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Article: Do common in silico tools predict the clinical consequences of amino-acid substitutions in the CFTR gene?

TitleDo common in silico tools predict the clinical consequences of amino-acid substitutions in the CFTR gene?
Authors
Issue Date2010
PublisherBlackwell Munksgaard. The Journal's web site is located at http://www.blackwellpublishing.com/journals/CGE
Citation
Clinical Genetics, 2010, v. 77 n. 5, p. 464-473 How to Cite?
AbstractComputational methods are used to predict the molecular consequences of amino-acid substitutions on the basis of evolutionary conservation or protein structure, but their utility in clinical diagnosis or prediction of disease outcome has not been well validated. We evaluated three popular computer programs, namely, PANTHER, SIFT and P. olyP. hen, by comparing the predicted clinical outcomes for a group of known CFTR missense mutations against the diagnosis of cystic fibrosis (CF) and clinical manifestations in cohorts of subjects with CF-disease and CFTR-related disorders carrying these mutations. Owing to poor specificity, none of tools reliably distinguished between individual mutations that confer CF disease from mutations found in subjects with a CFTR-related disorder or no disease. Prediction scores for CFTR mutations derived from PANTHER showed a significant overall statistical correlation with the spectrum of disease severity associated with mutations in the CFTR gene. In contrast, P. olyP. hen- and SIFT-derived scores only showed significant differences between CF-causing and non-CF variants. Current computational methods are not recommended for establishing or excluding a CF diagnosis, notably as a newborn screening strategy or in patients with equivocal test results. © 2010 John Wiley & Sons A/S.
Persistent Identifierhttp://hdl.handle.net/10722/178238
ISSN
2015 Impact Factor: 3.892
2015 SCImago Journal Rankings: 1.630
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorDorfman, Ren_US
dc.contributor.authorNalpathamkalam, Ten_US
dc.contributor.authorTaylor, Cen_US
dc.contributor.authorGonska, Ten_US
dc.contributor.authorKeenan, Ken_US
dc.contributor.authorYuan, XWen_US
dc.contributor.authorCorey, Men_US
dc.contributor.authorTsui, LCen_US
dc.contributor.authorZielenski, Jen_US
dc.contributor.authorDurie, Pen_US
dc.date.accessioned2012-12-19T09:43:39Z-
dc.date.available2012-12-19T09:43:39Z-
dc.date.issued2010en_US
dc.identifier.citationClinical Genetics, 2010, v. 77 n. 5, p. 464-473en_US
dc.identifier.issn0009-9163en_US
dc.identifier.urihttp://hdl.handle.net/10722/178238-
dc.description.abstractComputational methods are used to predict the molecular consequences of amino-acid substitutions on the basis of evolutionary conservation or protein structure, but their utility in clinical diagnosis or prediction of disease outcome has not been well validated. We evaluated three popular computer programs, namely, PANTHER, SIFT and P. olyP. hen, by comparing the predicted clinical outcomes for a group of known CFTR missense mutations against the diagnosis of cystic fibrosis (CF) and clinical manifestations in cohorts of subjects with CF-disease and CFTR-related disorders carrying these mutations. Owing to poor specificity, none of tools reliably distinguished between individual mutations that confer CF disease from mutations found in subjects with a CFTR-related disorder or no disease. Prediction scores for CFTR mutations derived from PANTHER showed a significant overall statistical correlation with the spectrum of disease severity associated with mutations in the CFTR gene. In contrast, P. olyP. hen- and SIFT-derived scores only showed significant differences between CF-causing and non-CF variants. Current computational methods are not recommended for establishing or excluding a CF diagnosis, notably as a newborn screening strategy or in patients with equivocal test results. © 2010 John Wiley & Sons A/S.en_US
dc.languageengen_US
dc.publisherBlackwell Munksgaard. The Journal's web site is located at http://www.blackwellpublishing.com/journals/CGEen_US
dc.relation.ispartofClinical Geneticsen_US
dc.subject.meshAlgorithmsen_US
dc.subject.meshAmino Acid Substitution - Geneticsen_US
dc.subject.meshCanadaen_US
dc.subject.meshComputational Biology - Methodsen_US
dc.subject.meshCystic Fibrosis - Diagnosis - Genetics - Pathologyen_US
dc.subject.meshCystic Fibrosis Transmembrane Conductance Regulator - Geneticsen_US
dc.subject.meshExocrine Pancreatic Insufficiency - Geneticsen_US
dc.subject.meshHumansen_US
dc.subject.meshMutation, Missense - Geneticsen_US
dc.subject.meshPancreas - Pathologyen_US
dc.subject.meshPhenotypeen_US
dc.subject.meshRoc Curveen_US
dc.titleDo common in silico tools predict the clinical consequences of amino-acid substitutions in the CFTR gene?en_US
dc.typeArticleen_US
dc.identifier.emailTsui, LC: tsuilc@hkucc.hku.hken_US
dc.identifier.authorityTsui, LC=rp00058en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1111/j.1399-0004.2009.01351.xen_US
dc.identifier.pmid20059485-
dc.identifier.scopuseid_2-s2.0-77953067567en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-77953067567&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume77en_US
dc.identifier.issue5en_US
dc.identifier.spage464en_US
dc.identifier.epage473en_US
dc.identifier.isiWOS:000276489700009-
dc.publisher.placeDenmarken_US
dc.identifier.f10003352957-
dc.identifier.scopusauthoridDorfman, R=8934686800en_US
dc.identifier.scopusauthoridNalpathamkalam, T=36515191400en_US
dc.identifier.scopusauthoridTaylor, C=7404823047en_US
dc.identifier.scopusauthoridGonska, T=6602316145en_US
dc.identifier.scopusauthoridKeenan, K=36514732000en_US
dc.identifier.scopusauthoridYuan, XW=19338202300en_US
dc.identifier.scopusauthoridCorey, M=7005819978en_US
dc.identifier.scopusauthoridTsui, LC=7102754167en_US
dc.identifier.scopusauthoridZielenski, J=7003732699en_US
dc.identifier.scopusauthoridDurie, P=7005360997en_US
dc.identifier.citeulike7035558-

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