Genome complexity reduction for SNP genotyping analysis.

Abstract:

: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.

authors

Jordan B,Charest A,Dowd JF,Blumenstiel JP,Yeh Rf RF,Osman A,Housman DE,Landers JE

doi

10.1073/pnas.261710699

keywords:

subject

Has Abstract

pub_date

2002-03-05 00:00:00

pages

2942-7

issue

5

eissn

0027-8424

issn

1091-6490

pii

99/5/2942

journal_volume

99

pub_type

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