We analyzed 67 short tandem repeat polymorphisms from the non-recombining part of the Y-chromosome (Y-STRs), including 49 rarely studied simple single-copy (ss)Y-STRs and 18 widely used Y-STRs, in 590 males from 51 populations belonging to 8 worldwide regions (HGDP-CEPH panel). Although autosomal DNA profiling provided no evidence for close relationship, we found 18 Y-STR haplotypes (defined by 67 Y-STRs) that were shared by two to five men in 13 worldwide populations, revealing high and widespread levels of cryptic male relatedness. Maximal (95.9%) haplotype resolution was achieved with the best 25 out of 67 Y-STRs in the global dataset, and with the best 3-16 markers in regional datasets (89.6-100% resolution). From the 49 rarely studied ssY-STRs, the 25 most informative markers were sufficient to reach the highest possible male lineage differentiation in the global (92.2% resolution), and 3-15 markers in the regional datasets (85.4-100%). Considerably lower haplotype resolutions were obtained with the three commonly used Y-STR sets (Minimal Haplotype, PowerPlex Y®, and AmpFlSTR® Yfiler®). Six ssY-STRs (DYS481, DYS533, DYS549, DYS570, DYS576 and DYS643) were most informative to supplement the existing Y-STR kits for increasing haplotype resolution, or - together with additional ssY-STRs - as a new set for maximizing male lineage differentiation. Mutation rates of the 49 ssY-STRs were estimated from 403 meiotic transfers in deep-rooted pedigrees, and ranged from ∼4.8 × 10-4 for 31 ssY-STRs with no mutations observed to 1.3 × 10-2 and 1.5 × 10-2 for DYS570 and DYS576, respectively, the latter representing the highest mutation rates reported for human Y-STRs so far. Our findings thus demonstrate that ssY-STRs are useful for maximizing global and regional resolution of male lineages, either as a new set, or when added to commonly used Y-STR sets, and support their application to forensic, genealogical and anthropological studies.

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Keywords HGDP-CEPH, Haplotype resolution, Lineage differentiation, Microsatellites, Mutation rates, Y chromosome, Y-STR, Y-chromosome, article, genetic analysis, genetic correlation, genetic marker, genetic polymorphism, genetic variability, haplotype, human, male, mutation rate, priority journal, short tandem repeat
Persistent URL dx.doi.org/10.1016/j.fsigen.2009.01.009, hdl.handle.net/1765/17080
Journal Forensic Science International: Genetics
Vermeulen, M, Wollstein, A, van der Gaag, K, Lao Grueso, O, Xue, Y, Wang, Q, … Kayser, M.H. (2009). Improving global and regional resolution of male lineage differentiation by simple single-copy Y-chromosomal short tandem repeat polymorphisms. Forensic Science International: Genetics, 3(4), 205–213. doi:10.1016/j.fsigen.2009.01.009