Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing

Abstract

Background: Whole-genome sequencing represents a promising approach to pinpoint chemically induced mutations in genetic model organisms, thereby short-cutting time-consuming genetic mapping efforts.

Principal findings: We 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.

Significance: In conclusion, whole-genome sequencing conducted by either platform is a viable approach for the identification of single-nucleotide variations in the C. elegans genome.

Figure 1. Distribution of depth-coverage.

The distribution of depth-coverage of the entire genome is shown for both SOLiD and GA. Poisson and gamma distributions with comparable average mean values are imposed on the observed distribution. Only reads that are mapped with no more three mismatches and without inconsistent mate-pairs are counted in the depth-coverage calculation.

Figure 2. The relationship between average depth-coverage and variant detection sensitivity.

The x-axis is the average depth-coverage. The y-axis is the theoretical fraction of genome where potential variants can be detected under the assumptions described above. The red dot marks 95% sensitivity at 13× coverage.