Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data

By W. Lai, Mark D. Johnson, R. Kucherlapati, P. Park. Bioinform., 2005

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High-resolution mapping of copy-number alterations with massively parallel sequencing (2008, methodology): “A simple approach would be to partition the genome into windows of fixed size, estimate the tumor-normal ratios for each window and use standard segmentation algorithms to decompose the genome into regions of equivalent copy numbe”
A robust approach for estimating change-points in the mean of an AR(1) process (2014, methodology): “Simulation design To assess the performance of the proposed method, we used a simulation design inspired from the one conceived by [19].”
ChIP-Seq: advantages and challenges of a maturing technology (2009, methodology): “However, many peak detection techniques used in ChIP–chip and DNA copy number analysi”
A review of change point detection methods (2018, methodology): “Practically, this method is used to detect changes in the mean of array-based DNA copy number data [86, 106, 132] (with the quadratic error cost function 9).”
changepoint: An R Package for Changepoint Analysis (2014, methodology): “Case study: Glioblastoma Lai et al. (2005) compare different methods for segmenting array comparative genomic hybridization (aCGH) data from Glioblastoma multiforme (GBM), a type of brain tumor. These arrays were developed to identify DNA copy number alteration corresponding to chromosomal aberratio”