Phenotype-aware prioritisation of rare Mendelian disease variants.
molecular diagnosis
phenotype
rare disease
variant prioritisation
variant prioritization
Journal
Trends in genetics : TIG
ISSN: 0168-9525
Titre abrégé: Trends Genet
Pays: England
ID NLM: 8507085
Informations de publication
Date de publication:
12 2022
12 2022
Historique:
received:
31
03
2022
revised:
06
06
2022
accepted:
05
07
2022
pubmed:
8
8
2022
medline:
19
11
2022
entrez:
7
8
2022
Statut:
ppublish
Résumé
A molecular diagnosis from the analysis of sequencing data in rare Mendelian diseases has a huge impact on the management of patients and their families. Numerous patient phenotype-aware variant prioritisation (VP) tools have been developed to help automate this process, and shorten the diagnostic odyssey, but performance statistics on real patient data are limited. Here we identify, assess, and compare the performance of all up-to-date, freely available, and programmatically accessible tools using a whole-exome, retinal disease dataset from 134 individuals with a molecular diagnosis. All tools were able to identify around two-thirds of the genetic diagnoses as the top-ranked candidate, with LIRICAL performing best overall. Finally, we discuss the challenges to overcome most cases remaining undiagnosed after current, state-of-the-art practices.
Identifiants
pubmed: 35934592
pii: S0168-9525(22)00179-2
doi: 10.1016/j.tig.2022.07.002
pmc: PMC9950798
mid: NIHMS1872532
pii:
doi:
Types de publication
Journal Article
Review
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1271-1283Subventions
Organisme : NICHD NIH HHS
ID : R01 HD103805
Pays : United States
Organisme : NIH HHS
ID : R24 OD011883
Pays : United States
Organisme : NHGRI NIH HHS
ID : U54 HG006370
Pays : United States
Organisme : Department of Health
ID : RG65966
Pays : United Kingdom
Informations de copyright
Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests The authors declare no conflict of interest.
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