Sequence-based mutation patterns at 41 Y chromosomal STRs in 2 548 father–son pairs

Abstract

A total of 2548 unrelated healthy father-son pairs from a Northern Han Chinese population were genotyped at 41 Y-STRs including DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS444, DYS447, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS522, DYS549, DYS533, DYS557, DYS570, DYS576, DYS593, DYS596, DYS627, DYS635, DYS643, DYS645, Y-GATA-H4, DYF387S1a/b, DYF404S1a/b, DYS385a/b and DYS527a/b. In 2548 father samples, 2387 unique haplotypes were detected with the haplotype diversity (HD) and discrimination capacity (DC) values of 0.999956608 and 0.967410 07. The average gene diversity (GD) value was 0.6934 with a range from 0.1051 at DYS645 to 0.9657 at DYS385a/b. When comparing alleles at 24 overlapped Y-STRs between the ForenSeq™ DNA Signature Prep Kit on the MiSeq FGx® Forensic Genomics System and the Goldeneye® DNA ID Y Plus Kit on the Applied Biosystems™ 3730 DNA Analyzer from 308 father samples in mutational pairs, 258 alleles were detected by massively parallel sequencing (MPS) typing including 156 length-based alleles that could be obtained by capillary electrophoresis (CE) typing, 95 repeat region (RR) variant alleles and 7 flanking region (FR) variant alleles. Hereof, we found 16 novel RR variant alleles and firstly identified two SNPs (rs2016239814 at DYS19 and rs2089968964 at DYS448) and one 4-bp deletion (rs2053269960 at DYS439) that had been validated by the Database of Short Genetic Variation (dbSNP). Sanger sequencing or MPS was employed to confirm 356 mutations from 104 468 allele transfers generated from CE, where 96.63% resulted in one-step mutations, 2.25% in two-step and 1.12% in multi-step, and the overall ratio of repeat gains versus losses was balanced (173 gains v.s. 183 losses). In 308 father-son pairs, 268 pairs occurred mutations at a single locus, 33 pairs at two loci, 6 pairs at three loci and 1 pair at four loci. The average Y-STR mutation rate at 41 Y-STRs was approximately 3.4 × 10−3 (95% CIs: 3.1 × 10−3–3.8 × 10−3). The mutation rates at DYS576 and DYS627 were higher than 1 × 10−2 in Northern Han Chinese, while the mutation rates at DYF387S1a/b, DYF404S1a/b, DYS449, DYS518 and DYS570 were lower than initially-defined. In this study, the classical molecular factors (the longer STR region, the more complex motif and the order father) were confirmed to drive Y-STR mutation rates increased, but the length of repeat unit did not conform to the convention. Lastly, the interactive graphical and installable StatsY was developed to facilitate forensic scientists to automatically calculate allele and haplotype frequencies, forensic parameters and mutation rates at Y-STRs.

Concordance study on Y-STRs typing between SeqStudio™ genetic analyzer for HID and MiSeq™ FGx forensic genomics system

“…An increase of at least 40% in the total number of alleles due to sequence allele variations detected by MPS compared to those identified by CE was also confirmed by other authors [26,46,48,49,[52][53][54], as well as the observation that the most varied allele sequences occurred in DYF387S1 and DYS389II markers [26,34,48,49,51,53]. Concerning the presence of N-1 stutter, the information recovered from other works that had evaluated them agreed with the findings of this study: for example, the highest value of the N-1 stutter ratio was observed at DYS481, which has a trinucleotide repeat [46,51].…”