Automated Processing of 2-D Gel Electrophoretograms of Genomic DNA for Hunting Pathogenic DNA Molecular Changes

Katsutoshi Takahashi[1] (sltaka@jaist.ac.jp)
Masayuki Nakazawa[2] (nakazawa@kanazawa-tc.ac.jp)
Yasuo Watanabe[3] (watanabe@infor.kanazawa-it.ac.jp)
Akihiko Konagaya[1] (kona@jaist.ac.jp)

[1] Japan Advanced Institute of Science and Technology (JAIST) Hokuriku
Asahidai 1-1, Tatsunokuchi, Ishikawa 923-1211, Japan
[2] Kanazawa Technical College
Hisayasu 2-270, Kanazawa, Ishikawa 921-8601, Japan
[3] Kanazawa Institute of Technology
Ohgigaoka 7-1, Nonoichi, Ishikawa 921-8501, Japan


Abstract

We have developed the automated processing algorithms for 2-dimensional (2-D) electrophoretograms of genomic DNA based on RLGS (Restriction Landmark Genomic Scanning) method, which scans the restriction enzyme recognition sites as the landmark and maps them onto a 2-D electrophoresis gel. Our powerful processing algorithms realize the automated spot recognition from RLGS electrophoretograms and the automated comparison of a huge number of such images. In the final stage of the automated processing, a master spot pattern, on which all the spots in the RLGS images are mapped at once, can be obtained. The spot pattern variations which seemed to be specific to the pathogenic DNA molecular changes can be easily detected by simply looking over the master spot pattern. When we applied our algorithms to the analysis of 33 RLGS images derived from human colon tissues, we successfully detected several colon tumor specific spot pattern changes.

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Japanese Society for Bioinformatics