Whole-genome sequencing and variant discovery in C. elegans

Massively parallel sequencing instruments enable rapid and inexpensive DNA sequence data production. Because these instruments are new, their data require characterization with respect to accuracy and utility. To address this, we sequenced a Caernohabditis elegans N2 Bristol strain isolate using the...

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Bibliographic Details
Published in:	Nature methods Vol. 5; no. 2; pp. 183 - 188
Main Authors:	Mardis, Elaine R, Hillier, LaDeana W, Marth, Gabor T, Quinlan, Aaron R, Dooling, David, Fewell, Ginger, Barnett, Derek, Fox, Paul, Glasscock, Jarret I, Hickenbotham, Matthew, Huang, Weichun, Magrini, Vincent J, Richt, Ryan J, Sander, Sacha N, Stewart, Donald A, Stromberg, Michael, Tsung, Eric F, Wylie, Todd, Schedl, Tim, Wilson, Richard K
Format:	Journal Article
Language:	English
Published:	New York Nature Publishing Group US 01-02-2008 Nature Publishing Group
Subjects:	Animals Base Sequence Bioinformatics Biological Microscopy Biological Techniques Biomedical and Life Sciences Biomedical Engineering/Biotechnology Caenorhabditis elegans Caenorhabditis elegans - genetics Chromosome Mapping - methods Deoxyribonucleic acid DNA DNA Mutational Analysis - methods DNA sequencing Gene expression Genetic Variation - genetics Genomics Life Sciences Molecular Sequence Data Nucleotide sequencing Polymorphism, Single Nucleotide - genetics Proteomics Scientific method Sequence Analysis, DNA - methods Single nucleotide polymorphisms Worms United States
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Summary:	Massively parallel sequencing instruments enable rapid and inexpensive DNA sequence data production. Because these instruments are new, their data require characterization with respect to accuracy and utility. To address this, we sequenced a Caernohabditis elegans N2 Bristol strain isolate using the Solexa Sequence Analyzer, and compared the reads to the reference genome to characterize the data and to evaluate coverage and representation. Massively parallel sequencing facilitates strain-to-reference comparison for genome-wide sequence variant discovery. Owing to the short-read-length sequences produced, we developed a revised approach to determine the regions of the genome to which short reads could be uniquely mapped. We then aligned Solexa reads from C. elegans strain CB4858 to the reference, and screened for single-nucleotide polymorphisms (SNPs) and small indels. This study demonstrates the utility of massively parallel short read sequencing for whole genome resequencing and for accurate discovery of genome-wide polymorphisms.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1548-7091 1548-7105
DOI:	10.1038/nmeth.1179