An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes.
BACKGROUND
With the development of new technology, it has recently become practical to resequence the genome of a bacterium after experimental manipulation. It is critical though to know the accuracy of the technique used, and to establish confidence that all of the mutations were detected.


RESULTS
In order to evaluate the accuracy of genome resequencing using the microarray-based Comparative Genome Sequencing service provided by Nimblegen Systems Inc., we resequenced the E. coli strain W3110 Kohara using MG1655 as a reference, both of which have been completely sequenced using traditional sequencing methods. CGS detected 7 of 8 small sequence differences, one large deletion, and 9 of 12 IS element insertions present in W3110, but did not detect a large chromosomal inversion. In addition, we confirmed that CGS also detected 2 SNPs, one deletion and 7 IS element insertions that are not present in the genome sequence, which we attribute to changes that occurred after the creation of the W3110 lambda clone library. The false positive rate for SNPs was one per 244 Kb of genome sequence.


CONCLUSIONS
CGS is an effective way to detect multiple mutations present in one bacterium relative to another, and while highly cost-effective, is prone to certain errors. Mutations occurring in repeated sequences or in sequences with a high degree of secondary structure may go undetected. It is also critical to follow up on regions of interest in which SNPs were not called because they often indicate deletions or IS element insertions.
Herring
Christopher D
CD
Department of Bioengineering, University of California San Diego, La Jolla, USA. cherring@mascoma.com
Palsson
Bernhard Ø
BØ
D007446:Chromosome Inversion; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D016297:Mutagenesis, Site-Directed; D020641:Polymorphism, Single Nucleotide
Nat Methods. 2005 Dec;2(12):951-3
16299480
Genome Res. 2001 Nov;11(11):1913-25
11691856
Mol Syst Biol. 2006;2:2006.0007
16738553
Genome Res. 2006 Jun;16(6):757-67
16606700
Genome Res. 2004 Mar;14(3):398-405
14993206
Proc Natl Acad Sci U S A. 2006 May 2;103(18):7059-64
16636287
Nat Genet. 2006 Dec;38(12):1406-12
17086184
Science. 2006 Mar 31;311(5769):1932-6
16527929
PLoS Pathog. 2006 Jan;2(1):e5
16446783
Hum Mutat. 2000 Oct;16(4):354-63
11013446
Proc IEEE Comput Syst Bioinform Conf. 2004;:69-79
16448001
Cell. 1987 Jul 31;50(3):495-508
3038334
Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):431-6
16387854
Nature. 2005 Sep 15;437(7057):376-80
16056220
J Bacteriol. 2003 Sep;185(18):5611-26
12949114
Genome Biol. 2005;6(1):R10
15642093
Science. 2005 Sep 9;309(5741):1728-32
16081699
Proc Natl Acad Sci U S A. 2006 May 23;103(21):8107-12
16707573