Efficient change-points detection for genomic sequences via cumulative segmented regression

• Published in: Bioinformatics 2022-01, Vol.38 (2), p.311-317
• Main Authors: Jia, Shengji, Shi, Lei
• Format: Article
• Language: English
• Subjects: Algorithms; DNA Copy Number Variations; Genome; Genomics
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btab685

Abstract Motivation Knowing the number and the exact locations of multiple change points in genomic sequences serves several biological needs. The cumulative-segmented algorithm (cumSeg) has been recently proposed as a computationally efficient approach for multiple change-points detection, which is based on a simple transformation of data and provides results quite robust to model mis-specifications. However, the errors are also accumulated in the transformed model so that heteroscedasticity and serial correlation will show up, and thus the variations of the estimated change points will be quite different, while the locations of the change points should be of the same importance in the original genomic sequences. Results In this study, we develop two new change-points detection procedures in the framework of cumulative segmented regression. Simulations reveal that the proposed methods not only improve the efficiency of each change point estimator substantially but also provide the estimators with similar variations for all the change points. By applying these proposed algorithms to Coriel and SNP genotyping data, we illustrate their performance on detecting copy number variations. Availability and implementation The proposed algorithms are implemented in R program and the codes are provided in the online supplementary material. Supplementary information Supplementary data are available at Bioinformatics online.