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Cystic Fibrosis pp 355–372Cite as

Evaluation of the Disease Liability of CFTR Variants

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 742))

Abstract

Over 1600 novel sequence variants in the CFTR gene have been reported to the CF Mutation Database (http://www.genet.sickkids.on.ca/cftr/Home.html). While about 25 mutations are well characterized by clinical studies and functional assays, the disease liability of most of the remaining mutations is either unclear or unknown. This gap in knowledge has implications for diagnosis, therapy selection, and counseling for patients and families carrying an uncharacterized CFTR mutation. This chapter will describe a critical approach to assessing the disease implications of CFTR mutations utilizing clinical data, literature review, functional testing, and bioinformatic in silico methods.

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References

  1. Grody, W. W., Cutting, G. R., Klinger, K. W., Richards, C. S., Watson, M. S., and Desnick, R. J. (2001) Laboratory standards and guidelines for population-based cystic fibrosis carrier screening. Genet Med 3, 149–154.

    Article  PubMed  CAS  Google Scholar 

  2. Watson, M. S., Cutting, G. R., Desnick, R. J., Driscoll, D. A., Klinger, K., Mennuti, M., et al. (2004) Cystic fibrosis population carrier screening: 2004 revision of american college of medical genetics mutation panel. Genet Med 6, 387–391.

    Article  PubMed  Google Scholar 

  3. Lebo, R. V., and Grody, W. W. (2007) Testing and reporting ACMG cystic fibrosis mutation panel results. Genet Test 11, 11–31.

    Article  PubMed  CAS  Google Scholar 

  4. Goldgar, D. E., Easton, D. F., Deffenbaugh, A. M., Monteiro, A. N., Tavtigian, S. V., and Couch, F. J. (2004) Integrated evaluation of DNA sequence variants of unknown clinical significance: application to BRCA1 and BRCA2. Am J Hum Genet 75, 535–544.

    Article  PubMed  CAS  Google Scholar 

  5. Mitchell, A. A., Chakravarti, A., and Cutler, D. J. (2005) On the probability that a novel variant is a disease-causing mutation. Genome Res 15, 960–966.

    Article  PubMed  CAS  Google Scholar 

  6. Castellani, C., Cuppens, H., Macek, M., Jr., Cassiman, J. J., Kerem, E., Durie, P., et al. (2008) Consensus on the use and interpretation of cystic fibrosis mutation analysis in clinical practice. J Cyst Fibros 7, 179–196.

    Article  PubMed  CAS  Google Scholar 

  7. Bobadilla, J. L., Macek, M., Fine, J. P., and Farrell, P. M. (2002) Cystic fibrosis: a worldwide analysis of CFTR mutations – correlation with incidence data and application to screening. Hum Mutat 19, 575–606.

    Article  PubMed  CAS  Google Scholar 

  8. Southern, K. W., Munck, A., Pollitt, R., Travert, G., Zanolla, L., Dankert-Roelse, J., et al. (2007) A survey of newborn screening for cystic fibrosis in Europe. J Cyst Fibros 6, 57–65.

    Article  PubMed  CAS  Google Scholar 

  9. Grody, W. W., Cutting, G. R., and Watson, M. S. (2007) The cystic fibrosis mutation “arms race”: when less is more. Genet Med 9, 739–744.

    Article  PubMed  Google Scholar 

  10. Pompei, F., Ciminelli, B. M., Bombieri, C., Ciccacci, C., Koudova, M., Giorgi, S., et al. (2006) Haplotype block structure study of the CFTR gene. Most variants are associated with the M470 allele in several European populations. Eur J Hum Genet 14, 85–93.

    PubMed  CAS  Google Scholar 

  11. Bombieri, C., Giorgi, S., Carles, S., de Cid, R., Belpinati, F., Tandoi, C., et al. (2000) A new approach for identifying non-pathogenic mutations. An analysis of the cystic fibrosis transmembrane regulator gene in normal individuals. Hum Genet 106, 172–178.

    Article  PubMed  CAS  Google Scholar 

  12. Wei, L., Vankeerberghen, A., Jaspers, M., Cassiman, J., Nilius, B., and Cuppens, H. (2000) Suppressive interactions between mutations located in the two nucleotide binding domains of CFTR. FEBS Lett 473, 149–153.

    Article  PubMed  CAS  Google Scholar 

  13. Zielenski, J. (2000) Genotype and phenotype in cystic fibrosis. Respiration 67, 117–133.

    Article  PubMed  CAS  Google Scholar 

  14. Stuppia, L., Antonucci, I., Binni, F., Brandi, A., Grifone, N., Colosimo, A., et al. (2005) Screening of mutations in the CFTR gene in 1195 couples entering assisted reproduction technique programs. Eur J Hum Genet 13, 959–964.

    Article  PubMed  CAS  Google Scholar 

  15. Wang, X. J., Moylan, B., Leopold, D. A., Zeitlin, P. L., Rubenstein, R. C., Proud, D., et al. (1998) An increased frequency of CF mutations in patients with chronic sinusitis. Am J Hum Genet 63, A55.

    Article  Google Scholar 

  16. Miller, P. W., Hamosh, A., Macek, M., Jr., Greenberger, P. A., MacLean, J., Walden, S., et al. (1996) Cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations in allergic bronchopulmonary aspergillosis. Am J Hum Genet 59, 45–51.

    PubMed  CAS  Google Scholar 

  17. Wilschanski, M., Dupuis, A., Ellis, L., Jarvi, K., Zielenski, J., Tullis, E., et al. (2006) Mutations in cystic fibrosis transmembrane regulator gene and in vivo transepithelial potentials. Am J Respir Crit Care Med 127, 705–710.

    Google Scholar 

  18. Anguiano, A., Oates, R. D., Amos, J. A., Dean, M., Gerrard, B., Stewart, C., et al. (1992) Congenital bilateral absence of the vas deferens – a primarily genital form of cystic fibrosis. J Am Med Assoc 267, 1794–1797.

    Article  CAS  Google Scholar 

  19. Welsh, M. J., and Smith, A. E. (1993) Molecular mechanisms of CFTR chloride channel dysfunction in cystic fibrosis. Cell 73, 1251–1254.

    Article  PubMed  CAS  Google Scholar 

  20. Kerem, E., and Kerem, B. (1995) The relationship between genotype and phenotype in cystic fibrosis. Curr Opin Pulm Med 1, 450–456.

    Article  PubMed  CAS  Google Scholar 

  21. Cheng, S. H., Gregory, R. J., Marshall, J., Paul, S., Souza, D. W., White, G. A., et al. (1990) Defective intracellular transport and processing of CFTR is the molecular basis of most cystic fibrosis. Cell 63, 827–834.

    Article  PubMed  CAS  Google Scholar 

  22. US Cystic Fibrosis Foundation (2008) US cystic fibrosis foundation patient registry annual data report for 2007.

    Google Scholar 

  23. The Cystic Fibrosis Genotype-Phenotype Consortium (1993) Correlation between genotype and phenotype in patients with cystic fibrosis. The cystic fibrosis genotype-phenotype consortium. N Engl J Med 329, 1308–1313.

    Article  Google Scholar 

  24. Mickle, J. E., and Cutting, G. R. (2000) Genotype-phenotype relationships in cystic fibrosis. Med Clin North Am 84, 597–607.

    Article  PubMed  CAS  Google Scholar 

  25. Taulan, M., Guittard, C., Theze, C., Claustres, M., and Georges, M. (2009) A novel double deletion underscores the importance of characterizing end points of the CFTR large rearrangements. Eur J Hum Genet 17, 1683–1687.

    Article  PubMed  Google Scholar 

  26. Rohlfs, E. M., Zhou, Z., Sugarman, E. A., Heim, R. A., Pace, R. G., Knowles, M. R., et al. (2002) The I148T CFTR allele occurs on multiple haplotypes: a complex allele is associated with cystic fibrosis. Genet Med 4, 319–323.

    Article  PubMed  CAS  Google Scholar 

  27. Strom, C. M., Huang, D., Buller, A., Redman, J., Crossley, B., Anderson, B., et al. (2002) Cystic fibrosis screening using the college panel: platform comparison and lessons learned from the first 20,000 samples. Genet Med 4, 289–296.

    Article  PubMed  CAS  Google Scholar 

  28. Kiesewetter, S., Macek, M., Jr., Davis, C., Curristin, S. M., Chu, C.-S., Graham, C., et al. (1993) A mutation in the cystic fibrosis transmembrane conductance regulator gene produces different phenotypes depending on chromosomal background. Nature Genet 5, 274–278.

    Article  PubMed  CAS  Google Scholar 

  29. Vanscoy, L. L., Lai, T., Bowers, A., and Cutting, G. R. (2006) Modifier genes may contribute substantially to variation in cystic fibrosis (cf) lung disease estimated by CF-Specific % for FEV1. Proc Am Thorac Soc 3, A408.

    Google Scholar 

  30. Gibson, L. E., and Cooke, R. E. (1959) A test for concentration of electrolytes in sweat in cystic fibrosis of the pancreas utilizing pilocarpine by iontophoresis. Pediatrics 23, 545–549.

    PubMed  CAS  Google Scholar 

  31. Beauchamp, M., and Lands, L. C. (2005) Sweat-testing: a review of current technical requirements. Pediatr Pulmonol 39, 507–511.

    Article  PubMed  CAS  Google Scholar 

  32. Stewart, B., Zabner, J., Shuber, A. P., Welsh, M. J., and McCray, P. B., Jr. (1995) Normal sweat chloride values do not exclude the diagnosis of cystic fibrosis. Am J Resp Crit Care Med 151, 899–903.

    PubMed  CAS  Google Scholar 

  33. US Cystic Fibrosis Foundation (2008) US cystic fibrosis foundation patient registry annual data report for 2007.

    Google Scholar 

  34. Farrell, P. M., Rosenstein, B. J., White, T. B., Accurso, F. J., Castellani, C., Cutting, G. R., et al. (2008) Guidelines for diagnosis of cystic fibrosis in newborns through older adults: cystic fibrosis foundation consensus report. J Pediatr 153, S4–S14.

    Article  PubMed  Google Scholar 

  35. Eng, W., LeGrys, V. A., Schechter, M. S., Laughon, M. M., and Barker, P. M. (2005) Sweat-testing in preterm and full-term infants less than 6 weeks of age. Pediatr Pulmonol 40, 64–67.

    Article  PubMed  Google Scholar 

  36. Rosenstein, B. J., and Cutting, G. R. (1998) The diagnosis of cystic fibrosis: a consensus statement. J Pediatr 132, 589–595.

    Article  PubMed  CAS  Google Scholar 

  37. Borowitz, D., Parad, R. B., Sharp, J. K., Sabadosa, K. A., Robinson, K. A., Rock, M. J., et al. (2009) Cystic fibrosis foundation practice guidelines for the management of infants with cystic fibrosis transmembrane conductance regulator-related metabolic syndrome during the first two years of life and beyond. J Pediatr 155, S106–S116.

    Article  PubMed  Google Scholar 

  38. Wilschanski, M., Zielenski, J., Markiewicz, D., Taui, L. C., Corey, M., Levison, H., et al. (1995) Correlation of sweat chloride concentration with classes of the cystic fibrosis transmembrane conductance regulator gene mutations. J Pediatr 127, 705–710.

    Article  PubMed  CAS  Google Scholar 

  39. Wilson, D. C., Ellis, L. E., Zielenski, J., Corey, M., Ip, W. F., Tsui, L. C., et al. (1998) Uncertainty in the diagnosis of cystic fibrosis: possible role of in vivo nasal potential difference measurements. J Pediatr 132, 596–599.

    Article  PubMed  CAS  Google Scholar 

  40. Sheridan, M. B., Fong, P., Groman, J. D., Conrad, C., Flume, P., Diaz, R., et al. (2005) Mutations in the beta subunit of the epithelial Na+ channel in patients with a cystic fibrosis-like syndrome. Hum Mol Genet 14, 3493–3498.

    Article  PubMed  CAS  Google Scholar 

  41. Wilschanski, M., Famini, H., Strauss-Liviatan, N., Rivlin, J., Blau, H., Bibi, H., et al. (2001) Nasal potential difference measurements in patients with atypical cystic fibrosis. Eur Respir J 17, 1208–1215.

    Article  PubMed  CAS  Google Scholar 

  42. Groman, J. D., Karczeski, B., Sheridan, M., Robinson, T. E., Fallin, M. D., and Cutting, G. R. (2005) Phenotypic and genetic characterization of patients with features of “nonclassic” forms of cystic fibrosis. J Pediatr 146, 675–680.

    Article  PubMed  Google Scholar 

  43. Burns, J. L., Emerson, J., Stapp, J. R., Yim, D. L., Krzewinski, J., Louden, L., et al. (1998) Microbiology of sputum from patients at cystic fibrosis centers in the United States. Clin Infect Dis 27, 158–163.

    Article  PubMed  CAS  Google Scholar 

  44. Wilschanski, M., and Durie, P. R. (2007) Patterns of GI disease in adulthood associated with mutations in the CFTR gene. Gut 56, 1153–1163.

    Article  PubMed  CAS  Google Scholar 

  45. Kerem, E., Corey, M., Kerem, B. -S., Rommens, J., Markiewicz, D., Levison, H., et al. (1990) The relation between genotype and phenotype in cystic fibrosis – analysis of the most common mutation (deltaF508). N Engl J Med 323, 1517–1522.

    Article  PubMed  CAS  Google Scholar 

  46. McKone, E. F., Emerson, S. S., Edwards, K. L., and Aitken, M. L. (2003) Effect of genotype on phenotype and mortality in cystic fibrosis: a retrospective cohort study. Lancet 361, 1671–1676.

    Article  PubMed  CAS  Google Scholar 

  47. Hamosh, A., Trapnell, B. C., Zeitlin, P. L., Montrose-Rafizadeh, C., Rosenstein, B. J., Crystal, R. G., et al. (1991) Severe deficiency of CFTR mRNA carrying nonsense mutations R553X and W1316X in respiratory epithelial cells of patients with cystic fibrosis. J Clin Invest 88, 1880–1885.

    Article  PubMed  CAS  Google Scholar 

  48. Hamosh, A., Rosenstein, B. J., and Cutting, G. R. (1992) CFTR nonsense mutations G542X and W1282X associated with severe reduction of CFTR mRNA in nasal epithelial cells. Hum Mol Genet 1, 542–544.

    Article  PubMed  CAS  Google Scholar 

  49. Ng, P. C., and Henikoff, S. (2006) Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 7, 61–80.

    Article  PubMed  CAS  Google Scholar 

  50. Thusberg, J., and Vihinen, M. (2009) Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods. Hum Mutat 30, 703–714.

    Article  PubMed  CAS  Google Scholar 

  51. Gomez Garcia, E. B., Oosterwijk, J. C., Timmermans, M., van Asperen, C. J., Hogervorst, F. B., Hoogerbrugge, N., et al. (2009) A method to assess the clinical significance of unclassified variants in the BRCA1 and BRCA2 genes based on cancer family history. Breast Cancer Res 11, R8.

    Article  PubMed  Google Scholar 

  52. Bao, L., and Cui, Y. (2005) Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information. Bioinformatics 21, 2185–2190.

    Article  PubMed  CAS  Google Scholar 

  53. Bromberg, Y., and Rost, B. (2007) SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res 35, 3823–3835.

    Article  PubMed  CAS  Google Scholar 

  54. Karchin, R., Diekhans, M., Kelly, L., Thomas, D. J., Pieper, U., Eswar, N., et al. (2005) LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics 21, 2814–2820.

    Article  PubMed  CAS  Google Scholar 

  55. Ramensky, V., Bork, P., and Sunyaev, S. (2002) Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30, 3894–3900.

    Article  PubMed  CAS  Google Scholar 

  56. Reumers, J., Maurer-Stroh, S., Schymkowitz, J., and Rousseau, F. (2006) SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs. Bioinformatics 22, 2183–2185.

    Article  PubMed  CAS  Google Scholar 

  57. Yue, P., Melamud, E., and Moult, J. (2006) SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics 7, 166.

    Article  PubMed  Google Scholar 

  58. George Priya, D. C., Rajasekaran, R., Sudandiradoss, C., Ramanathan, K., Purohit, R., and Sethumadhavan, R. (2008) A novel computational and structural analysis of nsSNPs in CFTR gene. Genomic Med 2, 23–32.

    Article  Google Scholar 

  59. Dorfman, R., Nalpathamkalam, T., Taylor, C., Gonska, T., Keenan, K., Yuan, X. W., et al. (2010) Do common in silico tools predict the clinical consequences of amino-acid substitutions in the CFTR gene? Clin Genet 77, 464–473.

    Article  PubMed  CAS  Google Scholar 

  60. Kelly, L., Fukushima, H., Karchin, R., Gow, J. M., Chinn, L. W., Pieper, U., et al. (2010) Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains. Protein Sci 19, 2110–2121.

    Article  PubMed  CAS  Google Scholar 

  61. Goldgar, D. E., Easton, D. F., Byrnes, G. B., Spurdle, A. B., Iversen, E. S., and Greenblatt, M. S. (2008) Genetic evidence and integration of various data sources for classifying uncertain variants into a single model. Hum Mutat 29, 1265–1272.

    Article  PubMed  Google Scholar 

  62. Karchin, R., Monteiro, A. N., Tavtigian, S. V., Carvalho, M. A., and Sali, A. (2007) Functional impact of missense variants in BRCA1 predicted by supervised learning. PLoS Comput Biol 3, e26.

    Article  PubMed  Google Scholar 

  63. Horaitis, O., Talbot, C. C., Jr., Phommarinh, M., Phillips, K. M., and Cotton, R. G. (2007) A database of locus-specific databases. Nat Genet 39, 425.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

The authors would like to thank Neeraj Sharma Ph.D. and Barbara Karczeski M.S., M.A. for their critical review of this manuscript. This work was supported by research grants from the US CF Foundation (CUTTING09A and SOSNAY10Q0) and from the National Institute of Health (HL68927 and DK44003).

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Authors and Affiliations

  1. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Patrick R. Sosnay & Garry R. Cutting

  2. Cystic Fibrosis Centre, Ospedale Civile Maggiore, Verona, Italy

    Carlo Castellani

  3. The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada

    Mary Corey, Ruslan Dorfman & Julian Zielenski

  4. Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA

    Rachel Karchin

  5. Cystic Fibrosis Foundation, Bethesda, MD, USA

    Christopher M. Penland

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  1. Patrick R. Sosnay
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  2. Carlo Castellani
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  4. Ruslan Dorfman
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  5. Julian Zielenski
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  8. Garry R. Cutting
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Correspondence to Garry R. Cutting .

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Editors and Affiliations

  1. Faculty of Sciences, Centre for Biodiversity & Functional, University of Lisboa, Campo Grande, Lisboa, 1749-016, Portugal

    Margarida D. Amaral

  2. , Department of Physiology, University of Regensburg, Universitätsstr. 31, Regensburg, 93053, Germany

    Karl Kunzelmann

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Sosnay, P.R. et al. (2011). Evaluation of the Disease Liability of CFTR Variants. In: Amaral, M., Kunzelmann, K. (eds) Cystic Fibrosis. Methods in Molecular Biology, vol 742. Humana Press. https://doi.org/10.1007/978-1-61779-120-8_21

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  • DOI: https://doi.org/10.1007/978-1-61779-120-8_21

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