Haplotypes and mutation analysis of 22 Y-chromosomal STRs in Korean father–son pairs

Abstract

We analyzed 369 Korean father/son haplotype transfers in 355 families at 22 Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS388, DYS437, DYS438, DYS439, DYS446, DYS447, DYS448, DYS449, DYS456, DYS458, DYS464, DYS635, and GATA H4.1). A total of 350 haplotypes were observed with an overall haplotype diversity of 0.9999. Among these, 345 were unique and five were found twice. Furthermore, 36 mutations were identified, giving locus-specific mutation rate estimates between 0.0 and 19.0 x 10(-3) per generation and an average mutation rate estimate of 3.9 x 10(-3) (95% CI 2.7-5.4 x 10(-3)). The compilation of Y-STR mutation events for the present study and previous studies demonstrates that DYS449, DYS458, DYS635, DYS456 and DYS439 are the most prone to mutations and that their overall average mutation rate estimate is 2.36 x 10(-3) (95% CI 2.03-2.73 x 10(-33)).

The Rate and Spectrum of Microsatellite Mutation in Caenorhabditis elegans and Daphnia pulex

“…On a per-generation basis, the mutation rates that we report for C. elegans and D. pulex are much lower than those previously estimated for humans (Heyer et al 1997;Brinkmann et al 1998;Sajantila et al 1999;Kayser et al 2000;Leopoldino and Pena 2003;Dupuy et al 2004;Ballard et al 2005;Gusmao et al 2005;Henke and Henke 2006;Yan et al 2006;Hohoff et al 2007;Lee et al 2007), but much higher than those for yeast (Henderson and Petes 1992;Strand et al 1993;Johnson et al 1996;Sia et al 1997Sia et al , 2001Wierdl et al 1997;Hawk et al 2005;Legendre et al 2007). In principle, such differences could simply arise as a consequence of the pronounced variation in the numbers of germline cell divisions per generation that exists among these species (1, 10, and $200, respectively, in Saccharomyces cerevisiae, C. elegans, and Homo sapiens; Kimble and Ward 1998;Crow 2000).…”

Analysis of mutations in father–son pairs with 17 Y-STR loci

“…In Table 3, we report the most current mutation rate information available on the 17 Y-STR loci in the Yfiler TM kit, as this will be important for laboratories using this technology. The final mutation rates for the Y-STR loci were determined by pooling the data in this study with mutation rate data provided by the Y Chromosome Haplotype Reference Database (YHRD) www.YHRD.org, published articles and papers in press [5][6][7][8][13][14][15][16][17]. Haplotype information for the 778 samples considered in this study across the 17 Yfiler loci is available in Supplementary material in Table S1.…”

Haplotype-assisted characterization of germline mutations at short tandem repeat loci

“…The following loci were selected: & D3S1358 (chromosomal localization: 3p21.31) shows a simple repeat structure: 5′-FR-TCTA-(TCTG) 2 -(TCTA) 9-11 -FR-3′ (alleles 12-14) 5′-FR-TCTA-(TCTG) 3 -(TCTA) 11-15 -FR-3′ (alleles [15][16][17][18][19] 5′-FR-TCTA-(TCTG) 2 -(TCTA) 12-14 -FR-3′ (alleles 15′-17′), FR=flanking region. The heterozygosity index is 0.78 [32], and the mutation rate is in the range of 0.12% [33] (STRbase; http://www.cstl.nist.gov/biotech/strbase/).…”

“…Microsatellites are often applied to investigate paternity cases [8][9][10][11][12][13][14][15]. Typically, a set consisting of approximately 15 STRs is applied [16][17][18][19][20][21][22].…”