title: A Novel Graph-based Algorithm to Infer Recurrent Copy Number Variations in Cancer.
abstract: Many cancers have been linked to copy number variations (CNVs) in the genomic DNA. Although there are existing methods to analyze CNVs from individual samples, cancer-causing genes are more frequently discovered in regions where CNVs are common among tumor samples, also known as recurrent CNVs. Integrating multiple samples and locating recurrent CNV regions remain a challenge, both computationally and conceptually. We propose a new graph-based algorithm for identifying recurrent CNVs using the maximal clique detection technique. The algorithm has an optimal solution, which means all maximal cliques can be identified, and guarantees that the identified CNV regions are the most frequent and that the minimal regions have been delineated among tumor samples. The algorithm has successfully been applied to analyze a large cohort of breast cancer samples and identified some breast cancer-associated genes and pathways.
authors: Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada; Centre for Healthcare Innovation, Winnipeg Regional Health Authority/University of Manitoba, Winnipeg, Canada.
authors: Chen
authors: C
authors: Chi
authors: Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada; Department of Computer Science, University of Manitoba, Winnipeg, Canada.
authors: Rasif
authors: R
authors: Ajwad
authors: Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada.
authors: Qin
authors: Q
authors: Kuang
authors: Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada; Centre for Healthcare Innovation, Winnipeg Regional Health Authority/University of Manitoba, Winnipeg, Canada; Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada.
authors: Pingzhao
authors: P
authors: Hu
keywords: cancer; interval graph; maximal clique; recurrent copy number variation