Abstract
Human identification systems such as criminal databases, forensic DNA testing and
genetic genealogy require reliable and cost-effective genotyping of autosomal, mitochondrial
and Y chromosome markers from different biological materials, including venous blood
and saliva. Although many such assays are available, few systems are capable of simultaneously
detecting all three targets in a single reaction. Employing the APEX-2 principle,
we have characterized a novel 124-plex assay, using specific primer extension, universal
primer amplification and single base extension on an oligonucleotide array. The assay
has been designed for simultaneous genotyping of SNPs from the single copy loci (46
autosomal and 29 Y chromosomal markers) side by side with SNPs from the mitochondrial
genome (49 markers) that appears in up to thousands of copies per cell in certain
tissue types. All the autosomal SNPs (from the SNPforID Consortium) included in the multiplex assay are unlinked and are distributed widely
across autosomes, enabling genetic fingerprints to be distinguished. Mitochondrial
DNA and Y chromosome polymorphisms that define haplogroups common in European populations
are included to allow for maternity and paternity testing and for the analysis of
genetic genealogies. After assay optimization we estimated the accuracy (99.83%) and
call rate (99.66%) of the protocol on 17 mother–father–child/children families and
five internal control DNAs. In addition, 79 unrelated Estonian and Swedish DNA samples
were genotyped and the accuracy of mtDNA and Y chromosome haplogroup inference by
the multiplex method was assessed using conventional genotyping methods and direct
sequencing.
Keywords
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Article info
Publication history
Published online: May 18, 2009
Accepted:
April 17,
2009
Received in revised form:
April 16,
2009
Received:
December 22,
2008
Identification
Copyright
© 2009 Elsevier Ireland Ltd. Published by Elsevier Inc. All rights reserved.
