Detecting simultaneous variant intervals in aligned sequences
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Publication:641121
DOI10.1214/10-AOAS400zbMATH Open1223.62166arXiv1108.3177MaRDI QIDQ641121FDOQ641121
Authors: B. Yakir, Nancy R. Zhang, David Siegmund 
Publication date: 21 October 2011
Published in: The Annals of Applied Statistics (Search for Journal in Brave)
Abstract: Given a set of aligned sequences of independent noisy observations, we are concerned with detecting intervals where the mean values of the observations change simultaneously in a subset of the sequences. The intervals of changed means are typically short relative to the length of the sequences, the subset where the change occurs, the "carriers," can be relatively small, and the sizes of the changes can vary from one sequence to another. This problem is motivated by the scientific problem of detecting inherited copy number variants in aligned DNA samples. We suggest a statistic based on the assumption that for any given interval of changed means there is a given fraction of samples that carry the change. We derive an analytic approximation for the false positive error probability of a scan, which is shown by simulations to be reasonably accurate. We show that the new method usually improves on methods that analyze a single sample at a time and on our earlier multi-sample method, which is most efficient when the carriers form a large fraction of the set of sequences. The proposed procedure is also shown to be robust with respect to the assumed fraction of carriers of the changes.
Full work available at URL: https://arxiv.org/abs/1108.3177
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Cites Work
- Circular binary segmentation for the analysis of array-based DNA copy number data
- A Modified Bayes Information Criterion with Applications to the Analysis of Comparative Genomic Hybridization Data
- Detecting simultaneous change points in multiple sequences
- The statistics of gene mapping
- Tail probabilities for the null distribution of scanning statistics
- Tail approximations for maxima of random fields by likelihood ratio transformations
- Error Distribution for Gene Expression Data
- A new representation for a renewal-theoretic constant appearing in asymptotic approximations of large deviations
- Self-organization and the dynamical nature of ventricular fibrillation
Cited In (31)
- BayesProject: fast computation of a projection direction for multivariate changepoint detection
- Sequential tests controlling generalized familywise error rates
- Sequential detection of transient signal by moving likelihood ratio statistic in an exponential family
- Graph-based change-point detection
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- Change-points: from sequential detection to biology and back
- Scan statistics for detecting a local change in variance for normal data with known variance
- On extremal index of max-stable random fields
- Multi-sensor slope change detection
- Higher criticism: \(p\)-values and criticism
- An online copy number variant detection method for short sequencing reads
- Detecting simultaneous change points in multiple sequences
- Scan statistics on Poisson random fields with applications in genomics
- Some clustering-based change-point detection methods applicable to high dimension, low sample size data
- Change-point model on nonhomogeneous Poisson processes with application in copy number profiling by next-generation DNA sequencing
- Collective Anomaly Detection in High-Dimensional Var Models
- A novel change-point approach for the detection of gas emission sources using remotely contained concentration data
- Author's response
- Sequential model selection-based segmentation to detect DNA copy number variation
- Title not available (Why is that?)
- A combined SR-CUSUM procedure for detecting common changes in panel data
- Simultaneous discovery of rare and common segment variants
- Testing randomness online
- A comparative study on sequential detection of random mean change in multivariate normal data stream
- Exact tests for offline changepoint detection in multichannel binary and count data with application to networks
- Online multivariate changepoint detection with type I error control and constant time/memory updates per series
- Discussion on “Change-Points: From Sequential Detection to Biology and Back” by David Siegmund
- Sequential multi-sensor change-point detection
- Detection of subtle variations as consensus motifs
- Optimal detection of multi-sample aligned sparse signals
- Asymptotic distribution-free change-point detection based on interpoint distances for high-dimensional data
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