DOI QR코드

DOI QR Code

Automatic Reading System for On-off Type DNA Chip

  • Ryu, Mun-Ho (Div. of Bionics and Bioinformatics, Chonbuk National University, Bioengineering Research Center for the Aged, Chonbuk National University) ;
  • Kim, Jong-Dae (Div. of Information Engineering & Telecommunications, Hallym University) ;
  • Kim, Jong-Won (Biomedlab Co., Ltd.)
  • 발행 : 2006.12.31

초록

In this study we propose an automatic reading system for diagnostic DNA chips. We define a general specification for an automatic reading system and propose a possible implementation method. The proposed system performs the whole reading process automatically without any user intervention, covering image acquisition, image analysis, and report generation. We applied the system for the automatic report generation of a commercialized DNA chip for cervical cancer detection. The fluorescence image of the hybridization result was acquired with a $GenePix^{TM}$ scanner using its library running in HTML pages. The processing of the acquired image and the report generation were executed by a component object module programmed with Microsoft Visual C++ 6.0. To generate the report document, we made an HWP 2002 document template with marker strings that were supposed to be searched and replaced with the corresponding information such as patient information and diagnosis results. The proposed system generates the report document by reading the template and changing the marker strings with the resultant contents. The system is expected to facilitate the usage of a diagnostic DNA chip for mass screening by the automation of a conventional manual reading process, shortening its processing time, and quantifying the reading criteria.

키워드

참고문헌

  1. R.S.H. Istepanian, 'Micro-array Image Processing: Current Status and Future Directions', IEEE Trans. Nanobioscience, vol.2, no.4, pp.173-175, Dec., 2003 https://doi.org/10.1109/TNB.2003.816224
  2. Y. Zhou, J. Liu, 'AVA: Visual Analysis of Gene Expression Micro-array Data', Bioinformatics, vol.19, no.2, pp.293-294, 2003 https://doi.org/10.1093/bioinformatics/19.2.293
  3. L.J. Ridley, 'Guide to the Radiology Report', Australasian Radiology, vol. 46, pp.366-369, Dec., 2002
  4. GenePix 4000A User's Guide, Axon Instruments, Inc., 1999
  5. Operators' Manual, GSI Lumonics, 1999
  6. M.R. Fielden, R. G. Halgren, E. Dere, T.R. Zacharewski, 'GP3: GenePix Post-processing Program for Automated Analysis of Raw Micro-array Data', Bioinformatics, vol.18, no.5, pp.771-773, May, 2002 https://doi.org/10.1093/bioinformatics/18.5.771
  7. D. Bozinov, 'Autonomous System for Web-based Micro-array Image Analysis', IEEE Transactions on Nanobioscience, vol. 2, no.4, pp.215-220, 2003 https://doi.org/10.1109/TNB.2003.817021
  8. Z.Z Zhou, J.A. Stein, Q.Z Ji, 'GLEAMS: A Novel Approach to High Throughput Genetic Micro-array Image Capture and Analysis,' Proceedings of the International Society for Optical Engineering (SPIE), vol.4266, pp.13-23, 2001
  9. C.J. Kim, J.K. Jeong, M. Park, T.S. Park, T.C. Park, S.E. Namkoong, J.S. Park, 'HPV Oligonucleotide Microarray-based Detection of HPV Genotypes in Cervical Neoplastic Lesions,' Gynecologic Oncology, vol.89, pp.210-217, 2003 https://doi.org/10.1016/S0090-8258(02)00069-0
  10. B.S. Choi, O. Kim, M.S. Park, K.S. Kim, J.K. Jeong, J.S. Lee, 'Genital Human Papillomavirus Genotyping by HPV Oligonucleotide Micro-array in Korean Commercial Sex Workers', Journal of Medical Virology, vol.71, pp.440-445, 2003 https://doi.org/10.1002/jmv.10498
  11. J.D. Kim, S.K. Kim, J.S. Cho, J. Kim, 'Knowledgebased Image Processing for On-off Type DNA Micro-array', Proceedings of the International Society for Optical Engineering (SPIE), vol.4623, pp.38-46, 2002
  12. M. Ryu, J.D. Kim, B.G. Min, 'Robust Templatematching Measurements for Variations in Signal Amplitude', Journal of Optical Engineering, vol.43, no.2, pp.482-488, Feb., 2004 https://doi.org/10.1117/1.1634294
  13. M. Ryu, J.D. Kim, B.G. Min, M.G. Pang, J. Kim, 'Non-linear Matching Measure for the Analysis of On-off Type DNA Micro-array Images', Journal of Biomedical Optics, vol.9, no.3, pp.482-438, May, 2004