Change-point model on nonhomogeneous Poisson processes with application in copy number profiling by next-generation DNA sequencing
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Publication:439133
DOI10.1214/11-AOAS517zbMATH Open1243.62112arXiv1206.6627MaRDI QIDQ439133FDOQ439133
Authors: Jeremy J. Shen, Nancy R. Zhang 
Publication date: 1 August 2012
Published in: The Annals of Applied Statistics (Search for Journal in Brave)
Abstract: We propose a flexible change-point model for inhomogeneous Poisson Processes, which arise naturally from next-generation DNA sequencing, and derive score and generalized likelihood statistics for shifts in intensity functions. We construct a modified Bayesian information criterion (mBIC) to guide model selection, and point-wise approximate Bayesian confidence intervals for assessing the confidence in the segmentation. The model is applied to DNA Copy Number profiling with sequencing data and evaluated on simulated spike-in and real data sets.
Full work available at URL: https://arxiv.org/abs/1206.6627
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Bayesian inference (62F15) Markov processes: estimation; hidden Markov models (62M05) Applications of statistics to biology and medical sciences; meta analysis (62P10) Parametric tolerance and confidence regions (62F25) Non-Markovian processes: estimation (62M09) Biochemistry, molecular biology (92C40)
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Cited In (15)
- Model selection for high dimensional multi-sequence change-point problems
- A Bayesian approach to inference about a change point model with application to DNA copy number experimental data
- A Bayesian approach for locating change points in a compound Poisson process with application to detecting DNA copy number variations
- Minimax and adaptive tests for detecting abrupt and possibly transitory changes in a Poisson process
- A Composite Likelihood-Based Approach for Change-Point Detection in Spatio-Temporal Processes
- Detecting abrupt changes in the spectra of high-energy astrophysical sources
- Scan statistics on Poisson random fields with applications in genomics
- Multiple changepoint fitting via quasilikelihood, with application to DNA sequence segmentation
- A penalized regression approach for DNA copy number study using the sequencing data
- Nonparametric intensity estimation from noisy observations of a Poisson process under unknown error distribution
- Modeling the next generation sequencing read count data for DNA copy number variant study
- A statistical change-point analysis approach for modeling the ratio of next generation sequencing reads
- Approximations of distributions of scan statistics of inhomogeneous Poisson processes
- A Modified Bayes Information Criterion with Applications to the Analysis of Comparative Genomic Hybridization Data
- Asymptotics for change-point models under varying degrees of mis-specification
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