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A continuous-index hidden Markov jump process for modeling DNA copy number data.

Stjernqvist, Susann LU and Rydén, Tobias LU (2009) In Biostatistics 10. p.773-778
Abstract
The number of copies of DNA in human cells can be measured using array comparative genomic hybridization (aCGH), which provides intensity ratios of sample to reference DNA at genomic locations corresponding to probes on a microarray. In the present paper, we devise a statistical model, based on a latent continuous-index Markov jump process, that is aimed to capture certain features of aCGH data, including probes that are unevenly long, unevenly spaced, and overlapping. The model has a continuous state space, with 1 state representing a normal copy number of 2, and the rest of the states being either amplifications or deletions. We adopt a Bayesian approach and apply Markov chain Monte Carlo (MCMC) methods for estimating the parameters and... (More)
The number of copies of DNA in human cells can be measured using array comparative genomic hybridization (aCGH), which provides intensity ratios of sample to reference DNA at genomic locations corresponding to probes on a microarray. In the present paper, we devise a statistical model, based on a latent continuous-index Markov jump process, that is aimed to capture certain features of aCGH data, including probes that are unevenly long, unevenly spaced, and overlapping. The model has a continuous state space, with 1 state representing a normal copy number of 2, and the rest of the states being either amplifications or deletions. We adopt a Bayesian approach and apply Markov chain Monte Carlo (MCMC) methods for estimating the parameters and the Markov process. The model can be applied to data from both tiling bacterial artificial chromosome arrays and oligonucleotide arrays. We also compare a model with normal distributed noise to a model with t-distributed noise, showing that the latter is more robust to outliers. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Biostatistics
volume
10
pages
773 - 778
publisher
Oxford University Press
external identifiers
  • wos:000269735000014
  • pmid:19628640
  • scopus:74349095473
ISSN
1468-4357
DOI
10.1093/biostatistics/kxp030
language
English
LU publication?
yes
id
454fdf3e-1bca-4837-8249-51d343cb285a (old id 1452847)
date added to LUP
2009-09-01 10:05:08
date last changed
2017-02-05 03:36:03
@article{454fdf3e-1bca-4837-8249-51d343cb285a,
  abstract     = {The number of copies of DNA in human cells can be measured using array comparative genomic hybridization (aCGH), which provides intensity ratios of sample to reference DNA at genomic locations corresponding to probes on a microarray. In the present paper, we devise a statistical model, based on a latent continuous-index Markov jump process, that is aimed to capture certain features of aCGH data, including probes that are unevenly long, unevenly spaced, and overlapping. The model has a continuous state space, with 1 state representing a normal copy number of 2, and the rest of the states being either amplifications or deletions. We adopt a Bayesian approach and apply Markov chain Monte Carlo (MCMC) methods for estimating the parameters and the Markov process. The model can be applied to data from both tiling bacterial artificial chromosome arrays and oligonucleotide arrays. We also compare a model with normal distributed noise to a model with t-distributed noise, showing that the latter is more robust to outliers.},
  author       = {Stjernqvist, Susann and Rydén, Tobias},
  issn         = {1468-4357},
  language     = {eng},
  pages        = {773--778},
  publisher    = {Oxford University Press},
  series       = {Biostatistics},
  title        = {A continuous-index hidden Markov jump process for modeling DNA copy number data.},
  url          = {http://dx.doi.org/10.1093/biostatistics/kxp030},
  volume       = {10},
  year         = {2009},
}