Scan statistics on Poisson random fields with applications in genomics

DOI10.1214/15-AOAS892zbMATH Open1400.62300arXiv1406.3258MaRDI QIDQ312915FDOQ312915

Authors: Nancy R. Zhang, B. Yakir, Li C. Xia, David Siegmund 

Publication date: 9 September 2016

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: The detection of local genomic signals using high-throughput DNA sequencing data can be cast as a problem of scanning a Poisson random field for local changes in the rate of the process. We propose a likelihood-based framework for for such scans, and derive formulas for false positive rate control and power calculations. The framework can also accommodate mixtures of Poisson processes to deal with over-dispersion. As a specific, detailed example, we consider the detection of insertions and deletions by paired-end DNA-sequencing. We propose several statistics for this problem, compare their power under current experimental designs, and illustrate their application on an Illumina Platinum Genomes data set.

Full work available at URL: https://arxiv.org/abs/1406.3258

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zbMATH Keywords

change-point detectionscan statisticsPoisson processesnext-generation sequencingstructural variation

Mathematics Subject Classification ID

Classification and discrimination; cluster analysis (statistical aspects) (62H30) Random fields; image analysis (62M40) Applications of statistics to biology and medical sciences; meta analysis (62P10) Protein sequences, DNA sequences (92D20)

Cites Work

• Sequential analysis. Tests and confidence intervals
• Detecting simultaneous variant intervals in aligned sequences
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• A spatial scan statistic
• Random Fields and Geometry
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• Testing for a signal with unknown location and scale in a stationary Gaussian random field
• The admixture model in linkage analysis
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• Extremes in random fields. A theory and its applications
• Scan statistics on Poisson random fields with applications in genomics
• Title not available (Why is that?)
• Change-point model on nonhomogeneous Poisson processes with application in copy number profiling by next-generation DNA sequencing
• Tail approximations for maxima of random fields by likelihood ratio transformations
• Scan Statistics With Weighted Observations
• Mapping quantitative trait loci in oligogenic models
• Statistical composition of high-scoring segments from molecular sequences

Cited In (8)

• Poisson approximations for conditional r-scan lengths of multiple renewal processes and application to marker arrays in biomolecular sequences
• \(r\)-scan extremal statistics of inhomogeneous Poisson processes
• Detecting mutations in mixed sample sequencing data using empirical Bayes
• Segmentation and estimation of change-point models: false positive control and confidence regions
• Scan statistics on Poisson random fields with applications in genomics
• Scan Statistics With Weighted Observations
• Translocation Detection from Hi-C Data via Scan Statistics
• Multidimensional multiscale scanning in exponential families: limit theory and statistical consequences

Uses Software

• seqCBS
• Delly
• Pindel

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