HumFES/FPS and HumF13B: Population genetic data from North Italy

DNA extracted from 119 unrelated individuals was analysed by the polymerase chain reaction at the polymorphic microsatellite loci HumFES/FPS (n = 115 individuals) and HumFl3B (n = 119 individuals). The samples were collected from Caucasians living in the area of Milano (northern Italy). After horizontal polyacrylamide electrophoresis, 8 alleles were observed for HumFES/FPS, and 5 for HumF13B. Testing for Hardy-Weinberg equilibrium showed no significant deviation. The allele frequency data were compared with a German and a Turkish population sample.     

Short tandem repeat polymorphism at the HUMCD4 and HUMF13B loci in a Croatian population

Population studies were carried out on unrelated individuals of Croatian ancestry. Genomic DNA was amplified by the polymerase chain reaction (PCR) at the polymorphic microsatellite loci HUMCD4 (n = 105 individuals) and HUMF13B (n = 108 individuals). After horizontal polyacrylamide gel electrophoresis followed by silver staining 6 alleles and 12 genotypes were observed for HUMCD4 and 6 alleles and 13 genotypes could be identified for HUMF13B. Data obtained were in concordance with the prediction of Hardy-Weinberg equilibrium. The allele frequency data were compared with Austrian and Italian population samples and no significant deviations between these populations were observed. Received: 16 September 1996 / Received in revised form: 17 February 1997     

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     

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     

Global population variability in Promega PowerPlex CS7, D6S1043, and Penta B STRs

Supplementary short tandem repeats (STRs) can be added to forensic DNA analyses when core markers fail to provide sufficient discrimination power in identity and relationship testing. We combined D6S1043 and Penta B with Promega's PowerPlex CS7 supplementary STR kit, comprising Pentas D and E plus LPL, F13A01, FES/FPS, F13B, and Penta C. The nine STRs were typed in 941 individuals from 51 diverse populations of the CEPH Human Genome Diversity Panel (HGDP-CEPH), and we report allele frequency estimates plus rare alleles identified. Both Penta B and D6S1043 show highly informative variation in all populations, exceeding most CS7 STRs and raising cumulative random match probabilities by at least two orders of magnitude. However, Penta B genotype distributions show an excess of homozygotes across all HGDP-CEPH population groups indicating likely allele dropout from uncharted SNP or Indel variation at the primer sites chosen to type this STR. The first sequence analysis of common regular and rare intermediate D6S1043 alleles is reported. D6S1043 .3 intermediate alleles were found to occur at a high frequency in Native Americans, providing scope for differentiation of this group.     

A new allele at the short tandem repeat locus HumF13A01

We investigated the (AAAG)n short tandem repeat (STR) polymorphism HumF13A01 an Austrian Caucasoid population sample (n = 674). PCR amplified fragments were detected on an automatic A.L.F. DNA sequencer using laser-induced fluorescence. A total of 14 alleles could be identified, including a new 179 bp allele which was designated allele 3. Sequence determination of allele 3 confirmed the typing results by revealing three continuous copies of the core repeat, whereas in sequencing of 54 additional alleles no further variants or microheterogeneities could be observed. The population data showed no significant deviation from Hardy-Weinberg equilibrium. Received: 3 December 1996 / Received in revised form: 23 April 1997     

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.     

Inter-alpha-trypsin inhibitor polymorphism

Serum samples treated with chondroitinase ABC and sialidase were investigated for the detection of inter-alpha-Typsin inhibitor (ITI) polymorphism. The improved phenotyping procedure has proved to be the most practical method for ITI phenotyping. The ITI allele frequencies were examined in 2 population samples from Japanese (n = 365) and Thais (n = 150). Three common alleles, ITI^*I, ITI^*2, and ITI^*3 were identified in both populations, but the Thai population showed a higher frequency of ITI^* 1 and a lower frequency of ITI^*3. Two new alleles were found, which were tentatively denoted ITI^*Y and ITI^*T. The ITI^*T allele frequency in Thais was 0.047.     

The STR systems FES/FPS and F13B in a Polish population

Allele frequencies for the STR systems FES/FPS and F13B were determined from 203 unrelated individuals from north-eastern Poland. After denaturing PAGE, 7 and 6 alleles were detected for FES/FPS and F13B, respectively. No deviations from Hardy-Weinberg equilibrium were observed. Received: 18 March 1997 / Received in revised form: 22 May 1997     

Allele frequencies of eight STRs in Japanese and Chinese

Allele frequencies for the eight STR loci Hum-CSF1P0, F13A01, F13B, FES/FPS, LPL, TH01, TPOX and VWA were investigated in Japanese and Chinese populations. No significant deviations from Hardy-Weinberg equilibrium could be found for all loci. In the Japanese population VWA, CSF1PO, TH01, FES/FPS and TPOX were found to be useful for forensic applications and in the Chinese population, VWA, CSF1PO, TH01 and TPOX were found to be useful. Allele distributions were similar between both populations except for FES/FPS. Received: 12 January 1998 / Received in revised form: 12 June 1998     

Tetranucleotide STR system D8S1132: sequencing data and population genetic comparisons

In the present investigation of the D8S1132 locus 31 selected alleles were sequenced. In total there were 9 distinguishable alleles found to increase in size by regular 4 bp increments from 134 to 170 bp with a repeat array following the pattern (TCTA)_n TCA (TCTA)_n. One-third of the sequenced alleles exhibited an altered repeat sequence TCTG TCTA at the 3′ flanking region of the repeat array. A nomenclature for the designation of D8S1132 alleles is proposed on the basis of this sequence data and in accordance with the ISFH recommendations. The allele distribution of the D8S1132 locus has been investigated in three German populations (Halle-, Münster-, and Wiesbaden area) with frequencies ranging from 0.004 to 0.24. No deviation from Hardy-Weinberg equilibrium could be observed. The heterozygosity was 0.83 and the discrimination power 0.96 for the Halle population. Received: 20 August 1997 / Received in revised form: 17 October 1997     

Further sequence and length variation at the STR loci HumFES/FPS, HumVWA, HumFGA and D12S391

This paper reports population data and statistics for the HumFES/FPS, HumVWA, HumFGA and D12S391 loci in Austria. The sequences of some rare and new variant alleles which have been identified in the course of the present population study and other investigations are described. Sequence variation occurred in a HumFES/FPS allele revealing an (ATTT)₉ structure and an A to C transversion in the 5′ flanking region. At the HumVWA locus the structural type of the common allele 14 has been found in one allele 13 and in three examples of allele 15. Additionally the TCTA (TCTG)₃(TCTA)_n structure has been observed in three examples of allele 13 and one allele 14, which is very uncommon. Another allele 14 showed a C to T transition in the third of nine TCTA repeats. The sequences of three length variations at the HumFGA locus, namely the alleles 16, 19.2 and 21.2 are reported. At the D12S391 locus a novel 19.1 allele was found in this study. An extended nomenclature is proposed for the HumVWA locus to denominate sequence variants in a precise but simple way. Received: 14 October 1998 / Received in revised form: 18 February 1999     

Phenotype differences of STRs in 7 human populations

A maximum of 6 STR systems (TH01, VWA, ACTBP2, FES, F13B, D21S11) was investigated in 7 human populations (Germans, Turks, Moroccans, Japanese, Chinese, Papuans, Ovambos). In each population no deviations from Hardy-Weinberg equilibrium were observed. Out of each population the phenotypes of 50 individuals (comprising 3 to 6 STRs) were randomly selected. Based on the phenotype frequencies interpopulation comparisons were carried out using the frequencies of each other population. Within major ethnic groups only minor differences in phenotype frequencies were found. Between major ethnic groups differences of up to several orders of magnitude could be observed. The most discriminative STRs for interpopulation comparisons were TH01, FES and F13B.     

F13B and CD4 allele frequencies in an Austrian population sample

Allele frequencies of the two short tandem repeat (STR) systems F13B and CD4 were determined in an Austrian population sample by PCR analysis. A total of 6 alleles for F13B and 8 alleles for CD4 could be observed in a population of 216 (F13B) and 198 (CD4) unrelated individuals. No significant deviations from Hardy-Weinberg equilibrium were observed.     

Turkish population data on the HLA-DQα, LDLR, GYPA, HBGG, D7S8, and GC loci

We have determined the allele and genotype frequencies of six PCR-based genetic markers HLA-DQα, LDLR, GYPA, HBGG, D7S8 and GC in the Turkish population (n = 361 for HLA-DQα, and n = 260 for PM). All loci meet Hardy-Weinberg expectations. The frequency data can be used in forensic analyses in the Turkish population. Received: 21 March 1996 / Received in revised form: 18 March 1997     

Identification of a rare off-ladder allele of the D13S325 locus during paternity testing

This study demonstrates an unusual rare allele of D13S325 that was falsely categorized as an allele of D12S391 under the STRtyper™-10F/G system. The parentage cases with these rare alleles were analyzed using the Sinofiler™ system and singleplex amplification system, and the alleles of D13S325 extracted from the electrophoresis gel were sequenced. 5 Cases with the rare alleles misread as allele 20 of D12S391 were identified in total 2618 cases (including 3200 unrelated parents). This rare allele was designated as allele 5.1 of D13S325 based on its DNA sequence. Its frequency in the Chinese population was 1.6 × 10⁻³. Because the rare allele 5.1 of D13S325 locus tends to be incorrectly labeled in the STRtyper™-10F/G system, particular attention should be paid when the system is used in paternity testing, personal identification, and DNA database comparisons.     

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     

Bimodal allele frequency distribution at Y-STR loci DYS392 and DYS438: no evidence for a deviation from the stepwise mutation model

A deviation from the stepwise mutation model (SMM) has been suggested for the trinucleotide Y-STR locus DYS392, based upon its bimodal allele frequency distribution in various populations. The same type of distribution is also observed for the pentanucleotide Y-STR DYS438. In order to verify whether a departure from an SMM is likely for these two loci, we studied a large number of Portuguese male DNA samples typed for the two loci and in addition, for the Y-STR loci DYS19, DYS389I/II, DYS390, DYS391 and DYS393. The compatibility of the observed allele frequency spectrum with an SMM was assessed by an apportionment of the molecular variance among, and consideration of the molecular distances between, haplotype groups defined according to their allelic state at each of the two markers of interest. For haplotypes carrying either modal alleles 11 or 13 of DYS392, 18.6% of the molecular variance of the remaining Y-STR background could be attributed to variation between the two groups. When all pairwise _st values between haplotype groups were compared, group 12 was found to be closer to 11 than to 13, and group 14 was much closer to 13 than to 12 and 11. It may therefore be concluded that DYS392 allele 13 represents an evolutionary lineage with little or no relationship to 11 and 12. Furthermore, allele 14 is a one-step neighbour of 13 and is therefore likely to represent an offshoot from group 13. For haplotypes carrying either modal allele 10 or modal allele 12 of DYS438, 27.7% of the molecular variance of the Y-STR background was found to be due to variation between the two groups. Comparison of the other pairwise _st values indicated that group 10 was closer to 9 and 11 than to 12, and that group 12 was closer to 11 and 13 than to 10. The lineages defined by the two modal alleles of DYS438 therefore also seem to be phylogenetically distant. When the two loci were analysed in combination, using the standardised linkage disequilibrium measure (D'), a strong association was noted between alleles DYS392*11 and DYS438*10 (D'=0.70) and between DYS392*13 and DYS438*12 (D'=0.72). Taken together, these results show that the bimodal allele frequency distributions of DYS392 and DYS438 are explicable in terms of (probably the same) historical and demographic causes, rather than a mutational mechanism other than SMM. The loci do therefore not appear to warrant any special attention when applied in population genetic or forensic studies.     

AHinfl polymorphism in the 5'flanking region of the human VNTR locus DIS80

A restriction fragment length polymorphism (RFLP) characterized by the presence (HinfI+) or absence (HinfI-) of aHitinfI site has been found in the 5 flanking region of the VNTR locus D 1 S80. RFLP-allele frequencies were determined from 82 unrelated individuals:HinfI+ = 0.49,HinfI- = 0.51. The RFLP/VNTR haplotype frequencies show an absolute association between theHinfI+ allele and the VNTR allele of 18 repeat units and an extreme association between theHinfI- allele and the VNTR allele of 24 repeat units. The remaining VNTR alleles associate more randomly with the 2 flankingHinfI alleles.     

Population data and forensic efficiency values for the STR systems HumVWA,HumMBP and HumFABP

Summary Population studies were carried out on Caucasians from north-west Germany using the short tandem repeat (STR) systems HumVWA (locus: 12p12-12pter), HumMBP (locus: 18q23-pter) and HumFABP (locus: 4q28-q31). After electrophoresis 9 alleles could be identified for HumVWA in a sample size of 321 unrelated individuals and 4 alleles were found for HumFABP in 106 individuals. For HumMBP-A 10 alleles and for HumMBPB 7 alleles and I intermediate allele were determined in a sample size of 143 individuals. No deviations from Hardy-Weinberg equilibrium could be observed. In a small family study (HumVWA –n = 129; HumMBP –n = 59; HumFABP –n = 48) no new mutations could be found for HumMBP-A and HumFABP whereas 2 mutations were found in HumMBP-B and one mutation in HumVWA. Positive results could be obtained from 1 ng-20pg (HumVWA, HumFABP) and 1 ng-100pg (HumMBP) template DNA.