Using the YHRD Database for Casework Analysis
Lutz Roewer
EDITOR'S NOTE:
Funded by the National Institute of Justice, the U.S. Y-STR Database has been managed by the National Center for Forensic Science at the University of Central Florida since 2007 (Ballantyne et al. 2006), and its Release 4.2.1 (January 26, 2018) contains 35,658 Y-STR haplotypes generated by thirty U.S. forensic, academic and commercial laboratories. As of November 26, 2018, 217,758 search queries of the database had been performed.
The U.S. Y-STR Database haplotypes have been permanently transferred to the Y- Chromosome Haplotype Reference Database and the U.S. Y-STR Database will be decommissioned. Decommission dates is scheduled for June 30, 2019. Further details can be found here, including a YHRD Users Guide to enable the user to access SWGDAM compliant data output.
To learn more about the YHRD database, please register for the webinar hosted by Promega on May 8, 2019 at 9am CST, in which Dr. Roewer will present on using the YHRD database in forensic laboratories … To register click on the button below.
Today, Y-chromosome typing is used to assist forensic investigations in a broad range of casework, such as for the rapid sexing of traces, the identification and profiling of masked male DNA component(s) in mixtures with an excess of female DNA, 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 have been populated over the past 20 years.
The YHRD project was 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 about 270,000 profiles from nearly 1,300 populations typed for up to 29 Y-STRs and a large number of phylogenetic Y-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.
More than 1,300 local population samples with more than 270,000 haplotypes in 136 countries
In contrast, variable estimators are independent of the database size but not from its allelic composition. The “Discrete Laplace method”, used 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 a suspect.
EDITOR'S NOTE:
Funded by the National Institute of Justice, the U.S. Y-STR Database has been managed by the National Center for Forensic Science at the University of Central Florida since 2007 (Ballantyne et al. 2006), and its Release 4.2.1 (January 26, 2018) contains 35,658 Y-STR haplotypes generated by thirty U.S. forensic, academic and commercial laboratories. As of November 26, 2018, 217,758 search queries of the database had been performed.
The U.S. Y-STR Database haplotypes have been permanently transferred to the Y- Chromosome Haplotype Reference Database and the U.S. Y-STR Database will be decommissioned. Decommission dates is scheduled for June 30, 2019. Further details can be found here, including a YHRD Users Guide to enable the user to access SWGDAM compliant data output.
To learn more about the YHRD database, please register for the webinar hosted by Promega on May 8, 2019 at 9am CST, in which Dr. Roewer will present on using the YHRD database in forensic laboratories … To register click on the button below.
Lutz Roewer studied biochemistry at the University of Leipzig (Germany) and received his Ph.D. degree for molecular biology at the Humboldt-University Berlin (Germany) in 1991. His is currently an Associate Professor for Forensic Genetics at the Institute of Legal Medicine, Humboldt-University Berlin (Germany) and Director of the Department of Forensic Genetics at this institute.
Dr. Roewer has worked as a forensic expert since 1987. He is a specialist in the field of Y-chromosome genetics and its forensic, genealogical and anthropological applications. He is currently curator of the Y Chromosome Haplotype Reference Database (YHRD).
He is member of the editorial boards of the journals, International Journal of Legal Medicine and Forensic Science International: Genetics. He has been a member of the SWGDAM Y-STR committee for the past 5 years.
Dr. Roewer has authored more than 100 peer-reviewed articles in scientific journals, and publishes regular reviews and chapters in various textbooks.
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