Advanced DNA fingerprint genotyping based on a model developed from real chip electrophoresis data
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Advanced DNA fingerprint genotyping based on a model developed from real chip electrophoresis data. 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.
Advanced DNA fingerprint genotyping based on a model developed from
real chip electrophoresis data
Helena Skutkovaa,⇑, Martin Viteka, Matej Bezdicekb, Eva Brhelovab, Martina Lengerovab
a Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic
b Department of Internal Medicine, Hematology and Oncology, Masaryk University and University Hospital Brno, Cernopolni 212/9, 662 63 Brno, Czech Republic
h i g h l i g h t s
g r a p h i c a l
a b s t r a c t
Mapping chip electrophoresis
distortion based on real data
measurement.
Determining the transformation
function for the adaptive correction of
band size deviation.
Improving the ability to distinguish
closely related DNA fingerprints.
Using hierarchical clustering to adjust
the global band position.
Genotyping all DNA fingerprints from
multiple runs at once.
a r t i c l e
i n f o
a b s t r a c t
Article history:
Large-scale comparative studies of DNA fingerprints prefer automated chip capillary electrophoresis over
Received 19 October 2018
Revised 6 January 2019
Accepted 10 January 2019
Available online 25 January 2019
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 match-
ing, 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
Keywords:
DNA fingerprinting
Automated chip capillary electrophoresis
Genotyping
Band matching
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 mul-
tiple 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 anal-
ysis of DNA fingerprint similarities for extensive epidemiological studies of bacterial strains, thereby
Gel sample distortion
helping to prevent the spread of dangerous microbial infections.
Pattern recognition
2019 The Authors. Published by Elsevier B.V. on behalf of Cairo University. This is an open access article