title: Evaluation of the 124-plex 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, 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.
authors: Department of Biotechnology, IMCB, University of Tartu, 23 Riia St, 51010 Tartu, Estonia. karlakrj@ut.ee
authors: Kaarel
authors: K
authors: Krjutskov
authors: Triin
authors: T
authors: Viltrop
authors: Priit
authors: P
authors: Palta
authors: Ene
authors: E
authors: Metspalu
authors: Erika
authors: E
authors: Tamm
authors: Siim
authors: S
authors: Suvi
authors: Katrin
authors: K
authors: Sak
authors: Alo
authors: A
authors: Merilo
authors: Helena
authors: H
authors: Sork
authors: Rita
authors: R
authors: Teek
authors: Tiit
authors: T
authors: Nikopensius
authors: Toomas
authors: T
authors: Kivisild
authors: Andres
authors: A
authors: Metspalu
mesh_terms: D041322:Chromosomes, Human, Y; D016172:DNA Fingerprinting; D004272:DNA, Mitochondrial; D005787:Gene Frequency; D005819:Genetic Markers; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D010334:Paternity; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide
chemical_list: D004272:DNA, Mitochondrial; D005819:Genetic Markers