Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel.
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.
Barker
David L
DL
Illumina, Inc., San Diego, California 92121, USA.
Hansen
Mark S T
MS
Faruqi
A Fawad
AF
Giannola
Diane
D
Irsula
Orlando R
OR
Lasken
Roger S
RS
Latterich
Martin
M
Makarov
Vladimir
V
Oliphant
Arnold
A
Pinter
Jonathon H
JH
Shen
Richard
R
Sleptsova
Irina
I
Ziehler
William
W
Lai
Eric
E
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
D004247:DNA