title: SBE-TAGS: an array-based method for efficient single-nucleotide polymorphism genotyping.
abstract: Generating human single-nucleotide polymorphisms (SNPs) is no longer a rate-limiting step for genetic studies of disease. The number of SNPs in public databases already exceeds 200,000, and the total is expected to exceed 1,000,000 within a year. Rather, progress is limited by the inability to genotype large numbers of SNPs. Current genotyping methods are suitable for studying individual loci or at most a handful at a time. Here, we describe a method for parallel genotyping of SNPs, called single base extension-tag array on glass slides, SBE-TAGS. The principle is as follows. SNPs are genotyped by single base extension (SBE), using bifunctional primers carrying a unique sequence tag in addition to a locus-specific sequence. Because each locus has a distinct tag, the genotyping reactions can be performed in a highly multiplexed fashion, and the resulting product can then be "demultiplexed" by hybridization to the reverse complements of the sequence tags arrayed on a glass slide. SBE-TAGS is simple and inexpensive because of the high degree of multiplexing and the use of an easily generated, generic tag array. The method is also highly accurate: we genotyped over 100 SNPs, obtaining over 5, 000 genotypes, with approximately 99% accuracy.
authors.affiliation: Whitehead Institute/MIT Center for Genome Research, One Kendall Square, Building 300, Cambridge, MA 02139, USA.
authors.forename: J N
authors.initials: JN
authors.lastname: Hirschhorn
authors.forename: P
authors.initials: P
authors.lastname: Sklar
authors.forename: K
authors.initials: K
authors.lastname: Lindblad-Toh
authors.forename: Y M
authors.initials: YM
authors.lastname: Lim
authors.forename: M
authors.initials: M
authors.lastname: Ruiz-Gutierrez
authors.forename: S
authors.initials: S
authors.lastname: Bolk
authors.forename: B
authors.initials: B
authors.lastname: Langhorst
authors.forename: S
authors.initials: S
authors.lastname: Schaffner
authors.forename: E
authors.initials: E
authors.lastname: Winchester
authors.forename: E S
authors.initials: ES
authors.lastname: Lander
mesh_terms: D000818:Animals; D017931:DNA Primers; D020869:Gene Expression Profiling; D005838:Genotype; D006801:Humans; D051379:Mice; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide
chemical_list: D017931:DNA Primers