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

J 2019

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

SKUTKOVA, Helena; Martin VITEK; Matěj BEZDÍČEK; Eva BRHELOVÁ; Martina LENGEROVÁ et al.

Základní údaje

Originální název

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

Autoři

SKUTKOVA, Helena; Martin VITEK; Matěj BEZDÍČEK; Eva BRHELOVÁ a Martina LENGEROVÁ

Vydání

JOURNAL OF ADVANCED RESEARCH, AMSTERDAM, ELSEVIER SCIENCE BV, 2019, 2090-1232

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

21100 2.11 Other engineering and technologies

Stát vydavatele

Nizozemské království

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 6.992

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14110/19:00110574

Organizační jednotka

Lékařská fakulta

Klíčová slova anglicky

DNA fingerprinting; Automated chip capillary electrophores; Genotyping; Band matching; Gel sample distortion; Pattern recognition

Štítky

14110212, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 4. 9. 2019 13:57, Mgr. Tereza Miškechová

Anotace

V originále

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.

Citovat

SKUTKOVA, Helena; Martin VITEK; Matěj BEZDÍČEK; Eva BRHELOVÁ a Martina LENGEROVÁ. Advanced DNA fingerprint genotyping based on a model developed from real chip electrophoresis data. JOURNAL OF ADVANCED RESEARCH. AMSTERDAM: ELSEVIER SCIENCE BV, 2019, roč. 18, JUL 2019, s. 9-18. ISSN 2090-1232. Dostupné z: https://doi.org/10.1016/j.jare.2019.01.005.

@article{1552356,
   author = {Skutkova, Helena and Vitek, Martin and Bezdíček, Matěj and Brhelová, Eva and Lengerová, Martina},
   article_location = {AMSTERDAM},
   article_number = {JUL 2019},
   doi = {https://doi.org/10.1016/j.jare.2019.01.005},
   keywords = {DNA fingerprinting; Automated chip capillary electrophores; Genotyping; Band matching; Gel sample distortion; Pattern recognition},
   language = {eng},
   issn = {2090-1232},
   journal = {JOURNAL OF ADVANCED RESEARCH},
   title = {Advanced DNA fingerprint genotyping based on a model developed from real chip electrophoresis data},
   url = {http://dx.doi.org/10.1016/j.jare.2019.01.005},
   volume = {18},
   year = {2019}
}

TY  - JOUR
ID  - 1552356
AU  - Skutkova, Helena - Vitek, Martin - Bezdíček, Matěj - Brhelová, Eva - Lengerová, Martina
PY  - 2019
TI  - Advanced DNA fingerprint genotyping based on a model developed from real chip electrophoresis data
JF  - JOURNAL OF ADVANCED RESEARCH
VL  - 18
IS  - JUL 2019
SP  - 9-18
EP  - 9-18
PB  - ELSEVIER SCIENCE BV
SN  - 20901232
KW  - DNA fingerprinting
KW  - Automated chip capillary electrophores
KW  - Genotyping
KW  - Band matching
KW  - Gel sample distortion
KW  - Pattern recognition
UR  - http://dx.doi.org/10.1016/j.jare.2019.01.005
L2  - http://dx.doi.org/10.1016/j.jare.2019.01.005
N2  - 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.
ER  -

SKUTKOVA, Helena; Martin VITEK; Matěj BEZDÍČEK; Eva BRHELOVÁ a Martina LENGEROVÁ. Advanced DNA fingerprint genotyping based on a model developed from real chip electrophoresis data. \textit{JOURNAL OF ADVANCED RESEARCH}. AMSTERDAM: ELSEVIER SCIENCE BV, 2019, roč.~18, JUL 2019, s.~9-18. ISSN~2090-1232. Dostupné z: https://doi.org/10.1016/j.jare.2019.01.005.

Přehled o publikaci