SNP Discovery in Pooled Samples With Mismatch Repair Detection
Abstract
A targeted discovery effort is required to identify low frequency single nucleotide polymorphisms (SNPs) in human coding and regulatory regions. We here describe combining mismatch repair detection (MRD) with dideoxy terminator sequencing to detect SNPs in pooled DNA samples. MRD enriches for variant alleles in the pooled sample, and sequencing determines the nature of the variants. By using a genomic DNA pool as a template, ∼100 fragments were amplified and subsequently combined and subjected en masse to the MRD procedure. The variant-enriched pool from this one MRD reaction is enriched for the population variants of all the tested fragments. Each fragment was amplified from the variant-enriched pool and sequenced, allowing the discovery of alleles with frequencies as low as 1% in the initial population. Our results support that MRD-based SNP discovery can be used for large-scale discovery of SNPs at low frequencies in a population.
Footnotes
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↵4 In order to ameliorate this problem, amplification primers specific for one member of the family need to be designed; we have implemented software that would accomplish that by performing BLAST on the primer sequences and changing primer pairs that were not unique.
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Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2373904.
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↵3 Corresponding author. E-MAIL malek{at}p-gene.com; FAX (650) 228-0350.
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- Accepted April 8, 2004.
- Received January 19, 2004.
- Cold Spring Harbor Laboratory Press
