Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data

Frontiers in Genetics
María de la PuenteMaría Victoria Lareu

Abstract

The development of microhaplotype (MH) panels for massively parallel sequencing (MPS) platforms is gaining increasing relevance for forensic analysis. Here, we expand the applicability of a 102 autosomal and 11 X-chromosome panel of MHs, previously validated with both MiSeq and Ion S5 MPS platforms and designed for identification purposes. We have broadened reference population data for identification purposes, including data from 240 HGDP-CEPH individuals of native populations from North Africa, the Middle East, Oceania and America. Using the enhanced population data, the panel was evaluated as a marker set for bio-geographical ancestry (BGA) inference, providing a clear differentiation of the five main continental groups of Africa, Europe, East Asia, Native America, and Oceania. An informative degree of differentiation was also achieved for the population variation encompassing North Africa, Middle East, Europe, South Asia, and East Asia. In addition, we explored the potential for individual BGA inference from simple mixed DNA, by simulation of mixed profiles followed by deconvolution of mixture components.

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Citations

May 6, 2021·Emerging Topics in Life Sciences·Christopher Phillips, Maria de la Puente
Oct 14, 2021·Human Genetics·Andrew J PakstisKenneth K Kidd

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Datasets Mentioned

BETA
PRJEB39413
PRJEB39574

Methods Mentioned

BETA
genotyping
Assay
AmpliSeq
MDS
chips
chip
PCR
electrophoresis

Software Mentioned

ME
Structure Harvester
HaplotypeCaller
microhaplot R package
R package pegas
SAS
Arlequin
MiSeq
Torrent
fastq

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