Genetic mapping of 15 human X chromosomal forensic short tandem repeat (STR) loci by means of multi-core parallelization

Abstract

Typing of X chromosomal short tandem repeat (X STR) markers has become a standard element of human forensic genetic analysis. Joint consideration of many X STR markers at a time increases their discriminatory power but, owing to physical linkage, requires inter-marker recombination rates to be accurately known. We estimated the recombination rates between 15 well established X STR markers using genotype data from 158 families (1041 individuals) and following a previously proposed likelihood-based approach that allows for single-step mutations. To meet the computational requirements of this family-based type of analysis, we modified a previous implementation so as to allow multi-core parallelization on a high-performance computing system. While we obtained recombination rate estimates larger than zero for all but one pair of adjacent markers within the four previously proposed linkage groups, none of the three X STR pairs defining the junctions of these groups yielded a recombination rate estimate of 0.50. Corroborating previous studies, our results therefore argue against a simple model of independent X chromosomal linkage groups. Moreover, the refined recombination fraction estimates obtained in our study will facilitate the appropriate joint consideration of all 15 investigated markers in forensic analysis.

Twenty Years Later: A Comprehensive Review of the X Chromosome Use in Forensic Genetics

“…Obviously, linked markers are more prone to be in LD. Segregation analyses in one or multi generation family studies were performed, aiming to estimate recombination rates between X-STRs of interest through proper bioinformatic pipelines that take into account the possibility of mutation ( Nothnagel et al, 2012 ; Diegoli et al, 2016 ; Bini et al, 2019 ), but population-based studies, as HapMap project ( The International HapMap Consortium, 2007 ), can also be considered ( Phillips et al, 2012 ). Mapping functions as Haldane’s ( Haldane, 1919 ) or Kosambi’s ( Kosambi, 1944 ) are used to convert genetic distances between markers in recombination rates.…”

Genetic diversity and haplotypic structure of a Saudi population sample using Investigator Argus X-12 amplification kit

“…Previous studies have demonstrated that loci inside each of the four X-STR linkage groups show reduced, but non-zero recombination rates [27]. In addition, recombination between linkage groups is less than 50% [7,28,29]. In fact, Diegoli and Rohde [7] argues against a simple model of independent X chromosomal linkage groups for these reasons.…”

“…In addition, recombination between linkage groups is less than 50% [7,28,29]. In fact, Diegoli and Rohde [7] argues against a simple model of independent X chromosomal linkage groups for these reasons.…”

“…They have shown great forensic ability and are, therefore, recognized as efficient tools in forensic investigations of kinship cases [2][3][4]. A variety of X-STR systems have been developed and added to the list of conventional markers for better results in complex kinship analysis and cases involving mother-son and father/daughter relationship [5][6][7].…”

“…DXS7423 and HPRTB loci were in LD with DXS10146, DXS10148, DXS10079, DXS10103 and DXS10148, DXS10101, DXS8378, respectively. DXS8378 was in LD with DXS10148 and DXS10101 as well as with DXS7132 and HPRTB.The 12 X-STR markers are clustered into four linkage groups based on their physical localization[5,7] :LG1 (Xp22) contains DXS8378-DXS10135-DXS10148, LG2 (Xq11) contains DXS7132-DXS10074-DXS10079, LG3 (Xq26) contains DXS10101-DXS10103-HPRTB and LG4 (Xq28) contains DXS7423-DXS10134-DXS10146.…”