Highlights
- •GeneMarker® HTS was developed as a comprehensive tool for analysis of mtDNA MPS data.
- •A novel alignment and motif file approach was used for development of GeneMarker® HTS.
- •Successful haplotype determination for 500 CR sequences with GeneMarker® HTS.
- •Successful heteroplasmy assessment for 500 CR sequences with GeneMarker® HTS.
- •Minimal manual analysis required when using GeneMarker® HTS.
Abstract
Existing software has not allowed for effective alignment of mitochondrial (mt) DNA
sequence data generated using a massively parallel sequencing (MPS) approach, combined
with the ability to perform a detailed assessment of the data. The regions of sequence
that are typically difficult to align are homopolymeric stretches, isolated patterns
of SNPs (single nucleotide polymorphisms), and INDELs (insertions/deletions). A custom
software solution, GeneMarker® HTS, was developed and evaluated to address these limitations, and to provide a user-friendly
interface for forensic practitioners and others interested in mtDNA analysis of MPS
data. GeneMarker® HTS generates an exportable consensus mtDNA sequence that produces phylogenetically
correct SNP and INDEL calls using a customizable motif-based alignment algorithm.
Sequence data from 500 individuals, with various alignment asymmetries and levels
of heteroplasmy, were used to assess the software. Accuracy in producing mtDNA haplotypes,
the ability to correctly identify low-level heteroplasmic sequence variants, and the
user-based features of the software were evaluated. Analyzed sequences yielded correct
mtDNA haplotypes, and heteroplasmic variants were properly identified with minimal
manual interpretation. The software offers numerous user-defined parameters for filtering
the data that address the interests of researchers and practitioners, and provides
multiple options for viewing and navigating through the data.
Graphical abstract
Graphical Abstract
Keywords
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Article info
Publication history
Published online: February 05, 2017
Accepted:
January 25,
2017
Received in revised form:
January 4,
2017
Received:
October 30,
2016
Identification
Copyright
© 2017 Elsevier B.V. All rights reserved.
