정보처리학회논문지B (The KIPS Transactions:PartB)

한국정보처리학회 (Korea Information Processing Society)
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템플릿 정합법을 이용한 온-오프 형태 DNA 칩의 탐색자 구분

Probe Classification of an On-Off Type DNA Chip Using Template Matching Method

  • 유문호 (전북대학교 공과대학 생체정보공학부)
  • 발행 : 2006.12.31
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초록

본 연구는 카운팅 정합도라 불리는, 비선형 정합도를 척도로 하는 템플릿 정합법을 이용하여 온-오프 형태 DNA칩의 탐색자를 구분하는 방법을 제안한다. 또한, 스팟 템플릿의 다양한 위치나 크기에 따른 응답의 최대값을 찾는 최대 응답 탐색법을 제안한다. 각 스팟의 교잡반응 여부만을 분류하는 온-오프 형태의 DNA 칩의 탐색자를 구분하는 용도에 제안된 방법을 적용하였다 2390명의 환자에 대한 인유두종 바이러스 DNA 칩 검사에 적용하여, 카운팅 정합도를 기존의 정규상관도나 메디안과 비교하였다. 카운팅 정합도가 최대 응답 탐색법에 관계없이 최고의 성능을 보였다. 실험결과 위치탐색을 결합한 카운팅 정합도가 가장 적절하였다.

This paper proposes a nonlinear template matching measure, called counting measure, as a signal detection measure that is defined as the number of on pixels in the spot area. It is applied to classify probes for an on-off type DNA chip, where each probe spot is classified as hybridized or not. The counting measure also incorporates the maximum response search method, where the expected signal is obtained by taking the maximum among the measured responses of the various positions and sizes of the spot template. The counting measure was compared to existing signal detection measures such as the normalized correlation and the median for 2390 patient samples tested on the human papiliomavirus (HPV) DNA chip. The counting measure performed the best regardless of whether or not the maximum response search method was used. The experimental results showed that the counting measure combined with the positional search was the most preferable.

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