Detection of structural disorders in colorectal cancer DNA with Fourier-transform infrared spectroscopy

• Published in: Vibrational spectroscopy Vol. 46; no. 2; pp. 150 - 157
• Main Authors: Kondepati, Venkata Radhakrishna, Heise, H. Michael, Oszinda, Thomas, Mueller, Ralf, Keese, Michael, Backhaus, Juergen
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 11.03.2008
• Subjects: Colorectal cancer; DNA; FTIR spectroscopy; Linear discriminant analysis; LDA; Linear discriminant analysis; DNA; FTIR; Colorectal cancer; FTIR spectroscopy
• ISSN: 0924-2031; 1873-3697
• DOI: 10.1016/j.vibspec.2007.12.010

The application of Fourier-transform infrared (FTIR) spectroscopy for the detection of structural disorders in colorectal cancer deoxyribonucleic acid (DNA) has been investigated. The DNA was isolated from cancer and its adjacent histological normal tissue of 43 colorectal cancer patients. Minor structural disorders in cancer DNA were detected by differences in the spectral regions assigned to nucleotide bases and phosphodiester-deoxyribose backbone. Spectral differences between grade 1, 2 and 3 cancers were also observed. Furthermore, the normal DNA spectra from patients above 50 years were observed to exhibit cancer like phenotype. The spectral data were further evaluated using linear discriminant analysis with different leave- n-out cross-validation schemes (up to n = 15) after reducing the number of spectral variables down to nine for classification using a heuristic optimisation procedure. Diagnostic accuracies between 70 and 86% were achieved using different validation strategies, the lowest achieved by using a variable selection scheme independent from the validation test data. For practical work and due to the small sample population studied also prior wavelength selection schemes based on cross-validation using the whole data set were tested leading to more optimistic accuracies. Our findings suggest that mid-infrared spectroscopy can be applied for clinical studies elucidating DNA structure relevance.