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Accommodating error analysis in comparison and clustering of molecular fingerprints.

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...

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Detalles Bibliográficos
Autores principales: Salamon, H, Segal, M R, Ponce de Leon, A, Small, P M
Formato: Texto
Lenguaje:English
Publicado: Centers for Disease Control and Prevention 1998
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2640126/
https://www.ncbi.nlm.nih.gov/pubmed/9621186
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author Salamon, H
Segal, M R
Ponce de Leon, A
Small, P M
author_facet Salamon, H
Segal, M R
Ponce de Leon, A
Small, P M
author_sort Salamon, H
collection PubMed
description 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.
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spelling pubmed-26401262009-05-20 Accommodating error analysis in comparison and clustering of molecular fingerprints. Salamon, H Segal, M R Ponce de Leon, A Small, P M Emerg Infect Dis Research Article 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. Centers for Disease Control and Prevention 1998 /pmc/articles/PMC2640126/ /pubmed/9621186 Text en https://creativecommons.org/licenses/by/4.0/This is a publication of the U.S. Government. This publication is in the public domain and is therefore without copyright. All text from this work may be reprinted freely. Use of these materials should be properly cited.
spellingShingle Research Article
Salamon, H
Segal, M R
Ponce de Leon, A
Small, P M
Accommodating error analysis in comparison and clustering of molecular fingerprints.
title Accommodating error analysis in comparison and clustering of molecular fingerprints.
title_full Accommodating error analysis in comparison and clustering of molecular fingerprints.
title_fullStr Accommodating error analysis in comparison and clustering of molecular fingerprints.
title_full_unstemmed Accommodating error analysis in comparison and clustering of molecular fingerprints.
title_short Accommodating error analysis in comparison and clustering of molecular fingerprints.
title_sort accommodating error analysis in comparison and clustering of molecular fingerprints.
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2640126/
https://www.ncbi.nlm.nih.gov/pubmed/9621186
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