Evaluation of an automated phenotyping algorithm for rheumatoid arthritis.
Computational phenotyping
PheKB
Phenotyping algorithm
Rheumatoid arthritis
Journal
Journal of biomedical informatics
ISSN: 1532-0480
Titre abrégé: J Biomed Inform
Pays: United States
ID NLM: 100970413
Informations de publication
Date de publication:
11 2022
11 2022
Historique:
received:
02
05
2022
revised:
24
09
2022
accepted:
26
09
2022
pubmed:
12
10
2022
medline:
16
11
2022
entrez:
11
10
2022
Statut:
ppublish
Résumé
To better understand the challenges of generally implementing and adapting computational phenotyping approaches, the performance of a Phenotype KnowledgeBase (PheKB) algorithm for rheumatoid arthritis (RA) was evaluated on a University of California, Los Angeles (UCLA) patient population, focusing on examining its performance on ambiguous cases. The algorithm was evaluated on a cohort of 4,766 patients, along with a chart review of 300 patients by rheumatologists against accepted diagnostic guidelines. The performance revealed low sensitivity towards specific subtypes of positive RA cases, which suggests revisions in features used for phenotyping. A close examination of select cases also indicated a significant portion of patients with missing data, drawing attention to the need to consider data integrity as an integral part of phenotyping pipelines, as well as issues around the usability of various codes for distinguishing cases. We use patterns in the PheKB algorithm's errors to further demonstrate important considerations when designing a phenotyping algorithm.
Identifiants
pubmed: 36220544
pii: S1532-0464(22)00219-2
doi: 10.1016/j.jbi.2022.104214
pmc: PMC10226612
mid: NIHMS1870075
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
104214Subventions
Organisme : NIBIB NIH HHS
ID : T32 EB016640
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR001881
Pays : United States
Informations de copyright
Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Références
J Am Med Inform Assoc. 2015 Sep;22(5):993-1000
pubmed: 25929596
J Am Heart Assoc. 2017 Nov 29;6(12):
pubmed: 29187390
BMC Med Genomics. 2011 Jan 26;4:13
pubmed: 21269473
NPJ Digit Med. 2018 Apr 6;1:15
pubmed: 31304300
EGEMS (Wash DC). 2013 Dec 17;1(3):1035
pubmed: 25848578
BMC Med Inform Decis Mak. 2014 Jun 11;14:51
pubmed: 24916006
Dig Dis Sci. 2016 Nov;61(11):3236-3245
pubmed: 27619390
Arthritis Rheum. 1988 Mar;31(3):315-24
pubmed: 3358796
J Am Med Inform Assoc. 2016 Nov;23(6):1046-1052
pubmed: 27026615
Arthritis Rheum. 2004 Dec 15;51(6):952-7
pubmed: 15593102
PLoS One. 2016 May 02;11(5):e0154515
pubmed: 27135409
Arthritis Rheum. 1994 Jun;37(6):821-3
pubmed: 8003054
J Am Med Inform Assoc. 2012 Jun;19(e1):e162-9
pubmed: 22374935
JCO Clin Cancer Inform. 2020 Jun;4:529-538
pubmed: 32543899
Arthritis Rheum. 2010 Sep;62(9):2569-81
pubmed: 20872595
Lancet. 2017 Feb 25;389(10071):815-822
pubmed: 28110982
J Nerv Ment Dis. 2019 Oct;207(10):893-896
pubmed: 31596769