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Journal of Clinical Microbiology, June 2002, p. 2192-2198, Vol. 40, No. 6
0095-1137/02/$04.00+0     DOI: 10.1128/JCM.40.6.2192-2198.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Determining the Genomic Locations of Repetitive DNA Sequences with a Whole-Genome Microarray: IS6110 in Mycobacterium tuberculosis

Mårten Kivi,1,{dagger} Xuemin Liu,1,{ddagger} Soumya Raychaudhuri,2 Russ B. Altman,2 and Peter M. Small1*

Division of Infectious Diseases and Geographic Medicine,1 Stanford Medical Informatics, Department of Medicine, Stanford University, Stanford, California 943052

Received 18 September 2001/ Returned for modification 29 December 2001/ Accepted 15 February 2002

The mycobacterial insertion sequence IS6110 has been exploited extensively as a clonal marker in molecular epidemiologic studies of tuberculosis. In addition, it has been hypothesized that this element is an important driving force behind genotypic variability that may have phenotypic consequences. We present here a novel, DNA microarray-based methodology, designated SiteMapping, that simultaneously maps the locations and orientations of multiple copies of IS6110 within the genome. To investigate the sensitivity, accuracy, and limitations of the technique, it was applied to eight Mycobacterium tuberculosis strains for which complete or partial IS6110 insertion site information had been determined previously. SiteMapping correctly located 64% (38 of 59) of the IS6110 copies predicted by restriction fragment length polymorphism analysis. The technique is highly specific; 97% of the predicted insertion sites were true insertions. Eight previously unknown insertions were identified and confirmed by PCR or sequencing. The performance could be improved by modifications in the experimental protocol and in the approach to data analysis. SiteMapping has general applicability and demonstrates an expansion in the applications of microarrays that complements conventional approaches in the study of genome architecture.

* Corresponding author. Mailing address: Medical Center, Rm. S-165, Stanford University, Stanford, CA 94305. Phone: (650) 725-7908. Fax: (650) 498-7011. E-mail: peter{at}molepi.stanford.edu.

{dagger} Present address: Department of Medical Epidemiology, Karolinska Institutet, 171 77 Stockholm, Sweden.

{ddagger} Present address: Biorobotics, Woburn, MA 01801.

Journal of Clinical Microbiology, June 2002, p. 2192-2198, Vol. 40, No. 6
0095-1137/02/$04.00+0     DOI: 10.1128/JCM.40.6.2192-2198.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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