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Emerg Infect Dis. 1998 Apr-Jun;4(2):159-68.

Accommodating error analysis in comparison and clustering of molecular fingerprints.

Author information

1
University of California, San Francisco, USA. hugh@molepi.stanford.edu

Erratum in

  • Emerg Infect Dis 1998 Jul-Sep;4(3):515.

Abstract

Molecular epidemiologic studies of infectious diseases rely on pathogen genotype comparisons, which usually yield patterns comprising sets of DNA fragments (DNA fingerprints). We use a highly developed genotyping system, IS6110-based restriction fragment length polymorphism analysis of Mycobacterium tuberculosis, to develop a computational method that automates comparison of large numbers of fingerprints. Because error in fragment length measurements is proportional to fragment length and is positively correlated for fragments within a lane, an align-and-count method that compensates for relative scaling of lanes reliably counts matching fragments between lanes. Results of a two-step method we developed to cluster identical fingerprints agree closely with 5 years of computer-assisted visual matching among 1,335 M. tuberculosis fingerprints. Fully documented and validated methods of automated comparison and clustering will greatly expand the scope of molecular epidemiology.

PMID:
9621186
PMCID:
PMC2640126
DOI:
10.3201/eid0402.980203
[Indexed for MEDLINE]
Free PMC Article

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