title: 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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Computer Science, Columbia University, New York, New York, United States of America.
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Shen
authors.forename: Sumeet
authors.initials: S
authors.lastname: Sarin
authors.forename: Ye
authors.initials: Y
authors.lastname: Liu
authors.forename: Oliver
authors.initials: O
authors.lastname: Hobert
authors.forename: Itsik
authors.initials: I
authors.lastname: Pe'er
mesh_terms: D000818:Animals; D030801:Animals, Genetically Modified; D017173:Caenorhabditis elegans / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods; D004252:DNA Mutational Analysis / Q000295:instrumentation / Q000379:methods*; D049751:Genome, Helminth; D055106:Genome-Wide Association Study / Q000379:methods; D054643:INDEL Mutation / Q000502:physiology; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity