Abstract
BackgroundWhole-genome sequencing represents a promising approach to pinpoint chemically induced mutations in genetic model organisms, thereby short-cutting time-consuming genetic mapping efforts.Principal FindingsWe compare here the ability of two leading high-throughput platforms for paired-end deep sequencing, SOLiD (ABI) and Genome Analyzer (Illumina; “Solexa”), to achieve the goal of mutant detection. As a test case we used a mutant C. elegans strain that harbors a mutation in the lsy-12 locus which we compare to the reference wild-type genome sequence. We analyzed the accuracy, sensitivity, and depth-coverage characteristics of the two platforms. Both platforms were able to identify the mutation that causes the phenotype of the mutant C. elegans strain, lsy-12. Based on a 4 MB genomic region in which individual variants were validated by Sanger sequencing, we observe tradeoffs between rates of false positives and false negatives when using both platforms under similar coverage and mapping criteria.SignificanceIn conclusion, whole-genome sequencing conducted by either platform is a viable approach for the identification of single-nucleotide variations in the C. elegans genome.
Highlights
Amenable model organisms have been extensively subjected to forward genetic screening approaches in which mutant individuals that are defective in a given biological process are isolated
We have previously shown that sequencing with the Genome Analyzer (GA) by Illumina is capable of identifying a molecular lesion in a C. elegans strain, lsy12(ot177), that results in a neuronal cell fate defect, thereby demonstrating the utility of whole-genome sequencing as a quick and cost-effective way to circumvent classic genetic mapping [1]
SOLiD reads at a size of 25 bp and GA reads at a size of 35 bp
Summary
Amenable model organisms have been extensively subjected to forward genetic screening approaches in which mutant individuals that are defective in a given biological process are isolated. In an effort to better inform the design, implementation and analysis of such genome-wide deep sequencing experiments, we report sequencing of the same lsy-12(ot177) mutant strain, but using another platform, SOLiD by ABI [3]. We compare these parallel datasets, putting special emphasis on a 4 MB interval around the functional mutation where we have validated the discovered variants using lower throughput Sanger re-sequencing. Whole-genome sequencing represents a promising approach to pinpoint chemically induced mutations in genetic model organisms, thereby short-cutting time-consuming genetic mapping efforts
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