SNP discovery in pooled samples with mismatch repair detection.
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, approximately 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.
Fakhrai-Rad
Hossein
H
ParAllele Bioscience, South San Francisco, California 94080, USA.
Zheng
Jianbiao
J
Willis
Thomas D
TD
Wong
Kee
K
Suyenaga
Kent
K
Moorhead
Martin
M
Eberle
Jim
J
Thorstenson
Yvonne R
YR
Jones
Ted
T
Davis
Ronald W
RW
Namsaraev
Eugeni
E
Faham
Malek
M
D000818:Animals; D020137:Base Pair Mismatch / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods; D002891:Chromosomes, Human, Pair 21 / Q000235:genetics; D003001:Cloning, Molecular / Q000379:methods; D004260:DNA Repair / Q000235:genetics*; D005188:False Negative Reactions; D005189:False Positive Reactions; D005787:Gene Frequency / Q000235:genetics; D019398:Genes, BRCA1; D024522:Genes, BRCA2; D014644:Genetic Variation / Q000235:genetics; D005828:Genetics, Population; D006801:Humans; D006822:Hybrid Cells; D051379:Mice; D021141:Nucleic Acid Amplification Techniques / Q000379:methods; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity