Document Detail


Repeatability and reproducibility of ribotyping and its computer interpretation.
MedLine Citation:
PMID:  15059627     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Many molecular typing methods are difficult to interpret because their repeatability (within-laboratory variance) and reproducibility (between-laboratory variance) have not been thoroughly studied. In the present work, ribotyping of coryneform bacteria was the basis of a study involving within-gel and between-gel repeatability and between-laboratory reproducibility (two laboratories involved). The effect of different technical protocols, different algorithms, and different software for fragment size determination was studied. Analysis of variance (ANOVA) showed, within a laboratory, that there was no significant added variance between gels. However, between-laboratory variance was significantly higher than within-laboratory variance. This may be due to the use of different protocols. An experimental function was calculated to transform the data and make them compatible (i.e., erase the between-laboratory variance). The use of different interpolation algorithms (spline, Schaffer and Sederoff) was a significant source of variation in one laboratory only. The use of either Taxotron (Institut Pasteur) or GelCompar (Applied Maths) was not a significant source of added variation when the same algorithm (spline) was used. However, the use of Bio-Gene (Vilber Lourmat) dramatically increased the error (within laboratory, within gel) in one laboratory, while decreasing the error in the other laboratory; this might be due to automatic normalization attempts. These results were taken into account for building a database and performing automatic pattern identification using Taxotron. Conversion of the data considerably improved the identification of patterns irrespective of the laboratory in which the data were obtained.
Authors:
Gwénola Lefresne; Eric Latrille; Françoise Irlinger; Patrick A D Grimont
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Publication Detail:
Type:  Evaluation Studies; Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Research in microbiology     Volume:  155     ISSN:  0923-2508     ISO Abbreviation:  Res. Microbiol.     Publication Date:  2004 Apr 
Date Detail:
Created Date:  2004-04-02     Completed Date:  2004-06-29     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  8907468     Medline TA:  Res Microbiol     Country:  France    
Other Details:
Languages:  eng     Pagination:  154-61     Citation Subset:  IM    
Affiliation:
UMR Génie et Microbiologie des Procédés Alimentaires INRA-INAPG, Institut National de la Recherche Agronomique, 78850 Thiverval-Grignon, France.
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Arthrobacter / genetics
Citrobacter / genetics
DNA, Bacterial / chemistry,  genetics
Data Interpretation, Statistical
Electrophoresis, Agar Gel
Nucleic Acid Hybridization
RNA, Ribosomal / chemistry,  genetics
Reproducibility of Results
Ribotyping / methods*,  standards
Software / standards
Chemical
Reg. No./Substance:
0/DNA, Bacterial; 0/RNA, Ribosomal

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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