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

Journal of Advanced Research
Helena SkutkovaMartina Lengerova

Abstract

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.

Citations

Feb 23, 2021·Frontiers in Microbiology·Marketa NykrynovaHelena Skutkova

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Methods Mentioned

BETA
electrophoresis
chip
genotyping
bacterial

Software Mentioned

MATLAB
GelClust
BioNumerics Data module
GeneRuler
DiversiLab
2100 Bioanalyzer Expert Software tool
2100 Bioanalyzer Expert
PyElph
GelJ
BioNumerics

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