Linkage and linkage disequilibrium analysis of X-STRs in Italian families
Introduction
X-chromosomal short tandem repeat (X-STR) loci can efficiently complement autosomal markers in paternity testing, especially in deficiency cases with female offspring and kinship analysis involving large and incomplete pedigrees [1]. The use of X-STRs requires a precise knowledge not only of allele and haplotype frequencies, but also of the genetic linkage and linkage disequilibrium (LD) status among markers. In the present study, we analyzed 80 informative families for 20 X-STR markers including six clusters of closely linked loci (each spanning < 3 cM): DXS10135–DXS10148–DXS8378 (Xp22); DXS7132–DXS10074–DXS10079 (Xq12); DXS6801–DXS6809–DXS6789 (Xq21); DXS7424–DXS101 (Xq22); DXS10103–HPRTB–DXS10101 (Xq26); DXS8377–DXS10134–DXS7423–DXS10146 (Xq28).
Section snippets
Materials and methods
Blood samples were collected from 80 families composed by mother and two or more sons (73 families with 2 sons, 4 with 3 sons and 3 with 5 sons), for a total of 93 meiosis. Genomic DNA was isolated using a standard salting out procedure, then quantified with the Quantifiler Human DNA Quantification Kit (Applied Biosystems, Forster City, CA, USA). An input of 1–10 ng of DNA was used in each PCR reaction. Amplification of loci DXS8378, DXS7132, DXS6800, DXS6801, DXS6809, DXS6789, DXS7424, DXS101,
Results and discussion
Allele frequencies for the 20 X-STR loci, calculated from the 160 analyzed maternal chromosomes, are reported in Supplemental Table S1. All loci were in HWE after Bonferroni's correction for multiple testing, with the exception of DXS10146 locus. In this case, deviation from HWE was caused by a reduction of observed heterozygosity (0.759) compared to expected heterozygosity (0.897). No significant differences in allele distribution were observed in comparison with an Italian sample previously
Conflict of interest
None.
Acknowledgment
The continuing support of the Compagnia di San Paolo to C. Torre's laboratory is gratefully acknowledged.
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2016, Forensic Science International: GeneticsCitation Excerpt :Interestingly, a recombination rate of 0.45 was inferred in that study between linkage groups (LGs) I and II that agrees very well with our own result (0.4521) despite the fact that the border of LG I was defined by different markers (DXS8378 and DXS6795). Evidence for free recombination between LGs I and II had been provided by another study of 20 X STRs in 80 two-generation families [39], where a recombination rate of 0.49980 was estimated for junction markers DXS8378 and DXS7132. Also in agreement with our findings, free recombination was found to be lacking between LGs II and III and between LGs III and IV [39], despite different junction markers being used compared to our study.
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2016, Forensic Science International: GeneticsCitation Excerpt :The markers included in the 17 X-STR panel [13] have been gathered into different clusters throughout the literature, such as the cluster DXS6807-DXS8378-DXS9902 in the region Xp22 [14]. In the region Xq21, the markers DXS6801, DXS6809, and DXS6789 have been considered linked by the majority of the authors [3,21,22] and additionally, DXS6799 has also been included in this cluster [14] . Finally, the markers DXS7132, DXS10079, and DXS10074 have typically been considered as a haplotype in the Xq12 region [21–23] and some authors have also considered the locus DXS10075 [14,24] as part of it.