Lung disease diagnosis from gene expression profiles

Shuyi Ma, Jaeyun Sung, Yuliang Wang, Nathan D. Price

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Lung diseases include some of the most widespread and deadly conditions known to affect people in the US today. One of the main challenges in treating lung disease is the difficulty of diagnosis. Clinical diagnosis remains largely dependent upon symptomatic-based diagnoses; many cases can be either misdiagnosed or undiagnosed until disease has progressed to a more severe stage. Most studies aimed at finding molecular-based diagnostics have focused on one or two diseases at a time, yielding limited success. Instead, we searched for biomarkers reflective of the global health state of the lung by studying data taken from a broad range of lung diseases. We used gene expression microarray data from five different lung diseases - lung adenocarcinoma, lung squamous cell carcinoma, malignant pleural mesothelioma, chronic obstructive pulmonary disease, and asthma - as well as a non-diseased phenotype, to train a classification tree scheme based on the Top Scoring Pair (TSP) algorithm (Geman et al., Stat Appl Genet Mol Biol. 2004; 3: Article 19). The algorithm identified 27 gene pair classifiers that classify the three cancers explicitly, and several of the markers have been previously cited in literature as linked to these cancers. Ten-fold cross validation yielded a classification accuracy of approximately 88%. Thus, a TSP-based classification tree scheme accurately identifies lung diseases from the relative expression of a few number of diagnostic gene pairs.

Original languageEnglish (US)
Title of host publication10AIChE - 2010 AIChE Annual Meeting, Conference Proceedings
StatePublished - Dec 1 2010
Event2010 AIChE Annual Meeting, 10AIChE - Salt Lake City, UT, United States
Duration: Nov 7 2010Nov 12 2010

Publication series

NameAIChE Annual Meeting, Conference Proceedings

Other

Other2010 AIChE Annual Meeting, 10AIChE
CountryUnited States
CitySalt Lake City, UT
Period11/7/1011/12/10

ASJC Scopus subject areas

  • Chemical Engineering(all)
  • Chemistry(all)

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  • Cite this

    Ma, S., Sung, J., Wang, Y., & Price, N. D. (2010). Lung disease diagnosis from gene expression profiles. In 10AIChE - 2010 AIChE Annual Meeting, Conference Proceedings (AIChE Annual Meeting, Conference Proceedings).