1. Genotyping African haplotypes in ATM using a co-spotted single-base extension assay.
- Author
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Jain M, Thorstenson YR, Faulkner DM, Pourmand N, Jones T, Au M, Oefner PJ, White KP, and Davis RW
- Subjects
- Africa, Eastern ethnology, Ataxia Telangiectasia ethnology, Ataxia Telangiectasia genetics, Ataxia Telangiectasia Mutated Proteins, Cell Cycle Proteins, Cluster Analysis, DNA-Binding Proteins, Genetics, Population economics, Genetics, Population methods, Genetics, Population statistics & numerical data, Genotype, Humans, Male, Oligonucleotide Array Sequence Analysis economics, Oligonucleotide Array Sequence Analysis methods, Oligonucleotide Array Sequence Analysis statistics & numerical data, Polymerase Chain Reaction economics, Polymerase Chain Reaction methods, Polymerase Chain Reaction statistics & numerical data, Polymorphism, Single Nucleotide genetics, Tumor Suppressor Proteins, Black People genetics, Haplotypes genetics, Protein Serine-Threonine Kinases genetics
- 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., (Copyright 2003 Wiley-Liss, Inc.)
- Published
- 2003
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