Short hypervariable microhaplotypes: A novel set of very short high discriminating power loci without stutter artefacts

•We present a novel set of 16 very short hypervariable microhaplotypes with four or more SNPs within a 70 bp span.•These 16 loci reach a discriminating power comparable to 9 STRs.•We show that wet lab validation is essential to reliably introduce new loci selected from genome reference data.•These m...

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Bibliographic Details
Published in:Forensic science international : genetics 2018-07, Vol.35, p.169-175
Main Authors: van der Gaag, Kristiaan J., de Leeuw, Rick H., Laros, Jeroen F.J., den Dunnen, Johan T., de Knijff, Peter
Format: Article
Language:English
Subjects:
Alleles
Degraded
Dna
DNA Fingerprinting - methods
Fdstools
Forensic
Gonl
Haplotypes
High-Throughput Nucleotide Sequencing
Humans
Ion pgm
Massively parallel sequencing
Microhaplotypes
Miseq
MPS
Multiplex Polymerase Chain Reaction
Next generation sequencing
NGS
Polymorphism, Single Nucleotide
Sequence Analysis, DNA
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Summary:•We present a novel set of 16 very short hypervariable microhaplotypes with four or more SNPs within a 70 bp span.•These 16 loci reach a discriminating power comparable to 9 STRs.•We show that wet lab validation is essential to reliably introduce new loci selected from genome reference data.•These microhaplotypes could differentiate 276 samples of three continents to their respective population. Since two decades, short tandem repeats (STRs) are the preferred markers for human identification, routinely analysed by fragment length analysis. Here we present a novel set of short hypervariable autosomal microhaplotypes (MH) that have four or more SNPs in a span of less than 70 nucleotides (nt). These MHs display a discriminating power approaching that of STRs and provide a powerful alternative for the analysis;1;is of forensic samples that are problematic when the STR fragment size range exceeds the integrity range of severely degraded DNA or when multiple donors contribute to an evidentiary stain and STR stutter artefacts complicate profile interpretation. MH typing was developed using the power of massively parallel sequencing (MPS) enabling new powerful, fast and efficient SNP-based approaches. MH candidates were obtained from queries in data of the 1000 Genomes, and Genome of the Netherlands (GoNL) projects. Wet-lab analysis of 276 globally dispersed samples and 97 samples of nine large CEPH families assisted locus selection and corroboration of informative value. We infer that MHs represent an alternative marker type with good discriminating power per locus (allowing the use of a limited number of loci), small amplicon sizes and absence of stutter artefacts that can be especially helpful when unbalanced mixed samples are submitted for human identification.
ISSN:1872-4973
1878-0326
DOI:10.1016/j.fsigen.2018.05.008