Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity

Human Molecular Genetics

Volumn 24, Issue 7, 2014, Pages 1908-1917

  Masica, David L ^a,b   Sosnay, Patrick R ^c   Raraigh, Karen S ^c   Cutting, Garry R ^c   Karchin, Rachel ^a,b,c  

^a Johns Hopkins University   (United States)

^b Johns Hopkins University   (United States)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHLORIDE; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR;

AMINO ACID SUBSTITUTION; ARTICLE; CHLORIDE CONDUCTANCE; CLASSIFIER; CONTROLLED STUDY; CYSTIC FIBROSIS; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR GENE; DATA BASE; DISEASE SEVERITY; ENDOPHENOTYPE; FORCED EXPIRATORY VOLUME; GENE; GENETIC VARIABILITY; HUMAN; LEARNING ALGORITHM; LUNG DISEASE; MEASUREMENT ACCURACY; MISSENSE MUTATION; PATHOGENESIS; PHENOTYPE; PRIORITY JOURNAL; PROTEIN DOMAIN; QUANTITATIVE ANALYSIS; QUANTITATIVE TRAIT; SWEAT; CHEMISTRY; GENETIC VARIATION; GENETICS; INJURY SCALE; METABOLISM; PATHOLOGY; PROTEIN TERTIARY STRUCTURE;

CYSTIC FIBROSIS; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR; GENETIC VARIATION; HUMANS; MUTATION, MISSENSE; PHENOTYPE; PROTEIN STRUCTURE, TERTIARY; TRAUMA SEVERITY INDICES;

EID: 84926484027     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddu607     Document Type: Article

References (37)

1. Hamburg, M.A. and Collins, F.S. (2010) The path to personalized medicine. N. Engl. J. Med., 363, 301-304.
2. Stitziel, N., Kiezun, A. and Sunyaev, S. (2011) Computational and statistical approaches to analyzing variants identified by exome sequencing. Genome Biol., 12, 227.
3. Cline, M.S. and Karchin, R. (2011) Using bioinformatics to predict the functional impact of SNVs. Bioinformatics, 27, 441-448.
4. Mah, J.T.L., Low, E.S.H. and Lee, E. (2011) In silico SNP analysis and bioinformatics tools: a review of the state of the art to aid drug discovery. Drug Discov. Today, 16, 800-809.
5. Thusberg, J., Olatubosun, A. and Vihinen, M. (2011) Performance of mutation pathogenicity prediction methods on missense variants. Hum. Mutat., 32, 358-368.
6. Chan, P.A., Duraisamy, S., Miller, P.J., Newell, J.A., McBride, C., Bond, J.P., Raevaara, T., Ollila, S., Nyström, M., Grimm, A.J. et al. (2007) Interpreting missense variants: comparing computational methods in human disease genes CDKN2A, MLH1, MSH2, MECP2, and tyrosinase (TYR). Hum. Mutat., 28, 683-693.
7. Shihab, H.A., Gough, J., Cooper, D.N., Stenson, P.D., Barker, G. L.A., Edwards, K.J., Day, I.N.M. and Gaunt, T.R. (2013) Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum. Mutat., 34, 57-65.
8. Hicks, S., Wheeler, D.A., Plon, S.E. and Kimmel, M. (2011) Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Hum. Mutat., 32, 661-668.
9. Wieckowska, A., Zein, N.N., Yerian, L.M., Lopez, A.R., McCullough, A.J. and Feldstein, A.E. (2006) In vivo assessment of liver cell apoptosis as a novel biomarker of disease severity in nonalcoholic fatty liver disease. Hepatology, 44, 27-33.
10. Bozza, F., Salluh, J., Japiassu, A., Soares, M., Assis, E., Gomes, R., Bozza, M., Castro-Faria-Neto, H. and Bozza, P. (2007) Cytokine profiles as markers of disease severity in sepsis: a multiplex analysis. Crit. Care, 11, R49.
11. Sakuntabhai, A., Turbpaiboon, C., Casademont, I., Chuansumrit, A., Lowhnoo, T., Kajaste-Rudnitski, A., Kalayanarooj, S.M., Tangnararatchakit, K., Tangthawornchaikul, N., Vasanawathana, S. et al. (2005) A variant in the CD209 promoter is associated with severity of dengue disease. Nat. Genet., 37, 507-513.
12. Stahl, E., Lindberg, A., Jansson, S.-A., Ronmark, E., Svensson, K., Andersson, F., Lofdahl, C. and Lundback, B. (2005) Healthrelated quality of life is related to COPD disease severity. Health Qual. Life Outcomes, 3, 56.
13. Nelson, P.T., Jicha, G.A., Schmitt, F.A., Liu, H., Davis, D.G., Mendiondo, M.S., Abner, E.L. and Markesbery, W.R. (2007) Clinicopathologic correlations in a large Alzheimer disease center autopsy cohort: neuritic plaques and neurofibrillary tangles "do count" when staging disease severity. J. Neuropathol. Exp. Neurol., 66, 1136.
14. Drumm, M.L., Konstan, M.W., Schluchter, M.D., Handler, A., Pace, R., Zou, F., Zariwala, M., Fargo, D., Xu, A., Dunn, J.M. et al. (2005) Genetic modifiers of lung disease in cystic fibrosis. N. Engl. J. Med., 353, 1443-1453.
15. Dorfman, R., Sandford, A., Taylor, C., Huang, B., Frangolias, D., Wang, Y., Sang, R., Pereira, L., Sun, L., Berthiaume, Y. et al. (2008) Complex two-gene modulation of lung disease severity in children with cystic fibrosis. J. Clin. Invest., 118, 1040-1049.
16. Stone, E.A. and Sidow, A. (2005) Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. Genome Res., 15, 978-986.
17. Tavtigian, S.V., Greenblatt, M.S., Lesueur, F. and Byrnes, G.B. (2008) In silico analysis of missense substitutions using sequence-alignment based methods. Hum. Mutat., 29, 1327-1336.
18. Cooper, D., Krawczak, M., Polychronakos, C., Tyler-Smith, C. and Kehrer-Sawatzki, H. (2013) Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum. Genet., 132, 1077-1130.
19. Almasy, L. and Blangero, J. (2001) Endophenotypes as quantitative risk factors for psychiatric disease: rationale and study design. Am. J. Med. Genet., 105, 42-44.
20. Waddington, J.L., Corvin, A.P., Donohoe, G., O'Tuathaigh, C.M. P., Mitchell, K.J. and Gill, M. (2007) Functional Genomics and Schizophrenia: endophenotypes and mutant models. Psychiatr. Clin. North Am., 30, 365-399.
21. Cannon, T.D. and Keller, M.C. (2006) Endophenotypes in the genetic analyses of mental disorders. Annu. Rev. Clin. Psychol., 2, 267-290.
22. Thaker, G. (2008) Psychosis endophenotypes in schizophrenia and bipolar disorder. Schizophr. Bull., 34, 720-721.
23. Anderson, R.D. and Pepine, C.J. (2013) Coronary angiography:is it time to reassess? Circulation, 127, 1760-1762.
24. Riordan, J.R. (2008) CFTR function and prospects for therapy. Annu. Rev. Biochem., 77, 701-726.
25. Sosnay, P.R., Siklosi, K.R., Van Goor, F., Kaniecki, K., Yu, H., Sharma, N., Ramalho, A.S., Amaral, M.D., Dorfman, R. and Zielenski, J. (2013) Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat. Genet., 45, 1160-1167.
26. Masica, D.L., Sosnay, P.R., Cutting, G.R. and Karchin, R. (2012) Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis. Hum. Mutat., 33, 1267-1274.
27. Strom, C.M., Huang, D., Chen, C., Buller, A., Peng, M., Quan, F., Redman, J. and Sun, W. (2003) Extensive sequencing of the cystic fibrosis transmembrane regulator gene: assay validation and unexpected benefits of developing a comprehensive test. Genet. Med., 5, 9-14.
28. Uppaluri, L., England, S.J. and Scanlin, T.F. (2012) Clinical evidence that V456A is a cystic fibrosis causing mutation in South Asians. J. Cyst. Fibrosis, 11, 312-315.
29. Vergani, P., Lockless, S.W., Nairn, A.C. and Gadsby, D.C. (2005) CFTR channel opening by ATP-driven tight dimerization of its nucleotide-binding domains. Nature, 433, 876-880.
30. Zolnerciks, J.K., Andress, E.J., Nicolaou, M. and Linton, K.J. (2011) Structure ofABC transporters. Essays Biochem., 50, 43-61.
31. Rahman, K.S., Cui, G., Harvey, S.C. and McCarty, N.A. (2013) Modeling the conformational changes underlying channel opening in CFTR. PLoS ONE, 8, e74574.
32. Rosenberg, M.F., Kamis, A.B., Aleksandrov, L.A., Ford, R.C. and Riordan, J.R. (2004) Purification and crystallization of the cystic fibrosis transmembrane conductance regulator (CFTR). J. Biol. Chem., 279, 39051-39057.
33. Kayaalp, E., Treacy, E., Waters, P.J., Byck, S., Nowacki, P. and Scriver, C.R. (1997) Human phenylalanine hydroxylase mutations and hyperphenylalaninemia phenotypes: a metanalysis of genotype-phenotype correlations. Am. J. Hum. Genet., 61, 1309-1317.
34. Hull, J. and Thomson, A.H. (1998) Contribution of genetic factors other than CFTR to disease severity in cystic fibrosis. Thorax, 53, 1018-1021.
35. Garred, P., Pressler, T., Madsen, H.O., Frederiksen, B., Svejgaard, A., Høiby, N., Schwartz, M. and Koch, C. (1999) Association of mannose-binding lectin gene heterogeneity with severity of lung disease and survival in cystic fibrosis. J. Clin. Invest., 104, 431-437.
36. Lehner, B. (2013) Genotype to phenotype: lessons from model organisms for human genetics. Nat. Rev. Genet., 14, 168-178.
37. Thompson, J.D., Gibson, T.J. and Higgins, D.G. (2002), Multiple sequence alignment using ClustalW and ClustalX. Curr. Protoc. Bioinformatics, chapter 2, unit 2.3, doi: 10.1002/0471250953.bi0203s00.