Bayesian probit regression model for the diagnosis of pulmonary fibrosis: Proof-of-principle

BMC Medical Genomics

Volumn 4, Issue , 2011, Pages

  Meltzer, Eric B ^a   Barry, William T ^a   D'Amico, Thomas A ^a   Davis, Robert D ^a   Lin, Shu S ^a   Onaitis, Mark W ^a   Morrison, Lake D ^a   Sporn, Thomas A ^a   Steele, Mark P ^a   Noble, Paul W ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; AGED; ARTICLE; BAYESIAN PROBIT REGRESSION MODEL; CLINICAL ARTICLE; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DIAGNOSTIC VALUE; FEMALE; GENE EXPRESSION PROFILING; HUMAN; HUMAN TISSUE; LUNG BIOPSY; LUNG FIBROSIS; LUNG LOBE; MALE; MATHEMATICAL MODEL; NUCLEOTIDE SEQUENCE; PHENOTYPE; PREDICTIVE VALUE; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; RECEIVER OPERATING CHARACTERISTIC; REGRESSION ANALYSIS; SENSITIVITY AND SPECIFICITY; AREA UNDER THE CURVE; BAYES THEOREM; CLUSTER ANALYSIS; COHORT ANALYSIS; DONOR; FIBROSING ALVEOLITIS; GENETICS; LUNG; LUNG TRANSPLANTATION; METABOLISM; MIDDLE AGED; PATHOLOGY;

ADULT; AGED; AREA UNDER CURVE; BAYES THEOREM; CLUSTER ANALYSIS; COHORT STUDIES; FEMALE; GENE EXPRESSION PROFILING; HUMANS; IDIOPATHIC PULMONARY FIBROSIS; LUNG; LUNG TRANSPLANTATION; MALE; MIDDLE AGED; PHENOTYPE; PREDICTIVE VALUE OF TESTS; REGRESSION ANALYSIS; ROC CURVE; SENSITIVITY AND SPECIFICITY; TISSUE DONORS;

EID: 80053472343     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-4-70     Document Type: Article

References (31)

1. Mortality from pulmonary fibrosis increased in the United States from 1992 to 2003. Olson AL, Swigris JJ, Lezotte DC, Norris JM, Wilson CG, Brown KK, Am J Respir Crit Care Med 2007 176 277 284 10.1164/rccm.200701-044OC 17478620 (Pubitemid 47195878)
2. American Thoracic Society/European Respiratory Society International Multidisciplinary Consensus Classification of the Idiopathic Interstitial Pneumonias. This joint statement of the American Thoracic Society (ATS), and the European Respiratory Society (ERS) was adopted by the ATS board of directors, June 2001 and by the ERS Executive Committee, June 2001. Am J Respir Crit Care Med 2002 165 277 304 11790668
3. Idiopathic pulmonary fibrosis: diagnosis and treatment. International consensus statement. American Thoracic Society (ATS), and the European Respiratory Society (ERS). American Thoracic Society, Am J Respir Crit Care Med 2000 161 646 664 10673212
4. Idiopathic pulmonary fibrosis. Meltzer EB, Noble PW, Orphanet J Rare Dis 2008 3 8 10.1186/1750-1172-3-8 18366757
5. Strategies for treating idiopathic pulmonary fibrosis. du Bois RM, Nat Rev Drug Discov 2010 9 129 140 10.1038/nrd2958 20094055
6. Idiopathic nonspecific interstitial pneumonia: report of an American Thoracic Society project. Travis WD, Hunninghake G, King TE Jr, Lynch DA, Colby TV, Galvin JR, Brown KK, Chung MP, Cordier JF, du Bois RM, et al. Am J Respir Crit Care Med 2008 177 1338 1347 10.1164/rccm.200611-1685OC 18388353 (Pubitemid 351860911)
7. Interstitial lung disease: clinical evaluation and keys to an accurate diagnosis. Raghu G, Brown KK, Clin Chest Med 2004 25 409 419 v 10.1016/j.ccm.2004.05.007 15331183 (Pubitemid 39149794)
8. Diagnostic approach to the patient with diffuse lung disease. Ryu JH, Olson EJ, Midthun DE, Swensen SJ, Mayo Clin Proc 2002 77 1221 1227 quiz 1227 10.4065/77.11.1221 12440558 (Pubitemid 35266370)
9. Evolving concepts in the early and accurate diagnosis of idiopathic pulmonary fibrosis. du Bois RM, Clin Chest Med 2006 27 17 25 v-vi 16545629
10. Idiopathic interstitial pneumonia: what is the effect of a multidisciplinary approach to diagnosis? Flaherty KR, King TE Jr, Raghu G, Lynch JP, Colby TV, Travis WD, Gross BH, Kazerooni EA, Toews GB, Long Q, et al. Am J Respir Crit Care Med 2004 170 904 910 10.1164/rccm.200402-147OC 15256390 (Pubitemid 39346487)
11. Multidisciplinary interobserver agreement in the diagnosis of idiopathic pulmonary fibrosis. Thomeer M, Demedts M, Behr J, Buhl R, Costabel U, Flower CD, Verschakelen J, Laurent F, Nicholson AG, Verbeken EK, et al. Eur Respir J 2008 31 585 591 10.1183/09031936.00063706 18057059
12. Idiopathic interstitial pneumonia: do community and academic physicians agree on diagnosis? Flaherty KR, Andrei AC, King TE Jr, Raghu G, Colby TV, Wells A, Bassily N, Brown K, du Bois R, Flint A, et al. Am J Respir Crit Care Med 2007 175 1054 1060 10.1164/rccm.200606-833OC 17255566 (Pubitemid 46741757)
13. Microarray analysis of early stage serous ovarian cancers shows profiles predictive of favorable outcome. Berchuck A, Iversen ES, Luo J, Clarke JP, Horne H, Levine DA, Boyd J, Alonso MA, Secord AA, Bernardini MQ, et al. Clin Cancer Res 2009 15 2448 2455 10.1158/1078-0432.CCR-08-2430 19318476
14. Genomic strategy for targeting therapy in castration-resistant prostate cancer. Mendiratta P, Mostaghel E, Guinney J, Tewari AK, Porrello A, Barry WT, Nelson PS, Febbo PG, J Clin Oncol 2009 27 2022 2029 10.1200/JCO.2008.17.2882 19289629
15. Gene expression profiles of acute exacerbations of idiopathic pulmonary fibrosis. Konishi K, Gibson KF, Lindell KO, Richards TJ, Zhang Y, Dhir R, Bisceglia M, Gilbert S, Yousem SA, Song JW, et al. Am J Respir Crit Care Med 2009 180 167 175 10.1164/rccm.200810-1596OC 19363140
16. MMP1 and MMP7 as potential peripheral blood biomarkers in idiopathic pulmonary fibrosis. Rosas IO, Richards TJ, Konishi K, Zhang Y, Gibson K, Lokshin AE, Lindell KO, Cisneros J, Macdonald SD, Pardo A, et al. PLoS Med 2008 5 93 10.1371/journal.pmed.0050093 18447576 (Pubitemid 351649261)
17. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bolstad BM, Irizarry RA, Astrand M, Speed TP, Bioinformatics 2003 19 185 193 10.1093/bioinformatics/19.2.185 12538238 (Pubitemid 36181903)
18. Summaries of Affymetrix GeneChip probe level data. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP, Nucleic Acids Res 2003 31 15 10.1093/nar/gng015 12582260
19. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP, Biostatistics 2003 4 249 264 10.1093/biostatistics/4.2.249 12925520
20. Predicting the clinical status of human breast cancer by using gene expression profiles. West M, Blanchette C, Dressman H, Huang E, Ishida S, Spang R, Zuzan H, Olson JA Jr, Marks JR, Nevins JR, Proc Natl Acad Sci USA 2001 98 11462 11467 10.1073/pnas.201162998 11562467 (Pubitemid 32928751)
21. limma: Linear Models for Microarray Data. Smyth GK, Bioinformatics and computational biology solutions using R and Bioconductor 2005 397 420
22. Statistical issues in cDNA microarray data analysis. Smyth GK, Yang YH, Speed T, Methods Mol Biol 2003 224 111 136 12710670
23. Controlling the False Discovery Rate-a Practical and Powerful Approach to Multiple Testing. Benjamini Y, Hochberg Y, J Roy Stat Soc B Met 1995 57 289 300
24. Up-regulation and profibrotic role of osteopontin in human idiopathic pulmonary fibrosis. Pardo A, Gibson K, Cisneros J, Richards TJ, Yang Y, Becerril C, Yousem S, Herrera I, Ruiz V, Selman M, Kaminski N, PLoS Med 2005 2 251 10.1371/journal.pmed.0020251 16128620 (Pubitemid 41382924)
25. Gene expression profiling of familial and sporadic interstitial pneumonia. Yang IV, Burch LH, Steele MP, Savov JD, Hollingsworth JW, McElvania-Tekippe E, Berman KG, Speer MC, Sporn TA, Brown KK, et al. Am J Respir Crit Care Med 2007 175 45 54 16998095 (Pubitemid 46105308)
26. Gene expression analysis reveals matrilysin as a key regulator of pulmonary fibrosis in mice and humans. Zuo F, Kaminski N, Eugui E, Allard J, Yakhini Z, Ben-Dor A, Lollini L, Morris D, Kim Y, DeLustro B, et al. Proc Natl Acad Sci USA 2002 99 6292 6297 10.1073/pnas.092134099 11983918 (Pubitemid 34493305)
27. Gene expression profiling as a window into idiopathic pulmonary fibrosis pathogenesis: can we identify the right target genes? Kaminski N, Rosas IO, Proc Am Thorac Soc 2006 3 339 344 10.1513/pats.200601-011TK 16738198 (Pubitemid 43852873)
28. When it comes to genes - IPF or NSIP, familial or sporadic - they're all the same. Rosas IO, Kaminski N, Am J Respir Crit Care Med 2007 175 5 6 17179494 (Pubitemid 46115934)
29. Molecular phenotypes distinguish patients with relatively stable from progressive idiopathic pulmonary fibrosis (IPF). Boon K, Bailey NW, Yang J, Steel MP, Groshong S, Kervitsky D, Brown KK, Schwarz MI, Schwartz DA, PLoS One 2009 4 5134 10.1371/journal.pone.0005134 19347046
30. Accelerated variant of idiopathic pulmonary fibrosis: clinical behavior and gene expression pattern. Selman M, Carrillo G, Estrada A, Mejia M, Becerril C, Cisneros J, Gaxiola M, Perez-Padilla R, Navarro C, Richards T, et al. PLoS One 2007 2 482 10.1371/journal.pone.0000482 17534432
31. Gene expression profiles distinguish idiopathic pulmonary fibrosis from hypersensitivity pneumonitis. Selman M, Pardo A, Barrera L, Estrada A, Watson SR, Wilson K, Aziz N, Kaminski N, Zlotnik A, Am J Respir Crit Care Med 2006 173 188 198 16166619 (Pubitemid 43187891)