The YHRD Database: How It Works and How to Use It in Casework

Today, Y chromosome typing is used to assist forensic investigations in a broad range of casework, either for rapid sexing of traces, for the identification and profiling of masked male DNA component(s) in mixtures with an excess of female DNA, for tracing male lineages in relationship testing or for analyzing the ancestry of unidentified corpses or unknown trace donors. Like any forensic DNA analysis, judging the significance of a match between the trace and a reference person depends upon the population frequency of the DNA profile. Y chromosomes are highly geographically structured and there is the further complication that all members of a patrilineage are expected to share Y haplotypes. The forensic community has been proactive in establishing large quality-assured and publicly accessible databases of Y-haplotypes to address these issues. The Y Chromosome Haplotype Reference Database (YHRD) now includes 135 national databases which were populated in the past 20 years. The YHRD project started in 1999 with a collection of 3,825 haplotypes typed in 48 populations for up to 13 Y-STRs. Currently, the 60th edition of the YHRD is online with 269,383 profiles from 1,262 populations typed for up to 29 Y-STRs and a large number of SNPs. These data facilitate statistical analyses for a range of casework applications and interpretation purposes (e.g. frequency estimation, kinship and mixture analysis, ancestry prediction). All incoming data are validated first by the submitter using YHRD online tools and then by the curators before being uploaded and accepted for publication. To calculate the Y-STR profile frequency constant and variable estimators can be used. Constant estimators (counts in a database accompanied by a confidence interval) are bound from below by the database size and are therefore often overly conservative. In contrast, variable estimators are independent of the database size but not from its allelic composition. The “Discrete Laplace method” which is implemented in the Y Chromosome Haplotype Reference Database (YHRD) is a model-based extrapolation method which makes use of an in-depth analysis of Y-STR profiles in more than thousand worldwide population samples. It can be used to estimate haplotype frequencies with a better approximation than the counting method. Moreover, the YHRD is a useful resource to infer the ancestry of an unknown male person due to the availability of a consensus phylogenetic tree and geographic and ethno-linguistic information assigned to each profile. Y-based ancestry prediction and familial searching can therefore provide important investigative leads in crime cases without suspect.