Genome complexity reduction for SNP genotyping analysis.
Efficient single nucleotide polymorphism (SNP) genotyping methods are necessary to accomplish many current gene discovery goals. A crucial element in large-scale SNP genotyping is the number of individual biochemical reactions that must be performed. An efficient method that can be used to simultaneously amplify a set of genetic loci across a genome with high reliability can provide a valuable tool for large-scale SNP genotyping studies. In this paper we describe and characterize a method that addresses this goal. We have developed a strategy for reducing genome complexity by using degenerate oligonucleotide primer (DOP)-PCR and applied this strategy to SNP genotyping in three complex eukaryotic genomes; human, mouse, and Arabidopsis thaliana. Using a single DOP-PCR primer, SNP loci spread throughout a genome can be amplified and accurately genotyped directly from a DOP-PCR product mixture. DOP-PCRs are extremely reproducible. The DOP-PCR method is transferable to many species of interest. Finally, we describe an in silico approach that can effectively predict the SNP loci amplified in a given DOP-PCR, permitting the design of an efficient set of reactions for large-scale, genome-wide SNP studies.
Jordan
Barbara
B
Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Charest
Alain
A
Dowd
John F
JF
Blumenstiel
Justin P
JP
Yeh Rf
Ru-fang
RF
Osman
Asiah
A
Housman
David E
DE
Landers
John E
JE
D000818:Animals; D017360:Arabidopsis; D001482:Base Composition; D002874:Chromosome Mapping; D017931:DNA Primers; D004583:Electrons; D015723:Gene Library; D016678:Genome; D005838:Genotype; D006801:Humans; D051379:Mice; D020161:Physical Chromosome Mapping; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide
D017931:DNA Primers