A phylogenetic framework facilitates Y-STR variant discovery and classification via massively parallel sequencing

Tunde I Huszar,Mark A Jobling,Jon H Wetton

doi:10.1016/j.fsigen.2018.03.012

Abstract

Short tandem repeats on the male-specific region of the Y chromosome (Y-STRs) are permanently linked as haplotypes, and therefore Y-STR sequence diversity can be considered within the robust framework of a phylogeny of haplogroups defined by single nucleotide polymorphisms (SNPs). Here we use massively parallel sequencing (MPS) to analyse the 23 Y-STRs in Promega’s prototype PowerSeq™ Auto/Mito/Y System kit (containing the markers of the PowerPlex® Y23 [PPY23] System) in a set of 100 diverse Y chromosomes whose phylogenetic relationships are known from previous megabase-scale resequencing. Including allele duplications and alleles resulting from likely somatic mutation, we characterised 2311 alleles, demonstrating 99.83% concordance with capillary electrophoresis (CE) data on the same sample set. The set contains 267 distinct sequence-based alleles (an increase of 58% compared to the 169 detectable by CE), including 60 novel Y-STR variants phased with their flanking sequences which have not been reported previously to our knowledge. Variation includes 46 distinct alleles containing non-reference variants of SNPs/indels in both repeat and flanking regions, and 145 distinct alleles containing repeat pattern variants (RPV). For DYS385a,b, DYS481 and DYS390 we observed repeat count variation in short flanking segments previously considered invariable, and suggest new MPS-based structural designations based on these. We considered the observed variation in the context of the Y phylogeny: several specific haplogroup associations were observed for SNPs and indels, reflecting the low mutation rates of such variant types; however, RPVs showed less phylogenetic coherence and more recurrence, reflecting their relatively high mutation rates. In conclusion, our study reveals considerable additional diversity at the Y-STRs of the PPY23 set via MPS analysis, demonstrates high concordance with CE data, facilitates nomenclature standardisation, and places Y-STR sequence variants in their phylogenetic context.

Highlights

Short tandem repeats (STRs) are divided into simple, compound, complex or even complex hypervariable types, reflecting the increasing complexity of the length, sequence and intermittent elements of building blocks [1]
While single nucleotide changes typically have very low mutation rates (∼10−8 per base per generation [3]) and are unlikely to be observed as independent recurrences, the repeat pattern variation (RPV) in STRs mainly results from a more rapid (∼10−3 per repeat array per generation [4]) mutation process driven by replication slippage, so that the same variants can arise multiple times independently
The published analysis had used massively parallel sequencing of ∼3.7 Mb of DNA in each of 448 diverse Y chromosomes, and constructed a maximum-parsimony tree based on a total of 13,261 single nucleotide polymorphism (SNP)

Summary

Introduction

Short tandem repeats (STRs) are divided into simple, compound, complex or even complex hypervariable types, reflecting the increasing complexity of the length, sequence and intermittent elements of building blocks [1]. One indication that increased allelic diversity is likely to be observed via MPS-based analysis of an STR is the complexity of the array [2], since repeat pattern variation (RPV) can arise from different numbers of repeat blocks with the same allele length (isometric alleles). Single nucleotide polymorphisms (SNPs) and insertions or deletions (indels) within repeat arrays can contribute to diversity. While single nucleotide changes typically have very low mutation rates (∼10−8 per base per generation [3]) and are unlikely to be observed as independent recurrences, the RPV in STRs mainly results from a more rapid (∼10−3 per repeat array per generation [4]) mutation process driven by replication slippage, so that the same variants can arise multiple times independently. SNPs and indels are not restricted to the repeat array, but are found in the flanking regions, providing further basis for discrimination

Methods

Results

Conclusion