Simultaneous discovery of rare and common segment variants

Copy number variant is an important type of genetic structural variation appearing in germline DNA, ranging from common to rare in a population. Both rare and common copy number variants have been reported to be associated with complex diseases, so it is therefore important to simultaneously identify both based on a large set of population samples. We develop a proportion adaptive segment selection procedure that automatically adjusts to the unknown proportions of the carriers of the segment variants. We characterize the detection boundary that separates the region where a segment variant is detectable by some method from the region where it cannot be detected. Although the detection boundaries are very different for the rare and common segment variants, it is shown that the proposed procedure can reliably identify both whenever they are detectable. Compared with methods for single sample analysis, this procedure gains power by pooling information from multiple samples. The method is applied to analyze neuroblastoma samples and identifies a large number of copy number variants that are missed by single-sample methods.