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DangerTrack: A scoring system to detect difficult-to-assess regions.

ABSTRACT: Over recent years, multiple groups have shown that a large number of structural variants, repeats, or problems with the underlying genome assembly have dramatic effects on the mapping, calling, and overall reliability of single nucleotide polymorphism calls. This project endeavored to develop an easy-to-use track for looking at structural variant and repeat regions. This track, DangerTrack, can be displayed alongside the existing Genome Reference Consortium assembly tracks to warn clinicians and biologists when variants of interest may be incorrectly called, of dubious quality, or on an insertion or copy number expansion. While mapping and variant calling can be automated, it is our opinion that when these regions are of interest to a particular clinical or research group, they warrant a careful examination, potentially involving localized reassembly. DangerTrack is available at https://github.com/DCGenomics/DangerTrack.

SUBMITTER: Dolgalev I

PROVIDER: S-EPMC5405793 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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DangerTrack: A scoring system to detect difficult-to-assess regions.

Dolgalev Igor I Sedlazeck Fritz F Busby Ben B

F1000Research 20170407

Over recent years, multiple groups have shown that a large number of structural variants, repeats, or problems with the underlying genome assembly have dramatic effects on the mapping, calling, and overall reliability of single nucleotide polymorphism calls. This project endeavored to develop an easy-to-use track for looking at structural variant and repeat regions. This track, DangerTrack, can be displayed alongside the existing Genome Reference Consortium assembly tracks to warn clinicians and ...[more]

PMID: 28503299

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Project description:BackgroundSeveral scoring systems are used to assess fecal incontinence (FI), among which, the most commonly used are Wexner and Vaizey's scoring systems. However, there are significant lacunae in these scoring systems, due to which they are neither accurate nor comprehensive.AimTo develop a new scoring system for FI that is accurate, comprehensive, and easy to use.MethodsA pro forma was made in which six types of FI were included: solid, liquid, flatus, mucous, stress, and urge. The weight for each FI was determined by asking a group of patients and laypersons to give a disability score to each type of FI from 0 to 100 (0- least, 100- maximum disability). The disability was assessed on a modified EQ-5D+ (EuroQol) description system, 4D3L (4 dimensions and 3 levels) for each FI. The average score of each FI was calculated, divided by 10, and rounded off to determine the weight of each FI type. The scores for the three levels of frequency of each FI were assigned as never = 0 (No episode of FI ever), occasional = 1 (≤ 1 episode of FI/ wk), and common = 2 (> 1 episode of FI/ wk), and was termed as frequency score. The score for each FI would be derived by multiplying the frequency score and the weight for that FI type. In the second phase of the study, a group of colorectal surgeons was asked to rank the six FI types in order of severity, and their ranking was compared with the patient and laypersons' rankings.ResultsFifty patients and 50 laypersons participated in the study. The weight was assigned to each FI (solid-8, liquid-8, urge-7, flatus-6, mucus-6, and stress-5), and an new scoring system was formulated. The maximum possible score was 80 (total incontinence), and the least 0 (no incontinence). The surgeons' ranking of FI severity did not correlate well with patients' and laypersons' rankings of FI, highlighting that surgeons and patients may perceive the severity of FI differently.ConclusionA new scoring system for FI was formulated, which was simple, logical, comprehensive, and easy to use, and eliminated previous shortcomings. Patients' and surgeons' perceptions of FI severity of FI did not correlate well.

Dataset Information

DangerTrack: A scoring system to detect difficult-to-assess regions.

Publications

DangerTrack: A scoring system to detect difficult-to-assess regions.

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