Detail publikačního výsledku

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

ŠKUTKOVÁ, H.; VÍTEK, M.; BEZDÍČEK, M.; BRHELOVÁ, E.; LENGEROVÁ, M.

Originální název

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

Anglický název

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

Druh

Článek WoS

Originální abstrakt

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.

Anglický abstrakt

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.

Klíčová slova

DNA fingerprintingautomated chip capillary electrophoresisgenotypingband matchinggel sample distortionpattern recognition

Klíčová slova v angličtině

DNA fingerprintingautomated chip capillary electrophoresisgenotypingband matchinggel sample distortionpattern recognition

Autoři

ŠKUTKOVÁ, H.; VÍTEK, M.; BEZDÍČEK, M.; BRHELOVÁ, E.; LENGEROVÁ, M.

Rok RIV

2019

Vydáno

25.01.2019

Nakladatel

Elsevier

ISSN

2090-1232

Periodikum

Journal of Advanced Research

Svazek

18

Číslo

18

Stát

Egyptská arabská republika

Strany od

9

Strany do

18

Strany počet

10

URL

http://www.sciencedirect.com/science/article/pii/S2090123219300050

BibTex

@article{BUT155605,
  author="Helena {Vítková} and Martin {Vítek} and Matěj {Bezdíček} and Eva {Brhelová} and Martina {Lengerová}",
  title="Advanced DNA fingerprint genotyping based on a model developed from real chip electrophoresis data",
  journal="Journal of Advanced Research",
  year="2019",
  volume="18",
  number="18",
  pages="9--18",
  doi="10.1016/j.jare.2019.01.005",
  issn="2090-1232",
  url="http://www.sciencedirect.com/science/article/pii/S2090123219300050"
}