The algorithm of equal acceptance region for detecting copy number alterations: Applications to next-generation sequencing data

The information of copy number alterations (gains and losses) in tumour genomes can be used to discovery cancer-causing genes. The estimate of copy number can be obtained from the estimate copy number ratio. The higher the depth of underlying sequencing data, the more accurate the estimate of copy number ratio. At the same time, the higher depth of a sequencing data used in copy number analysis, the more cost of data analysis. To develop a method for identifying a necessary depth of sequencing data for copy number analysis before test data are produced is of interest. In this paper, we proposed an algorithm of equal acceptance regions for detecting copy number ratios. This algorithm can be used to determine the depth of sequencing data required for copy number analysis. Copyright © 2012 Inderscience Enterprises Ltd.