De Novo Identification of Single Nucleotide Mutations in Caenorhabditis Elegans Using Array Comparative Genomic Hybridization

Overview

Journal Genetics

Publisher Oxford University Press

Specialty Genetics

Date 2009 Feb 5

PMID 19189945

Citations 13

Authors

Jason S Maydan

H Mark Okada

Stephane Flibotte

Mark L Edgley

Donald G Moerman

Affiliations

Soon will be listed here.

Abstract

Array comparative genomic hybridization (aCGH) has been used primarily to detect copy-number variants between two genomes. Here we report using aCGH to detect single nucleotide mutations on oligonucleotide microarrays with overlapping 50-mer probes. This technique represents a powerful method for rapidly detecting novel homozygous single nucleotide mutations in any organism with a sequenced reference genome.

Citing Articles

Ribosomal Protein S12e Has a Distinct Function in Cell Competition.

Kale A, Ji Z, Kiparaki M, Blanco J, Rimesso G, Flibotte S Dev Cell. 2018; 44(1):42-55.e4.

PMID: 29316439 PMC: 5784854. DOI: 10.1016/j.devcel.2017.12.007.

Next-Generation Sequencing-Based Approaches for Mutation Mapping and Identification in Caenorhabditis elegans.

Doitsidou M, Jarriault S, Poole R Genetics. 2016; 204(2):451-474.

PMID: 27729495 PMC: 5068839. DOI: 10.1534/genetics.115.186197.

Random and targeted transgene insertion in Caenorhabditis elegans using a modified Mos1 transposon.

Frokjaer-Jensen C, Davis M, Sarov M, Taylor J, Flibotte S, LaBella M Nat Methods. 2014; 11(5):529-34.

PMID: 24820376 PMC: 4126194. DOI: 10.1038/nmeth.2889.

Forward and reverse mutagenesis in C. elegans.

Kutscher L, Shaham S WormBook. 2014; :1-26.

PMID: 24449699 PMC: 4078664. DOI: 10.1895/wormbook.1.167.1.

From genes to function: the C. elegans genetic toolbox.

Boulin T, Hobert O Wiley Interdiscip Rev Dev Biol. 2013; 1(1):114-37.

PMID: 23801671 PMC: 3694748. DOI: 10.1002/wdev.1.

References

Maydan J, Flibotte S, Edgley M, Lau J, Selzer R, Richmond T . Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization. Genome Res. 2007; 17(3):337-47. PMC: 1800925. DOI: 10.1101/gr.5690307. View

Sharp A, Itsara A, Cheng Z, Alkan C, Schwartz S, Eichler E . Optimal design of oligonucleotide microarrays for measurement of DNA copy-number. Hum Mol Genet. 2007; 16(22):2770-9. DOI: 10.1093/hmg/ddm234. View

Wei H, Kuan P, Tian S, Yang C, Nie J, Sengupta S . A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets. Nucleic Acids Res. 2008; 36(9):2926-38. PMC: 2396435. DOI: 10.1093/nar/gkn133. View

Cuppen E, Gort E, Hazendonk E, Mudde J, van de Belt J, Nijman I . Efficient target-selected mutagenesis in Caenorhabditis elegans: toward a knockout for every gene. Genome Res. 2007; 17(5):649-58. PMC: 1855173. DOI: 10.1101/gr.6080607. View

Flibotte S, Moerman D . Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization. BMC Genomics. 2008; 9:497. PMC: 2577661. DOI: 10.1186/1471-2164-9-497. View

Flibotte S, Edgley M, Maydan J, Taylor J, Zapf R, Waterston R . Rapid high resolution single nucleotide polymorphism-comparative genome hybridization mapping in Caenorhabditis elegans. Genetics. 2008; 181(1):33-7. PMC: 2621182. DOI: 10.1534/genetics.108.096487. View

Edgley M, Riddle D . LG II balancer chromosomes in Caenorhabditis elegans: mT1(II;III) and the mIn1 set of dominantly and recessively marked inversions. Mol Genet Genomics. 2001; 266(3):385-95. DOI: 10.1007/s004380100523. View

Barnes T, Kohara Y, Coulson A, Hekimi S . Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans. Genetics. 1995; 141(1):159-79. PMC: 1206715. DOI: 10.1093/genetics/141.1.159. View

OMeara M, Bigelow H, Flibotte S, Etchberger J, Moerman D, Hobert O . Cis-regulatory mutations in the Caenorhabditis elegans homeobox gene locus cog-1 affect neuronal development. Genetics. 2009; 181(4):1679-86. PMC: 2666530. DOI: 10.1534/genetics.108.097832. View

10.

Gresham D, Dunham M, Botstein D . Comparing whole genomes using DNA microarrays. Nat Rev Genet. 2008; 9(4):291-302. PMC: 7097741. DOI: 10.1038/nrg2335. View

11.

Hillier L, Marth G, Quinlan A, Dooling D, Fewell G, Barnett D . Whole-genome sequencing and variant discovery in C. elegans. Nat Methods. 2008; 5(2):183-8. DOI: 10.1038/nmeth.1179. View

12.

Li H, Ruan J, Durbin R . Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008; 18(11):1851-8. PMC: 2577856. DOI: 10.1101/gr.078212.108. View

13.

Gresham D, Ruderfer D, Pratt S, Schacherer J, Dunham M, Botstein D . Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science. 2006; 311(5769):1932-6. DOI: 10.1126/science.1123726. View

14.

Selzer R, Richmond T, Pofahl N, Green R, Eis P, Nair P . Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer. 2005; 44(3):305-19. DOI: 10.1002/gcc.20243. View

15.

Anderson P . Mutagenesis. Methods Cell Biol. 1995; 48:31-58. View

16.

Sarin S, Prabhu S, OMeara M, Peer I, Hobert O . Caenorhabditis elegans mutant allele identification by whole-genome sequencing. Nat Methods. 2008; 5(10):865-7. PMC: 2574580. DOI: 10.1038/nmeth.1249. View