Spanish population data on seven loci: D1S80, D17S5, HUMTH01, HUMVWA, ACTBP2, D21S11 and HLA-DQA1

D1S80 VNTR locus genotypes in a population of Southeastern Sicily: Distribution and genetic disequilibrium

Locus D1S80 is one of the best-known polymorphic loci, showing a variable number of tandem repeats. This article presents the results on D1S80 allele distributions in a sample of 324 unrelated Sicilian individuals, collected and analyzed in two distinct laboratory centers. Although, as expected, the two most frequent alleles were those with 18 and 24 repeat units, the population sample from southeastern Sicily showed a relatively low frequency of allele 29 (2.9%) and allele 31 (3.4%) and a relatively high frequency of allele 25 (6.0%), allele 30 (1.9%), and allele 32 (1.5%) in comparison with other populations. Statistical analysis performed by the five alleles model provided evidence that the population did not follow the Hardy-Weinberg equilibrium expectations (observed heterozygosity 70.99% vs. expected heterozygosity 76.31%). The calculated F (fixation index), as a measure of heterozygote deficiency or excess, was positive for four allele groups and negative for one allele group. This finding was consistent with a substantial diversity of human ethnic groups when tested with VNTR systems and might represent a genuine inconsistency, not due to a methodological bias. This scenario deserves further investigation, i.e., by performing a short tandem repeat (STR) units analysis on a greater number of loci in the same population sample.

Sequence analysis of STR polymorphisms at locus ACTBP2 in the Taiwanese population

A highly polymorphic sequence structure is reported in the human beta-actin related pseudogene 2 (ACTBP2) (SE33) locus in members of the Taiwanese Han population. A total of 100 unrelated members of the Taiwanese Han population were used in the study. Alleles that shared the same size but differ in their sequence are described to allow for inter laboratory sharing of data. PCR products amplified from this locus were separated by single-strand conformation polymorphism electrophoresis, the single-stranded DNA bands were excised from the gels, a second amplification performed, and then the PCR products were sequenced. All the alleles differed by either 2 or 4 bp. Sequence variations were observed as deletions or insertions in the repeat units AG (or AA) and AAAG. Additionally, transitions in the flanking regions were recorded. A total of 27 alleles with 71 associated genotypes were recorded if the alleles were defined by size, but 68 alleles with 88 associated genotypes were noted with the alleles were scored on the basis of sequence variation. The power of discrimination (Pd) of this single locus was 0.9874 making the human ACTBP2 a good alternative marker for individual identification and paternity testing.

African-derived South American populations: A history of symmetrical and asymmetrical matings according to sex revealed by bi- and uni-parental genetic markers

Estimates of African, European, and Amerindian contributions to the gene pool of 11 predominantly African-derived South American populations were obtained using five autosomal and one Y chromosome hypervariable loci, as well as mitochondrial DNA (sequences of the first hypervariable segment of the control region, plus two restriction sites and the presence or absence of the CoII/tRNA(Lys) intergenic 9-bp deletion). The three latter characteristics are reported here for the first time for 42 individuals living in three Brazilian populations. Thirty-eight sequences were identified in these persons; 17 (45%) could be classified as being of African, 4 (11%) of Amerindian, and 2 (5%) of European origin. Evidence for asymmetrical matings in relation to sex and ethnic group was obtained for nine of the 11 populations. The most consistent finding was the introduction of European genes through males, but the results differ in the several communities, indicating the importance of local factors in such interactions. Am. J. Hum. Biol. 11:551-563, 1999. Copyright 1999 Wiley-Liss, Inc.

Evaluation of chimerism in DNA samples by PCR amplification of D1S80 with detection by capillary electrophoresis

BACKGROUND

Analysis of the relative amounts of donor and recipient DNA in bone marrow after bone marrow transplantation is frequently used to determine the status of the transplant. We studied the performance of an assay to quantify chimerism based on amplification of the D1S80 variable number tandem repeat marker by PCR with detection of PCR products by capillary electrophoresis (CE).

METHODS AND RESULTS

Samples from potential bone marrow donors and recipients were analyzed separately and in mixtures to simulate various degrees of chimerism from 10% to 90% and subjected to PCR/CE analysis. There was excellent agreement between the measured and known relative proportions of DNA components in chimeric samples. The lower limit of sensitivity for detection of chimerism was 1%; between-runs coefficients of variation were <5%.

CONCLUSIONS

Amplification of the D1S80 minisatellite by PCR with CE detection is a reliable method for determination of the relative contribution of different DNAs in mixed samples. This method is fast, quantitative, and extremely reproducible.

Fluorescent multiplex analysis of nine STR loci: Spanish population data

A total of 171 Caucasians living in Andalucia (southern Spain) have been typed for nine short tandem repeat (STR) loci by multiplex PCR amplification using a commercially available kit (Profiler Plus; Perkin-Elmer, Norwalk, CT, USA) and semi-automatic electrophoresis (ABI Prism 377 DNA Sequencer, Applied Biosystems, Foster City, CA, USA). The kit enables typing of the STR loci D3S1358, VWA, FGA, D5S818, D13S317, D7S820, D8S1179, D21S11, and D18S51. All loci, except D7S820, meet Hardy-Weinberg equilibrium. Because of the large number of loci that can be analyzed, the power of discrimination (PD) is greater than 0.99999, and the probability of exclusion (PE) reaches 0.99991 in our population sample.