A novel approach to detect copy number variation using segmentation and genetic algorithm

ABSTRACT

Among many forms of genomic variations, copy-number variations (CNVs) can be defined as gains or losses of several kilobases to hundreds of kilobases of genomic DNA. Since many CNVs include genes that result in differential levels of gene expression, CNVs may account for a significant proportion of normal phenotypic variation. Some scientists demonstrated that a large portion of overlapping, currently known common human CNVs, were smaller in his dataset. However, previous experimental studies, performed primarily by a-CGH techniques, are limited to detection of CNVs of large-sized CNVs. Efficient algorithms for finding small-sized CNVs are essential. In our paper, we propose a novel approach to find small-sized CNVs on a-CGH data which is a sequential 2-dimensional clustering method. The algorithm we propose is robust to some level of noise. And regardless of the size of probes, our algorithm can find CNVs consisting of small number of probes.

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INDEX TERMS

Primary Classification:
  H. Information Systems
  H.2 DATABASE MANAGEMENT
      H.2.8 Database applications
          Subjects: Data mining

Additional Classification:
  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES
      Subjects: Biology and genetics

Keywords:
WGTP, a-CGH, copy number variation, genetic algorithm, parameter estimation, segmentation