Population genetic characteristics of the STR Loci D21S11 and FGA in eight diverse human populations.

A highly polymorphic multiplex short tandem repeat (STR) system composed of D21S11, FGA, and the sex-typing system amelogenin (AMG) has been used to investigate allele frequency distributions in two Canadian Caucasian samples (British Columbia and Alberta), three Canadian aboriginal populations (Coastal Salishans from British Columbia, Ojibwa from northern Ontario, and Cree from Saskatchewan), and three ethnic groups from Singapore (Chinese, Malays, and Asian Indians). Using the automated fluorescence detection approach on an ABD 373A DNA Sequencer, we distinguished 20 D21S11 and 22 FGA alleles with a nearly equal representation of two- and four-base variants. An overlap in allele sizes for both STR loci across populations was observed, but frequency differences were noted. Statistical analysis revealed that (1) both D21S11 and FGA loci conform to Hardy-Weinberg equilibrium in all eight surveyed populations based on five different tests and (2) both STR loci are in linkage equilibrium. Results from the 2 x N contingency table exact tests for population differentiation demonstrated that the Canadian samples from two different provinces were not distinguishable from one another at either STR locus and therefore could be combined to form one Caucasian group. Likewise, Chinese and Malays from Singapore did not show significant differences at either STR locus. In contrast, all other examined populations exhibited differences deemed statistically significant. As a complement to our study, we compared D21S11 allele frequency distributions in 21 worldwide populations and FGA allele frequency distributions in 14 populations. Many alleles never previously reported in worldwide populations were identified in Canadian aboriginal and Asian samples from this study. Twenty-four D21S11 and 29 FGA alleles were distinguished in worldwide groups. Interesting similarities in allele frequency distribution patterns across populations suggest that the STR polymorphism at these loci predates the geographic dispersal of ancestral human populations. This study further demonstrates the utility of highly informative STR loci such as D21S11 and FGA in human population evolutionary history and in forensic medicine.

Validation studies for the genetic typing of the D1S80 locus for implementation into forensic casework.

A series of validation experiments were designed to evaluate, according to the Technical Working Group on DNA Analysis Methods (TWGDAM) guidelines, the analysis of the D1S80 locus for casework implementation. Approximately 400 samples from three different populations (Minnesota Caucasian, Minnesota African Americans, and Minnesota Native Americans) were typed to determine allele frequencies. Simulated forensic type specimens (blood, saliva, hair and semen, or vaginal secretions) were typed to demonstrate that deoxyribonucleic acid (DNA) extracted from various tissues of an individual yield the same D1S80 type. Dilution studies were performed and it was determined that a wide range of input DNA (0.5 ng to 40.0 ng) will consistently yield typeable results. The evaluation of DNA from various animals showed that the D1S80 locus is specific to human DNA within the limits of the parameters tested. The reproducibility of the system was tested by duplicate analysis of approximately 200 population samples. Duplicate samples were analyzed on both horizontal and vertical gel systems. In addition, simulated forensic specimens were analyzed by two independent laboratories: the Minnesota Forensic Science Laboratory (MFSL) and the Roche Biomedical Laboratories (RBL). All analyses, including extraction, quantitation, amplification and typing, were performed independently. All typing results for both laboratories were in agreement. By the analysis of mixtures from various simulated casework type mixtures, it was demonstrated that the D1S80 typing system is suitable for analyzing mixtures. In addition to the simulated casework, evidentiary samples from several adjudicated cases previously analyzed by restriction fragment length polymorphism (RFLP) analysis and/or DQA1 were typed at the D1S80 locus. The D1S80 results were consistent with previous RFLP and/or DQA1 results regarding inclusions/exclusions.

Trinucleotide repeat polymorphism within the human antithrombin gene (AT3): allele frequency data for three population groups.

The fifth intron of the human antithrombin gene (AT3) of chromosome 1q23 contains a highly polymorphic short tandem repeat based on the trinucleotide repeat [ATT]. Alleles range in size from [ATT]5 to [ATT]18, and can be typed using the polymerase chain reaction. Here we report allele frequency population data for Caucasians, Blacks and Southeast Asians. Statistical analyses demonstrate consistency with Hardy-Weinberg equilibrium for all three databases, and that the allele frequencies of all three population groups are significantly different from each other. This locus reveals 76% to 87% heterozygosity and therefore may be useful for forensic identity testing and paternity determination.

Allele frequency data for VNTR locus D17S79: identification of an internal HaeIII polymorphism in the black population.

D17S79 is one of several highly polymorphic VNTR loci commonly used to generate DNA profiles for forensic identity testing and parentage determination. In this study, we used Southern hybridization analysis of HaeIII-digested genomic DNA to compile D17S79 allele frequency databases for the Caucasian, Southeast Asian, East Indian, and Black populations of Southern Ontario. In our Black population sample, low-molecular-weight D17S79 alleles are relatively common and approximately 7% of the individuals have three-band hybridization patterns due to a HaeIII restriction site polymorphism within a common D17S79 allele. The internal HaeIII site generates an allele consisting of two HaeIII fragments of approximately 980 and 420 bp. The estimated frequency of this "split-allele" in our Black population is 0.035. Since this allele was not observed in the other population groups, the internal HaeIII polymorphism probably originated within the Black population. Although the existence of low-molecular-weight alleles and the internal HaeIII polymorphism could affect the interpretation of some VNTR patterns, they are of little or no forensic consequence to the frequencies assigned to VNTR profiles.

Electrophoretic and heat-stability polymorphism at the phosphoglucomutase (Pgm) locus in natural populations of Drosophila melanogaster.

Genetic polymorphism for electrophoretic and heart-sensitive alleles is known at the phosphoglucomutase (Pgm) locus in Drosophila melanogaster. Analysis of the distribution of electrophoretic and thermosensitive (ts) alleles was carried out in natural populations from Canada and West Africa and compared with already known data on Italian populations [Trippa, G., Loverre, A., and Catamo, A. (1976). Nature 260:42]. The data show the existence of five common alleles, Pgm1.00,tr, Pmg1.00,ts, Pgm0.70,ts, Pgm1.20,ts, and Pgm1.50,tr, and two rare alleles, Pgm0.55,ts and Pgm1.20,tr. The most frequent allele is always Pgm1.00,tr; the second most common allele is always of the ts type. The cumulated frequencies of ts alleles in the populations varies between 11 and 32%. The heat stability polymorphism is present in all populations examined and shows again the uniform geographic pattern that has been found for electrophoretic variation at this locus.