COMMUNICATION Application of Linear Discriminant Analysis and Attenuated Total Reflectance Fourier Transform Infrared Microspectroscopy for Diagnosis of Colon Cancer Mohammadreza Khanmohammadi & Amir Bagheri Garmarudi & Simin Samani & Keyvan Ghasemi & Ahmad Ashuri Received: 18 March 2009 / Accepted: 21 October 2010 / Published online: 31 December 2010 # Arányi Lajos Foundation 2010 Abstract Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) microspectroscopy was applied for detection of colon cancer according to the spectral features of colon tissues. Supervised classification models can be trained to identify the tissue type based on the spectroscopic fingerprint. A total of 78 colon tissues were used in spectroscopy studies. Major spectral differences were observed in 1,740–900 cm -1 spectral region. Several chemometric methods such as analysis of variance (ANOVA), cluster analysis (CA) and linear discriminate analysis (LDA) were applied for classifi- cation of IR spectra. Utilizing the chemometric techniques, clear and reproducible differences were observed between the spectra of normal and cancer cases, suggesting that infrared microspectroscopy in conjunction with spectral data process- ing would be useful for diagnostic classification. Using LDA technique, the spectra were classified into cancer and normal tissue classes with an accuracy of 95.8%. The sensitivity and specificity was 100 and 93.1%, respectively. Keywords Colon cancer . Diagnosis . ATR-FTIR . Chemometrics . LDA Introduction Cancer is one of the main causes of death all around the world and it will soon be the leading cause of death. In the United States, over 1.5 million cases of cancer are estimated to be diagnosed in 2009 [1]. Colon cancer has allocated one of the highest mortality rates. Abnormal cell proliferation has been known to be an indicator of the initiation of malignancy [2]. The detection of abnormal crypts becomes essential for diagnosis of colon cancer and its effective management [3, 4]. Hitherto the detection of premalignant conditions in the colon has been associated with abnormal crypt proliferation [5–8]. Various techniques have been utilized to identify abnormal crypt proliferation in colon tissues [9, 10]. The presence of certain molecular markers in the crypt has been used to detect abnormal proliferation [7, 8, 10, 11]. In some studies, abnormality was identified using sensitive markers, which were defined at molecular levels [12]. Despite the identification of certain specific markers for abnormal cell proliferation [13], the actual maturation of the crypt in terms of total biochemical changes has not been established. The “gold standard” in most cancer diagnostics is microscopic evaluation, by a pathologist, of a stained tissue obtained from biopsy of a particular organ. The differences between “malignant” and “normal” have many observations in common e.g. morphology and size of cells that are different and more variable than those of normal cells, nucleus of a cell that is larger than the nucleus of a normal cell, large cells with multiple nuclei, and the invasion of normal tissue by a neoplasm. Although many pathologists are exceptionally good at what they do, this analysis is somewhat subjective. “Misdiagnosis”, with a false negative or false positive result is common in tissue evaluation. Additionally, in some cases (about 10%), a pathologic examination may not produce a M. Khanmohammadi (*) : A. Bagheri Garmarudi : K. Ghasemi : A. Ashuri Chemistry Department, Faculty of Science, Imam Khomeini International University, 34149-1-6818, Qazvin, Iran e-mail: mrkhanmohammadi@gmail.com A. Bagheri Garmarudi Department of Chemistry & Polymer Laboratories, Engineering Research Institute, Tehran, Iran S. Samani Pathology Department, Qazvin University of Medical Sciences, Qazvin, Iran Pathol. Oncol. Res. (2011) 17:435–441 DOI 10.1007/s12253-010-9326-y