Dinucleotide (CA)n tandem repeats on the human X-chromosome and the history of the Mediterranean populations.

BACKGROUND: Tandem repeats (STRs) are genomic markers of particular interest in forensic and population genetics. Most of the population data currently available correspond to the variation of STRs of forensic panels, which barely include dinucleotide tandem repeats. AIMS: The aim of the study is to test the usefulness of a battery of dinucleotide STRs on the X chromosome for population and forensic studies. SUBJECTS AND METHODS: A total of 672 individuals from 12 Mediterranean populations and two external references were analysed for 15 X-STR following the instructions of the commercial company and using control DNA from the CEPH centre whose sequences are published in GenBank. Genotypic results were analysed using standard population genetics methods including estimates of linkage disequilibrium, population structure and gene flow. Common forensic efficiency parameters were calculated. RESULTS: The analysed X-STRs show high values of genetic diversity, comparable to other STRs of more common use. No significant associations between markers were found. A slight population structure was detected between the two shores of the Mediterranean. The X-STRs studied here present a similar degree of variability to that of other X-STRs used in forensics. CONCLUSION: Tandem-repeated dinucleotides are a good tool for evidencing population differences here. Forensic parameters indicate that the dinucleotide X-STRs are suitable for forensic use.

Population variation of LIN28B in the Mediterranean: Novel markers for microgeographic discrimination.

OBJECTIVES: The aim of this study is to determine whether the LIN28B gene is differentially distributed in the Mediterranean region through the analysis of the allele distribution of three single nucleotide polymorphisms (SNPs), namely rs7759938, rs314277, and rs221639, in 24 populations. These SNPs have been recently related to the age at menarche, pubertal height growth, peripubertal body mass index, levels of prenatal testosterone exposure, and cancer survival. METHODS: A total of 1,197 DNA samples were genotyped. The allele frequencies were used to determine the relationship between populations, with data from the 1000 Genomes Project being used for external comparisons. The genotype distributions and the population structure between populations and groups of populations were determined. RESULTS: The population results indicate a significant degree of variation (FST = 0.043, P < 0.0001). Allele frequencies show significant differences among populations. A hierarchical variance analysis is consistent with a primary differentiation between populations on the North and South coasts of the Mediterranean. This difference is especially evident in the unexpected distribution of the SNP rs221639, which shows one of the highest FST (11.5%, P < 0.0001) values described in the Mediterranean region thus far. CONCLUSION: The population differentiation and the structuring of the genetic variance, in agreement with previous studies, indicate that the SNPs in question are good tools for the study of human populations, even at a microgeographic level. Am. J. Hum. Biol. 28:905-912, 2016. © 2016Wiley Periodicals, Inc.

An unexpected world population variation of MCT1 polymorphism 1470T > A involved in lactate transport.

A common missense mutation (1470T > A) in gene SLC16A1 responsible for an amino acid substitution in protein MCT1 has been associated with differential lactate transport and hence, differences in physical performance and muscle injuries in relation to physical exercise. This study describes, for the first time, the worldwide variation of MCT1 variant 1470T > A at an intra- and inter-continental level. Two thousand five hundred and four individual genotypes of 26 populations clustered in 5 population groups have been analysed with data downloaded from the public database 1000 Genomes Phase 3 Browser. Several parameters of population differentiation and structure have been explored as well as selection signatures in the whole gene. Allele T, the common variant, shows extremely high values in Sub-Saharan African groups (frequencies 86-91%) as compared with the remaining world regions (69-49%). TT genotype also predominates in African groups, showing significant differences with the rest of world populations. In view of the evidence that the TT genotype is associated with clinical implications and a better predisposition to sprint/power performances, we suggest that the high presence of the TT genotype in African populations should be taken into account in future association studies at both medical and sports fields.

A survey of sub-Saharan gene flow into the Mediterranean at risk loci for coronary artery disease.

This study tries to find detectable signals of gene flow of Sub-Saharan origin into the Mediterranean in four genomic regions previously associated with coronary artery disease. A total of 366 single-nucleotide polymorphisms were genotyped in 772 individuals from 10 Mediterranean countries. Population structure analyses were performed, in which a noticeable Sub-Saharan component was found in the studied samples. The overall percentage of this Sub-Saharan component presents differences between the two Mediterranean coasts. D-statistics suggest possible Sub-Saharan introgression into one of the studied genomic regions (10q11). We also found differences in linkage disequilibrium patterns between the two Mediterranean coasts, possibly attributable to differential Sub-Saharan admixture. Our results confirm the potentially important role of human demographic history when performing epidemiological studies.