Highlights
- •The SifaMPS 381 Y-SNP panel was designed to simultaneously target 381 Y-SNPs using the Illumina MiSeq System.
- •A high-resolution haplogroup tree defining 359 different haplogroups aimed at Chinese males was built.
- •High-resolution SifaMPS 381 Y-SNP panel could facilitate paternal lineage classification, familial searching and so forth.
Abstract
Y-chromosome single nucleotide polymorphism (Y-SNP) shows great variation in geographical
distribution and population heterogeneity and can be used to map population genetics
around the world. Massive parallel sequencing (MPS) methodology enables high-resolution
Y-SNP haplogrouping for a certain male and is widely used in forensic genetics and
evolutionary studies. In this present study, we used MPS to develop a customized 381
Y-SNP panel (SifaMPS 381 Y-SNP panel) to investigate the basic structure and subbranches
of the haplogroup tree of the Chinese populations. The SifaMPS 381 Y-SNP panel covers
all the Y-SNPs from our previously designed 183 Y-SNP panel and additional SNPs under
the predominant haplogroups in the Chinese populations based on certain criteria.
We also evaluated the sequencing matrix, concordance, sensitivity, repeatability of
this panel and the ability to analyze mixed and case-type samples based on the Illumina
MiSeq System. The results demonstrated that the novel MPS Y-SNP panel possessed good
sequencing performance and generated accurate Y-SNP genotyping results. Although the
recommended DNA input was greater than 1.25 ng, we observed that a lower DNA amount
could still be used to analyze haplogroups correctly. In addition, this panel could
handle mixed samples and common case-type samples and had higher resolution among
Chinese Han males than previously reported. In conclusion, the SifaMPS 381 Y-SNP panel
showed an overall good performance and offers a better choice for Y-SNP haplogrouping
of the Chinese population, thereby facilitating paternal lineage classification, familial
searching and other forensic applications.
Keywords
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Article info
Publication history
Published online: October 29, 2022
Accepted:
October 26,
2022
Received in revised form:
September 19,
2022
Received:
January 19,
2022
Identification
Copyright
© 2022 Elsevier B.V. All rights reserved.
