title: Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel.
abstract: Comprehensive genome scans involving many thousands of SNP assays will require significant amounts of genomic DNA from each sample. We report two successful methods for amplifying whole-genomic DNA prior to SNP analysis, multiple displacement amplification, and OmniPlex technology. We determined the coverage of amplification by analyzing a SNP linkage marker set that contained 2320 SNP markers spread across the genome at an average distance of 2.5 cM. We observed a concordance of >99.8% in genotyping results from genomic DNA and amplified DNA, strongly indicating the ability of both methods used to amplify genomic DNA in a highly representative manner. Furthermore, we were able to achieve a SNP call rate of >98% in both genomic and amplified DNA. The combination of whole-genome amplification and comprehensive SNP linkage analysis offers new opportunities for genetic analysis in clinical trials, disease association studies, and archiving of DNA samples.
authors.affiliation: Illumina, Inc., San Diego, California 92121, USA.
authors.forename: David L
authors.initials: DL
authors.lastname: Barker
authors.forename: Mark S T
authors.initials: MS
authors.lastname: Hansen
authors.forename: A Fawad
authors.initials: AF
authors.lastname: Faruqi
authors.forename: Diane
authors.initials: D
authors.lastname: Giannola
authors.forename: Orlando R
authors.initials: OR
authors.lastname: Irsula
authors.forename: Roger S
authors.initials: RS
authors.lastname: Lasken
authors.forename: Martin
authors.initials: M
authors.lastname: Latterich
authors.forename: Vladimir
authors.initials: V
authors.lastname: Makarov
authors.forename: Arnold
authors.initials: A
authors.lastname: Oliphant
authors.forename: Jonathon H
authors.initials: JH
authors.lastname: Pinter
authors.forename: Richard
authors.initials: R
authors.lastname: Shen
authors.forename: Irina
authors.initials: I
authors.lastname: Sleptsova
authors.forename: William
authors.initials: W
authors.lastname: Ziehler
authors.forename: Eric
authors.initials: E
authors.lastname: Lai
mesh_terms: D004247:DNA / Q000235:genetics; D008040:Genetic Linkage / Q000235:genetics*; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D021141:Nucleic Acid Amplification Techniques / Q000379:methods* / Q000592:standards; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results
chemical_list: D004247:DNA