Assessing Population Level Genetic Instability via Moving Average

Samuel McDaniel, Jessica Minnier, Rebecca Betensky, Gayatry Mohapatra, Yiping Shen, James F. Gusella, David N. Louis, Tianxi Cai

Research output: Contribution to journalArticle

Abstract

Tumoral tissues tend to generally exhibit aberrations in DNA copy number that are associated with the development and progression of cancer. Genotyping methods such as array-based comparative genomic hybridization (aCGH) provide means to identify copy number variation across the entire genome. To address some of the shortfalls of existing methods of DNA copy number data analysis, including strong model assumptions, lack of accounting for sampling variability of estimators, and the assumption that clones are independent, we propose a simple graphical approach to assess population-level genetic alterations over the entire genome based on moving average. Furthermore, existing methods primarily focus on segmentation and do not examine the association of covariates with genetic instability. In our methods, covariates are incorporated through a possibly mis-specified working model and sampling variabilities of estimators are approximated using a resampling method that is based on perturbing observed processes. Our proposal, which is applicable to partial, entire or multiple chromosomes, is illustrated through application to aCGH studies of two brain tumor types, meningioma and glioma.

Original languageEnglish (US)
Pages (from-to)120-136
Number of pages17
JournalStatistics in Biosciences
Volume2
Issue number2
DOIs
StatePublished - Dec 1 2010

Fingerprint

Moving Average
Population Genetics
Genes
Sampling
Comparative Genomics
DNA
Entire
Chromosomes
Aberrations
Comparative Genomic Hybridization
Covariates
Tumors
Brain
Genome
Tissue
Estimator
Brain Tumor
Resampling Methods
Aberration
Progression

Keywords

  • aCGH data
  • Gaussian process
  • Genomic data
  • Moving average
  • Perturbation method

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Statistics and Probability

Cite this

McDaniel, S., Minnier, J., Betensky, R., Mohapatra, G., Shen, Y., Gusella, J. F., ... Cai, T. (2010). Assessing Population Level Genetic Instability via Moving Average. Statistics in Biosciences, 2(2), 120-136. https://doi.org/10.1007/s12561-010-9028-8

Assessing Population Level Genetic Instability via Moving Average. / McDaniel, Samuel; Minnier, Jessica; Betensky, Rebecca; Mohapatra, Gayatry; Shen, Yiping; Gusella, James F.; Louis, David N.; Cai, Tianxi.

In: Statistics in Biosciences, Vol. 2, No. 2, 01.12.2010, p. 120-136.

Research output: Contribution to journalArticle

McDaniel, S, Minnier, J, Betensky, R, Mohapatra, G, Shen, Y, Gusella, JF, Louis, DN & Cai, T 2010, 'Assessing Population Level Genetic Instability via Moving Average', Statistics in Biosciences, vol. 2, no. 2, pp. 120-136. https://doi.org/10.1007/s12561-010-9028-8
McDaniel, Samuel ; Minnier, Jessica ; Betensky, Rebecca ; Mohapatra, Gayatry ; Shen, Yiping ; Gusella, James F. ; Louis, David N. ; Cai, Tianxi. / Assessing Population Level Genetic Instability via Moving Average. In: Statistics in Biosciences. 2010 ; Vol. 2, No. 2. pp. 120-136.
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