Human tandem repeat sequences in forensic DNA typing

It has been 20 years since the first development of DNA fingerprinting and the start of forensic DNA typing. Ever since, human tandem repeat DNA sequences have been the main targets for forensic DNA analysis. These repeat sequences are classified into minisatellites (or VNTRs) and microsatellites (or STRs). In this brief review, we discuss the historical and current forensic applications of such tandem repeats.

Genetic variability at the D1S80 minisatellite: predominance of allele 18 among some indian populations

BACKGROUND

Hypervariable minisatellites are considered as useful genetic markers in population studies because they are highly polymorphic, multiallelic and co-dominant in nature. The D1S80 minisatellite is one of the well studied markers, and has been used for differentiating population groups of various geographic, linguistic, cultural and genetic origins.

OBJECTIVE

The present study reports the genetic variation observed at the D1S80 minisatellite among seven anthropologically distinct ethnic groups from Kerala state in south India and is compared with other reported Indian and world populations.

SUBJECTS AND METHODS

DNA was isolated from the peripheral blood samples of 282 random, normal and healthy volunteers, PCR amplified and electrophoresed on 4% PAGE followed by silver staining.

RESULTS

A total of 22 alleles (14-39 repeats) were detected with high heterozygosity (0.63-0.84) and Polymorphic Information Content (PIC) values (0.63-0.83). Allele 18 was the predominant allele, except in Ezhavas. The comparison of allele frequency data with world populations including other studied Indian ethnic groups has revealed that the majority of Indian populations possessed allele 18 as the predominant allele. In contrast, allele 24 was reported to be the predominant allele worldwide with a few exceptions.

CONCLUSIONS

This study at the D1S80 minisatellite on seven ethnic groups will provide useful information for the Indian population genetic database. However, the most important observation was the predominance of allele 18 among the majority of Indian ethnic groups. The reason is not clear yet and thus further studies on Indian ethnic groups from different regions are necessary to find out the importance of allele 18 as the predominant allele in Indian population.

HLA-DQA1 polymorphism in autochthonous Basques from Navarre (Spain): genetic position within European and Mediterranean scopes

In this work, a sample of 112 individuals from an autochthonous Basque population (Northern Navarre, Spain) were typed at the DNA level for the HLA-DQA1 locus, with the aim of characterizing its polymorphism and analyzing the genetic relationships of Basque Navarrese with other Caucasian populations. Northern Navarre is a neighboring area with Guipúzcoa, a province located in the core of the Basque territory having the highest proportion of Basque-speakers. In Navarrese population, the most frequent alleles were DQA1*01 (0.375) and DQA1*02 (0.259). Frequency clines for both DQA1*0103 allele and DQA1*04* allele cluster (including DQA1*0401, DQA1*0501 and DQA1*0601) among the European and Mediterranean populations considered are reported for the first time. Furthermore, a spatial structuring previously described for DQA1*02 allele is corroborated. The information provided by the highly polymorphic HLA-DQA1 locus was stressed by using genetic distances and non-metrical multidimensional scaling (MDS). The analysis of genetic relationships among populations showed a high genetic affinity between the Basque subpopulations of Northern Navarre and Guipúzcoa, which in turn tended to plot separately from the remaining European and Mediterranean populations. In the same way, the Basques showed no clear relationship to North African populations, as postulated in several previous HLA studies. The observed genetic heterogeneity seems to be conditioned by the high frequencies of the DQA1*02 allele in Basques from Guipúzcoa and North Navarre. These two subpopulations seem to show low levels of admixture with other non-Basque neighboring populations, probably because of their deeply rooted ethnicity and the existence of a linguistic barrier to random mating.

Genetic admixture in three Mexican Mestizo populations based on D1S80 and HLA-DQA1 loci

This study compares genetic polymorphisms at the D1S80 and HLA-DQA1 loci in three Mexican Mestizo populations from three large states (Nuevo León, Jalisco, and the Federal District). Allele frequency distributions are relatively homogenous in the three samples; only the Federal District population shows minor differences of the HLA-DQA1 allele frequencies compared with the other two. In terms of genetic composition, these Mestizo populations show evidence of admixture with predominantly Spanish-European (50-60%) and Amerindian (37-49%) contributions; the African contribution (1-3%) is minor. Together with the observation that in Nuevo León, the admixture estimates based on D1S80 and HLA-DQA1, are virtually the same as those reported earlier from blood group loci, suggests that DNA markers, such as D1S80 and HLA-DQA1 are useful for examining genetic homogeneity/heterogeneity across Mestizo populations of Mexico. The inverse relationship of the proportion of gene diversity due to population differences (Gst) to within population gene diversity (Hs) is also consistent with theoretical predictions, supporting the use of these markers for population genetics studies.