Collaborative genetic mapping of 12 forensic short tandem repeat (STR) loci on the human X chromosome

Abstract

A large number of short tandem repeat (STR) markers spanning the entire human X chromosome have been described and established for use in forensic genetic testing. Due to their particular mode of inheritance, X-STRs often allow easy and informative haplotyping in kinship analyses. Moreover, some X-STRs are known to be tightly linked so that, in combination, they constitute even more complex genetic markers than each STR taken individually. As a consequence, X-STRs have proven particularly powerful in solving complex cases of disputed blood relatedness. However, valid quantification of the evidence provided by X-STR genotypes in the form of likelihood ratios requires that the recombination rates between markers are exactly known. In a collaborative family study, we used X-STR genotype data from 401 two- and three-generation families to derive valid estimates of the recombination rates between 12 forensic markers widely used in forensic testing, namely DXS10148, DXS10135, DXS8378 (together constituting linkage group I), DXS7132, DXS10079, DXS10074 (linkage group II), DXS10103, HPRTB, DXS10101 (linkage group III), DXS10146, DXS10134 and DXS7423 (linkage group IV). Our study is the first to simultaneously allow for mutation and recombination in the underlying likelihood calculations, thereby obviating the bias-prone practice of excluding ambiguous transmission events from further consideration. The statistical analysis confirms that linkage groups I and II are transmitted independently from one another whereas linkage groups II, III and IV are characterised by inter-group recombination fractions that are notably smaller than 50%. Evidence was also found for recombination within all four linkage groups, with recombination fraction estimates ranging as high as 2% in the case of DXS10146 and DXS10134.

Introduction

Genotyping of X-chromosomal short tandem repeats (X-STRs) has become a useful tool in forensic genetics, and a large number of X-STRs spanning the entire human X chromosome have been described in the past [1], [2], [3], [4], [5]. Moreover, joint consideration of X-STRs yields even more complex and informative genetic markers than individual STRs taken on their own, provided that the probability of inter-marker recombination is negligible and that haplotypes therefore segregate stably within families. In fact, sharing of rare X-STRs haplotypes has been recognised as being strongly indicative of kinship [6].

Haplotyping is easier with X-STRs than with autosomal markers. Since males are hemizygous for all relevant X-chromosomal loci, their X-STR haplotypes are revealed directly by genotyping. In addition, for pedigrees in which critical kinship relationships are beyond doubt, it may be possible to determine female X-STR haplotypes with sufficient accuracy as well. Women always carry the entire paternal X chromosome so that their X-STR haplotypes can be assessed, for example, by genotyping their biological father. Likewise, genotyping of a mother and at least one son may also reveal both maternal haplotypes albeit with some residual uncertainty due to the possibility of female recombination.

In 2008, eight X-STRs were evaluated for forensic use and included into the Mentype^® Argus X-8 PCR amplification kit [7]. For practical purposes, these eight markers were grouped into pairs constituting four (presumably) independent ‘linkage groups’, namely DXS10135–DXS8378, DXS7132–DXS10074, HPRTB–DXS10101, and DXS10134–DXS7423 [6]. Linkage within groups was generally regarded as sufficiently tight for the chance of intra-pair recombination to be negligible in practice. These two postulates complied with published recombination data [8], [9], [10], including our own earlier family studies [6], [11], although only a small number of meioses were studied. Recently, the Mentype^® Argus X-8 kit was extended (into the Investigator^® Argus X-12 PCR amplification kit, Qiagen) so as to include four additional markers, DXS10148 [12], DXS10079 [3], DXS10103 [2] and DXS10146 [13], with one novel marker located in each previously defined linkage group (Table 1).

To allow female recombination to be taken properly into account in quantitative kinship analyses using X-STRs, the recombination fractions between the markers of interest need to be known precisely [14]. Recently, two studies [15], [16] strongly suggested that the estimates of the pair-wise recombination fractions available for the Mentype^® Argus X-8 markers needed to be revised. This realisation prompted some of us to publish the recombination pattern of 39 X-STRs as observed in German three-generation families, comprising a total of 135 meioses [17]. However, since the accuracy of the recombination fraction estimates ensuing from such studies is critically dependent upon the number of meioses included, we choose to expand our previous work accordingly. Here, we present the results of an international multi-center study of recombination between the Investigator^® Argus X-12 markers. Using a largely expanded family data set, we were able to obtain much more precise estimates of the recombination fractions involved. Moreover, by following a comprehensive likelihood-based approach, we were able for the first time to allow for meiotic mutation in the estimation of X-STR recombination fractions.