Comprehensive annotated STR physical map of the human Y chromosome

A plethora of Y-STR makers from diverse sources have been deposited in public databases and represent potential candidates for incorporation into the next generation of Y-STR multiplexes for forensic use. Based upon all of the Y-STR loci that have been deposited in the human genome database (>400), we have sequentially positioned each one along the Y chromosome using the most current human genome sequencing data (NCBI Build 36.1; March 2006). The information derived from this work defines the number and relative position of all potentially forensically relevant Y-STR loci, their location within the physical linkage map of the Y chromosome and their relationship to structural genes. We conclude that there exists at present at least 417 separate Y-STR markers available for potential forensic use, although many of these will be found to be unsuitable for other reasons. However, from this data, we were able to identify 28 pairs of duplicated loci that were given separate DYS designations and four pairs of loci with overlapping flanking regions. Removing one locus from each set of duplicates reduced the number of potentially useful loci from 417 to 389. The derived information should be useful for workers who are designing novel Y-STR multiplexes to ensure the presence of non-synonymous loci and, if so desired, to avoid loci that lie within structural genes. It may also be useful for forensic casework practitioners (or molecular anthropologist) to aid in distinguishing between chromosomal rearrangements (such as duplications and deletions) and bona fide DNA admixtures or null alleles caused by primer binding site mutations.

Publication:
Hanson, E.K., and Ballantyne, J. Comprehensive annotated STR physical map of the human Y chromosome: Forensic Implications. Legal Medicine 2006; 8: 110-120.

Figure 1. Annotated Physical map of >300 Y-STRs. The precise chromosomal location of each STR, determined by a BLAT search (NCBI Build 36.1; March 2006), is indicated. The boxes demarcate loci that are present in different chromosomal segments. Colored loci comprise Y-STRs that have been incorporated into National Center for Forensic Science multiplex systems (MPI-MPX).