Evidence map›Paper›PMID 30788173›Full record

ArticleJournal of advanced research2019

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

Helena Skutkova, Martin Vitek, Matej Bezdicek, Eva Brhelova, Martina Lengerova

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of advanced research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.4field-weighted citation impact, top 39% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed, 6 citations in OpenAlex.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors at 2 institutions in 1 country.

Helena SkutkovaDepartment of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic.
Martin VitekDepartment of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic.
Matej BezdicekDepartment of Internal Medicine, Hematology and Oncology, Masaryk University and University Hospital Brno, Cernopolni 212/9, 662 63 Brno, Czech Republic.
Eva BrhelovaDepartment of Internal Medicine, Hematology and Oncology, Masaryk University and University Hospital Brno, Cernopolni 212/9, 662 63 Brno, Czech Republic.
Martina LengerovaDepartment of Internal Medicine, Hematology and Oncology, Masaryk University and University Hospital Brno, Cernopolni 212/9, 662 63 Brno, Czech Republic.
Masaryk University · CZBrno University of Technology · CZ

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Automated chip capillary electrophoresisBand matchingDBSCAN, density-based spatial clustering of applications with noiseDNA fingerprintingDTW, dynamic time warpingESBL, extended spectrum beta-lactamasesGel sample distortionGenotypingKLPN, Klebsiella pneumoniaMALDI-TOF, matrix assisted laser desorption ionization – time of flightPattern recognitionrep-PCR, repetitive element palindromic polymerase chain reactionRMSE, root mean squared errorR-square, ratio of the sum of squaresSD, standard deviationSLINK, single linkageSSE, sum of squares due to errorUPGMA, unweighted pair group method with arithmetic mean

Identifiers

PMID30788173
PMCPMC6369143
OpenAlexW2914786907

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.