Informace o publikaci

Advanced DNA fingerprint genotyping based on a model developed from real chip electrophoresis data

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SKUTKOVA Helena VITEK Martin BEZDÍČEK Matěj BRHELOVÁ Eva LENGEROVÁ Martina

Rok publikování 2019
Druh Článek v odborném periodiku
Časopis / Zdroj JOURNAL OF ADVANCED RESEARCH
Fakulta / Pracoviště MU

Lékařská fakulta

Citace
www http://dx.doi.org/10.1016/j.jare.2019.01.005
Doi http://dx.doi.org/10.1016/j.jare.2019.01.005
Klíčová slova DNA fingerprinting; Automated chip capillary electrophores; Genotyping; Band matching; Gel sample distortion; Pattern recognition
Popis Large-scale comparative studies of DNA fingerprints prefer automated chip capillary electrophoresis over conventional gel planar electrophoresis due to the higher precision of the digitalization process. However, the determination of band sizes is still limited by the device resolution and sizing accuracy. Band matching, therefore, remains the key step in DNA fingerprint analysis. Most current methods evaluate only the pairwise similarity of the samples, using heuristically determined constant thresholds to evaluate the maximum allowed band size deviation; unfortunately, that approach significantly reduces the ability to distinguish between closely related samples. This study presents a new approach based on global multiple alignments of bands of all samples, with an adaptive threshold derived from the detailed migration analysis of a large number of real samples. The proposed approach allows the accurate automated analysis of DNA fingerprint similarities for extensive epidemiological studies of bacterial strains, thereby helping to prevent the spread of dangerous microbial infections. (C) 2019 The Authors. Published by Elsevier B.V. on behalf of Cairo University.