data from American caucasians, Hispanics and black Americans (Eisenberg and Maha 1991). All populations with the exception or black Americans, showed good agreement.     

Allele frequency distribution of the D1S80 (pMCT118) locus polymorphism in the Japanese population by the polymerase chain reaction

Summary Population studies among Japanese were carried out at the D1S80 locus by the polymerase chain reaction and subsequent analysis in agarose gel electrophoresis. A total of 58 genotypes and 25 alleles ranging from 16 to 45 repeat units were observed in a population group of 121 unrelated individuals. The alleles with 18, 24 and 30 repeat units were found to be most common. Some large alleles with more than 42 repeat units were first observed in this study. Statistical tests for Hardy-Weinberg equilibrium showed that no significant deviations could be found in this Japanese population sample. The values of the mean exclusion chance and the discriminating power (DP) were calculated to be 0.76 and 0.91, respectively. The observed heterozygosity was 0.91.     

Frequency of D1S80 and HLA DQα alleles in a Chinese population

Allele frequency distributions for the D1S80 (MCT118) and HLA DQ loci were determined in a Chinese population sample using the polymerase chain reaction (PCR). A total of 25 alleles and 100 phenotypes were observed for D 1 S80. The frequency of allele 18 was higher than allele 24 only in this Chinese population when compared to other reported populations. A total of 6 alleles and 21 possible phenotypes were observed for HLA DQ. The power of discrimination was 0.97 and 0.93 for D1S80 and HLA DQ, respectively.     

Population genetic data,comparison of the repeat structure and mutation events of two short STRs

The short tandem repeat (STR) systems D3S1545 and D7S1517, both small size STRs (fragment lengths <160 bp), were investigated in a population sample of German Caucasoids. New primer sequences more closely flanking the repetitive region were designed for D3S1545. For D3S1545, 7 alleles could be found (heterozygosity 0.68) while 11 alleles could be typed for D7S1517 (heterozygosity 0.83). Additionally, sequencing of selected alleles was carried out to establish the allele nomenclature and to clarify the structure of the tandem repeat arrays. D3S1545 showed a uniform GATA repeat structure but, in contrast, the repeat stretch of D7S1517 showed a compound structure characterised by different numbers of GAAA and CAAA repeats. Two isolated cases of a new mutation could be confirmed for D7S1517. The alleles of these two family constellations were characterised by sequencing and the probable mutational events were demonstrated.     

Microvariation at the human D1S80 locus

The minisatellite locus D1S80, (location: 1p35– p36), GenBank sequence accession # D28507), is a variable number of tandem repeat (VNTR) locus with a 16 base pair repeat size. The sequence of the predominant core repeat region and variants of the D1S80 locus were determined to ascertain whether sequence variation or size variation is the cause of altered migration of some D1S80 alleles. A total of 23 alleles from 14 individuals, previously typed based on the number of repeats (i.e. nominal alleles) for the D1S80 locus, were selected for sequence analysis. The individuals were from African American, Caucasian, and Hispanic databases. From these, 18 different repeat unit sequences were observed and arbitrarily designated A–R. Structural relationships between the alleles became more apparent when the arrays of repeat units were divided into common motifs or super-repeat domains. Six motifs ranging from 3 to 9 repeat units were identified. Several of the alleles included repeat arrays which were too diverse to predict an evolutionary relationship, however, there are two general repeat motif arrays and each has some relationship with either the 18 or the 24 repeat allele. The D1S80 allelic polymorphism is primarily due to variation in the number of repeat units and to sequence variation among repeats, however, it can not be ruled out that some rare alleles may be due to insertions or deletions.     

The STR locus D11S554: allele frequencies and sequence data in a Japanese population

A population study on the short tandem repeat (STR) locus D11S554 was carried out in a sample of 362 unrelated Japanese individuals living in the Gifu Prefecture. A total of 46 different alleles ranging from 180 bp to 340 bp and 135 genotypes were revealed. Sequence analysis of alleles was carried out for 185 samples. The sequence structures of the repeat regions of the alleles were found to be complex and the alleles were classified into nine sequence types, including four new sequence types. According to the system of Adams et al. (1993), we designated the new sequence types IA³, IA⁴, IA⁵ and IB³, respectively. Out of the 46 different alleles, 11 showed sequence heterogeneity. The results of this study demonstrated that the D11S554 locus is a powerful and useful genetic marker for forensic practice in the Japanese population. Received: 6 December 2000 / Accepted: 31 May 2001     

Subtyping and characterization of D1S80 alleles in a Japanese population using PCR-RFLP

In a Japanese population study of the D1S80 locus 24 alleles ranging from allele16 to allele43 were analysed using PCR-RFLP. As two repeat units were found to contain the restriction cleavage site (CCAGG) for EcoRII, we digested the alleles with EcoRII, separated the digested fragments on polyacrylamide gels and stained with ethidium bromide. Of the 24 alleles 11 band patterns were identified and tentatively labeled E1 to E11. A total of 42 subtypes were detected in a population group of 111 unrelated individuals. All samples of allele18 were of the E3 type, while about 60% of the allele 24 samples were of the E4 type and about 40% were of the E8 type. The third most frequent allele (allele30) contained four types, E4, E8, E5 and E6. No deviations from Hardy-Weinberg equilibrium were observed. Since this method could differentiate those samples which had the same length but different sequences, it is quite useful for paternity testing and individual identification. Received: 12 June 1997 / Received in revised form: 8 December 1997     

Population studies of three AMPFLPs systems in a North Polish population

Allele and phenotype frequencies for D1S80, D17S5 and ApoB were determined in a population sample of more than 200 unrelated persons from North Poland using the PCR method. For D1S80, D17S5 and ApoB 19, 13 and 21 alleles respectively were observed. No deviations from Hardy-Weinberg equilibrium were detected. All three systems have discrimination values above 92% and a cumulative discrimination index of 4.5 × 10⁴.Dedicated to Prof. Dr. J. Gerchow on the occasion of his 75th anniversary     

D1S80 (pMCT118) allele frequencies in a Malay population sample from Malaysia

The D1S80 allele frequencies in 124 unrelated Malays from the Malaysian population were determined and 51 genotypes and 19 alleles were encountered. The D1S80 frequency distribution met Hardy-Weinberg expectations. The observed heterozygosity was 0.80 and the power of discrimination was 0.96. Received: 17 June 1996 / Received in revised form: 16 October 1996     

Swiss population data and forensic efficiency values on 3 tetrameric short tandem repeat loci-HUMTH01, TPOX,and CSFIPO - derived using a STR multiplex system

Allele and genotype frequencies for 3 tetrameric short tandem repeat loci were determined in a Swiss population sample (n = 100) using the GenePrint STR Multiplex System, electrophoresis of the PCR products in DNA sequencing gels and subsequent detection of allelic fragments by silver staining. The loci are HUMTH01, TPOX, and CSFIPO. The observed heterozygosities are 83.0%, 60.0%, and 72.0%, respectively. The discrimination power determined for the individual loci is 0.914, 0.780, and 0.860, respectively, and the combined discrimination power for the triplex is 0.997. All loci meet Hardy-Weinberg expectations and after Bonferroni correction there was no evidence that the population sample deviates from expectations of independence. Moreover, independence of alleles at these STR loci with other PCR-based loci derived from the same Swiss population sample, previously reported, were considered. These loci were DQA1, LDLR, GYPA, HBGG, D7S8, GC and D1S80. Again, after Bonferroni correction there was no evidence that the population sample deviates from expectations of independence among alleles at the 10 different PCR-based loci. Thus, the allelic frequency data can be used in human identity testing to estimate the frequency of a multiple PCR-based DNA profile in the Swiss population.     

Non-amplification of an allele of the D8S1179 locus due to a point mutation

During a population study of 128 Korean families (626 persons) with the AmpFlSTR Profiler Plus PCR amplification system, we found an unusual homozygous genotype at the D8S1179 locus in 4 families. Therefore, a new pair of primers was designed for the D8S1179 locus from GenBank data (GenBank Accession No. G08710) to evaluate the cause. The newly designed primers amplified alleles that were not amplified with the AmpFlSTR Profiler Plus PCR amplification system. We sequenced alleles of the family members who had non-amplified alleles and we found a G-to-A transition at the position of the 147th base of the GenBank sequence. Received: 10 August 2000 / Accepted: 7 January 2001     

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.     

D1S80 subtyping by PCR-RFLP: new nomenclature and further characterization

In a previous study, we screened out sequence variations within alleles at the D1S80 locus of a Japanese population using PCR-RFLP with EcoRII as a restriction enzyme. In the present study, through analyzing the alleles in a Chinese population, we were able to demonstrate four new electrophoretic band patterns that were complementary to the Japanese data. After summarizing the band patterns and sequencing results of these two populations, we established a new nomenclature for the PCR-RFLP band patterns, closely relating them to their corresponding sequences so that the new types could be designated easily and accurately. After PCR-RFLP subtyping, nineteen alleles in the Chinese population were revealed to have a total of thirty-seven subtypes. The discrimination power of this locus in the Chinese population was elevated from 0.974 to 0.988, and the Hardy-Weinberg equilibrium in this population showed no deviation when checked. Two samples typed as homozygotes 24/24 and 30/30 were identified to be actually heterozygous according to their band patterns. The result was supported by the sequencing analysis of the two samples in which overlapping of eight and eleven repeat units, respectively, were revealed. The heterozygosity was thus elevated from 0.85 to 0.87. The present study proved that PCR-RFLP was an effective method for subtyping D1S80 alleles in the Chinese.     

The distribution of HLA DQA1 and D1S80 (pMCT118) alleles and genotypes in the populations of Galicia and Central Portugal

Summary Two South-West European populations (Galicia and Central Portugal) have been studied for the HLA DQA1 and D1S80 systems. The allele and genotype frequencies found have been compared with other previously published data. The distribution of the observed genotypes is in Hardy-Weinberg equilibrium for both systems. In the D1S80 system, no significant differences were found between both populations, although in the HLA DQA1 system the allele DQA1*0301 is twice as frequent in the Galician population. Other populations that have been compared showed a certain degree of divergence for the HLA DQA1 system. The combined chance of exclusion for both systems is 0.84 in Galicia and 0.85 in Central Portugal, and the combined power of discrimination is 0.993 in the 2 populations studied.