title: Genotyping African haplotypes in ATM using a co-spotted single-base extension assay.
abstract: Human genetic analysis, including population genetic studies, increasingly calls for cost-effective, high-throughput methods for the rapid screening of single nucleotide polymorphisms (SNPs) across many individuals. The modified single-base extension assay described here (arrayed SBE) is a highly accurate and robust method for SNP genotyping that can deliver genotypes at 3.5 cents each, following PCR. Specifically, amino-modified probe/target pairs were prehybridized, then co-spotted in a microarray format prior to enzymatic addition of allele-specific nucleotides. Probe/target identity was determined solely by its physical location on the array rather than by hybridization to a complementary target, resulting in a call rate of 99-100%. These innovations result in an inexpensive, accurate assay with exceptional signal-to-noise ratios, depending on the glass surface employed. Comparison of glass slides from three different manufacturers indicated that aldehyde-based Zyomyx slides provided superior performance for this assay. Arrayed SBE was applied to study the geographic distribution of three African-specific haplotypes in the human ATM gene. Four selectively neutral markers, which define the haplotypes H5, H6, and H7, were screened in a total of 415 individuals. Region-specific haplotype frequencies were consistent with patterns of human migration across and outside of Africa, suggesting a possible haplotype origin in East Africa. Arrayed SBE was a robust tool for this analysis that could be applied to any situation requiring the genotyping of a few SNPs in many individuals.
authors.affiliation: Stanford Genome Technology Center, Palo Alto, California 94304, USA.
authors.forename: Maneesh
authors.initials: M
authors.lastname: Jain
authors.forename: Yvonne R
authors.initials: YR
authors.lastname: Thorstenson
authors.forename: David M
authors.initials: DM
authors.lastname: Faulkner
authors.forename: Nader
authors.initials: N
authors.lastname: Pourmand
authors.forename: Ted
authors.initials: T
authors.lastname: Jones
authors.forename: Melinda
authors.initials: M
authors.lastname: Au
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Oefner
authors.forename: Kevin P
authors.initials: KP
authors.lastname: White
authors.forename: Ronald W
authors.initials: RW
authors.lastname: Davis
mesh_terms: D000351:Africa, Eastern / Q000208:ethnology; D001260:Ataxia Telangiectasia / Q000208:ethnology / Q000235:genetics; D064007:Ataxia Telangiectasia Mutated Proteins; D044383:Black People / Q000235:genetics*; D018797:Cell Cycle Proteins; D016000:Cluster Analysis; D004268:DNA-Binding Proteins; D005828:Genetics, Population / Q000191:economics / Q000379:methods / Q000706:statistics & numerical data; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000191:economics / Q000379:methods / Q000706:statistics & numerical data; D016133:Polymerase Chain Reaction / Q000191:economics / Q000379:methods / Q000706:statistics & numerical data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017346:Protein Serine-Threonine Kinases / Q000235:genetics*; D025521:Tumor Suppressor Proteins
chemical_list: D018797:Cell Cycle Proteins; D004268:DNA-Binding Proteins; D025521:Tumor Suppressor Proteins; C576324:ATM protein, human; D064007:Ataxia Telangiectasia Mutated Proteins; D017346:Protein Serine-Threonine Kinases