A Strategy for Direct Mapping and Identification of Mutations by Whole-Genome Sequencing

Mutant screens have proven powerful for genetic dissection of a myriad of biological processes, but subsequent identification and isolation of the causative mutations are usually complex and time consuming. We have made the process easier by establishing a novel strategy that employs whole-genome sequencing to simultaneously map and identify mutations without the need for any prior genetic mapping.

[1]  Detlef Weigel,et al.  SHOREmap: simultaneous mapping and mutation identification by deep sequencing , 2009, Nature Methods.

[2]  P. Zipperlen,et al.  Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans , 2000, Genome Biology.

[3]  B. Rosenthal,et al.  Deep resequencing of Trichinella spiralis reveals previously un-described single nucleotide polymorphisms and intra-isolate variation within the mitochondrial genome. , 2010, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[4]  Gabor T. Marth,et al.  Whole-genome sequencing and variant discovery in C. elegans , 2008, Nature Methods.

[5]  T. Mockler,et al.  Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology , 2008, Nucleic acids research.

[6]  Patrick W. Hullett,et al.  BMC Genomics BioMed Central Methodology article Rapid single nucleotide polymorphism mapping in C. elegans , 2005 .

[7]  Gabor T. Marth,et al.  Rapid whole-genome mutational profiling using next-generation sequencing technologies. , 2008, Genome research.

[8]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[9]  Ewan Birney,et al.  A new strategy for genome assembly using short sequence reads and reduced representation libraries. , 2010, Genome research.

[10]  W. Gish,et al.  Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map , 2001, Nature Genetics.

[11]  I. Pe’er,et al.  Caenorhabditis elegans mutant allele identification by whole-genome sequencing , 2008, Nature Methods.

[12]  Dee R. Denver,et al.  High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome , 2004, Nature.

[13]  Richard Gibbs,et al.  High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies , 2008, PLoS genetics.

[14]  N. Munakata [Genetics of Caenorhabditis elegans]. , 1989, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.

[15]  J. Newberg,et al.  Identification of EMS-Induced Mutations in Drosophila melanogaster by Whole-Genome Sequencing , 2009, Genetics.

[16]  J. Drake,et al.  The biochemistry of mutagenesis. , 1976, Annual review of biochemistry.

[17]  Dawei Li,et al.  The sequence and de novo assembly of the giant panda genome , 2010, Nature.

[18]  Henry R. Bigelow,et al.  MAQGene: software to facilitate C. elegans mutant genome sequence analysis , 2009, Nature Methods.

[19]  I. Greenwald,et al.  A Caenorhabditis elegans model for epithelial–neuronal transdifferentiation , 2008, Proceedings of the National Academy of Sciences.

[20]  D. Beier Sequence-based analysis of mutagenized mice , 2000, Mammalian Genome.

[21]  Yufeng Shen,et al.  Comparing Platforms for C. elegans Mutant Identification Using High-Throughput Whole-Genome Sequencing , 2008, PloS one.

[22]  J. Stajich,et al.  De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis , 2010, PLoS genetics.

[23]  Oliver Hobert,et al.  Analysis of Multiple Ethyl Methanesulfonate-Mutagenized Caenorhabditis elegans Strains by Whole-Genome Sequencing , 2010, Genetics.

[24]  Matthew W Vaughn,et al.  Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing. , 2009, Genome research.