Evaluation of the 124-Plex SNP Typing Microarray for Forensic Testing

• NCJ Number: 229594
• Journal: Forensic Science International: Genetics Volume: 4 Issue: 1 Dated: December 2009 Pages: 43-48
• Author(s): Kaarel Krjutskov; Triin Viltrop; Priit Palta; Ene Metspalu; Erika Tamm; Siim Suvi; Katrin Sak; Alo Merilo; Helena Sork; Rita Teek; Tiit Nikopensious; Toomas Kivisld; Andres Metspalu
• Date Published: December 2009
• Length: 6 pages
• Publication Format: Article
• Publication Type: Report (Study/Research)
• Language: English
• Country: Ireland

Annotation

Results are presented from the evaluation of the 124-plex single nucleotide polymorphism (SNP) typing microarray for forensic testing.

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, this study 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 single nucleotide polymorphisms (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, the accuracy (99.83 percent) and call rate (99.66 percent) of the protocol on 17 mother-father-child/children families and 5 internal control DNAs were estimated. 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. Tables, figures, appendix and references (Published Abstract)