SNP Discovery in Pooled Samples With Mismatch Repair Detection
AUTOR(ES)
Fakhrai-Rad, Hossein
FONTE
Cold Spring Harbor Laboratory Press
RESUMO
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.
ACESSO AO ARTIGO
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=442157Documentos Relacionados
- Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system
- High-Throughput SNP Allele-Frequency Determination in Pooled DNA Samples by Kinetic PCR
- Real-time closed tube single nucleotide polymorphism (SNP) quantification in pooled samples by quencher extension (QEXT)
- VarScan: variant detection in massively parallel sequencing of individual and pooled samples
- Comparison of pooled formalin-preserved fecal specimens with three individual samples for detection of intestinal parasites.