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Computer matching of oligonucleotide patterns on electrophoretic gels: an application to the epidemiology of cytomegalovirus

Published online by Cambridge University Press:  19 October 2009

A. E. Ades ,
A. J. Garrett ,
J. Cowell ,
K. S. Chin  and
C. S. Peckham
A. E. Ades
Affiliation:
Department of Paediatric Epidemiology, Institute of Child Health, 30 Guilford St, London WC1N 1EH
A. J. Garrett
Affiliation:
National Institute for Biological Standards and Control, Holly Hill, London NW3 6RB
J. Cowell
Affiliation:
Department of Child Health, Charing Cross Hospital Medical School, London W6 8RP
K. S. Chin
Affiliation:
Department of Child Health, Charing Cross Hospital Medical School, London W6 8RP
C. S. Peckham
Affiliation:
Department of Paediatric Epidemiology, Institute of Child Health, 30 Guilford St, London WC1N 1EH
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Summary

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A computer program was written to analyse oligonucleotide patterns displayed by gel electrophoresis following restriction endonuclease digestion of human cytomegaloviral DNA, and was applied to an epidemiological study of the transmission of infection in a hospital special care baby unit, with regard to infant-to-infant and mother-to-infant transmission.

The program calculates the molecular weight of oligonucleotides from their mobilities, using a cubic spline curve based on the mobilities of oligonucleotides from the AD169 strain. A matching algorithm then calculates the number of unmatched fragments for each pair of viral isolates. This was used as a similarity measure which successfully distinguished mother and infant isolate pairs from epidemiologically unrelated pairs.

The program is not intended to provide fully automatic matching, but could be recommended as a screening device to pick out pairs of strains which are sufficiently similar to suggest a common source of infection, and which may warrant closer comparison. Other applications are discussed, and the possible use of densitometers to automate data entry is considered.

Type
Research Article
Information
Epidemiology & Infection , Volume 100 , Issue 3 , June 1988 , pp. 467 - 479
Copyright
Copyright © Cambridge University Press 1988

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