Detection of Heterozygous Mutations in the Genome of Mismatch Repair Defective Diploid Yeast Using a Bayesian Approach

摘要: DNA replication errors that escape polymerase proofreading and mismatch repair (MMR) can lead to base substitution frameshift mutations. Such mutations disrupt gene function, reduce fitness, promote diseases such as cancer are also the raw material of molecular evolution. To analyze with limited bias genomic features associated errors, we performed a genome-wide analysis accumulate in MMR-deficient diploid lines Saccharomyces cerevisiae. These were derived from common ancestor grown for 160 generations, bottlenecks reducing population one cell every 20 generations. We sequenced between 8- 20-fold coverage wild-type three mutator using Illumina Solexa 36-bp reads. Using an experimentally aware Bayesian genotype caller developed pool experimental data across sequencing runs all strains, detected 28 heterozygous single-nucleotide polymorphisms (SNPs) 48 single-nt insertion/deletions (indels) set. This method was evaluated on simulated sets found have very low false-positive rate (∼6 × 10−5) false-negative 0.08 within unique mapping regions genome contained at least sevenfold coverage. The identified by confirmed Sanger sequencing. All given line, except deletion mutation which occurred independently two lines. indels, composed 46 deletions insertions, homopolymer (HP) tracts [i.e., 47 poly(A) or (T) tracts, 1 poly(G) (C) tract] 5 13 bp long. Our findings interest because HP present high levels yeast (>77,400 5- 20-nt tracts), these likely function. In addition, they demonstrate pattern seen previously defective strains number reporters holds true entire genome.