Exploitation of a novel slowly mutating Y‐STRs set and evaluation of slowly mutating Y‐STRs plus Y‐SNPs typing strategy in forensic genetics and evolutionary research

Abstract

The Y‐chromosome short tandem repeats (Y‐STRs) loci with different mutation rates existing in the Y chromosome non‐recombination region (NRY) allow to be applied in human forensics, genealogical researches, historical investigations and evolutionary studies. Currently, there is a high demand for pedigree search to narrow the scope of crime investigations. However, the commonly used Y‐STRs kits generally contain Y‐STRs with high mutation rates that could cause individuals from the same pedigree to display different haplotypes. Herein, we put forward a new strategy of Slowly Mutating (SM) Y‐STRs plus Y‐SNPs typing, which could not only improve the resolution and accuracy of pedigree search, but also be applicable to evolutionary research. First, we developed a nine SM Y‐STRs assay by evaluating their mutation rates in 210 pedigrees. Then the gene diversity and efficiency of the SM Y‐STRs and 172 Y‐SNPs sets were investigated by 2304 unrelated males from 24 populations. Furthermore, network and time estimation analyses were performed to evaluate the new strategy's capability to reconstruct phylogenetic tree and reliability to infer the time to the most recent common ancestor (TMRCA). The nine SM Y‐STRs assay even had a higher resolution and a comparable capacity of revealing population genetic differentiation compared to 172 Y‐SNPs system. This new strategy could optimize the phylogenetic tree generated by commonly used Y‐STR panels and obtain a quite consistent time estimations with the published dating.

Development and validation of a new multiplex Y‐STR panel designed to increase the power of discrimination

“…To satisfy such a requirement as much as possible, we developed this novel Y34plex panel that contained both slow to moderate mutation and rapid mutation markers. In details, Y-STR loci with slow-moderate mutations such as DYS593, DYS596, and DYS643 could be used for male pedigree searches [10,17,27]. Besides, the lineage resolution and total haplotype diversity were increased due to more markers incorporated, especially the addition of rapidly mutated markers [28].…”

“…The Y34plex is designed to incorporate 31 single-copy loci, including DYS456, DYS627, DYS390, DYS570, DYS635, DYS448, DYS437, DYS533, DYS449, DYS481, DYS392, DYS391, DYS389I, DYS460, YGATAH4, DYS438, DYS389II, DYS19, DYS458, DYS439, DYS393, DYS576, DYS518, DYS557, DYS593, DYS444, DYS596, DYS643, DYS447, DYS549, and DYS645, and three multi-copy loci, including DYF387S1a/b, DYS527a/b, and DYS385a/b. All loci in Y34plex are chosen from the previously published literatures [15][16][17][18]. Then, markers are selected by the following criteria and procedures: (i) First, markers contained in widely used commercial kits are selected compulsively; (ii) the mutation rates of newly added markers should be less than 1.00E − 03, and the gene diversity values should be greater than 0.5 as far as possible; (iii) the nucleotide number of the core repeat motif cannot be less than three; (iv) the flank region of the selected loci should be suitable for primer design.…”

“…Genetic polymorphisms of 34 Y-STR were evaluated in 434 unrelated healthy Wuxi Han male individuals by calculating haplotype frequencies, haplotype diversities, and haplotype DCs and comparing these forensic parameters with those of other data sets. Forensic parameters were computed according to the method reported by Liu et al [17].…”

“…Therefore, a novel Y chromosome typing system Y-STR 34plex (Y34plex) is designed and developed in the present study, which is aimed to increase the DC for a Y-STR panel and reduce the probability of an adventitious hit. The Y34plex is a 6-dye multiplex system that allows simultaneous amplification and detection of 34 Y-STR markers, including 25 markers in the Yfiler Plus kit [9] and nine Y-STR markers with slow or moderate mutations [15][16][17]. Subsequently, the applicability and robustness of the Y34plex were evaluated according to the guidelines issued by the Scientific Working Group on DNA Analysis Methods (http://swgdam.org/SWGDAM_YSTR_Guidelines_ APPROVED_01092014_v_02112014_FINAL.pdf and http://swgdam.org/SWGDAM_Validation_Guidelines_ APPROVED_Dec_2012.pdf).…”

The Validation of a Single Multiplex Typing System With 45 Y-STR Markers for Familial Searching and Database Construction

“…A previous study indicated that added RM Y-STRs would improve the efficiency of the system (Ballantyne et al, 2014) but mistakenly exclude male individuals from the same familial lineages, which could increase the difficulties of conducting paternal searching in the Y-STR database (Kayser, 2017). The SM Y-STRs are less likely to mutate among male relatives in the same pedigree, which makes this marker more suitable for forensic pedigree searches (Kayser, 2017;Liu et al, 2021). Therefore, we attempt to design a novel Y-STR panel with relatively low mutation rates of Y-STRs.…”