Linkage and linkage disequilibrium analysis of X-STRs in Italian families

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Abstract

Twenty X-chromosomal short tandem repeat (STR) loci were typed in 80 families of Italian descent, composed by mother and two or more sons, for a total of 93 meiosis. The analyzed X-STR panel included six clusters of closely linked markers (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).

Recombination fractions between pairs of markers calculated by pedigree analysis were compared with those obtained from the second-generation Rutgers combined linkage-physical map of the human genome. The observed differences confirm that recombination is not homogeneous along the X chromosome and that the conventional subdivision of X-STRs in four groups of completely unlinked markers cannot be regarded as true.

Significant linkage disequilibrium was found between markers DXS6801 and DXS6809 (p = 0.017). The effect on likelihood calculations of inferring haplotype frequencies from allele distributions rather than haplotype count in the relevant population was evaluated.

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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