Consistent testing for recurrent genomic aberrations

DOI10.1093/BIOMET/ASV046zbMATH Open1372.62087arXiv1403.1876OpenAlexW2594180712WikidataQ57435272 ScholiaQ57435272MaRDI QIDQ72647FDOQ72647

Authors: V. Walter, F. A. Wright, A. B. Nobel 

Publication date: 17 November 2015

Published in: Biometrika (Search for Journal in Brave)

Abstract: Genomic aberrations, such as somatic copy number alterations, are frequently observed in tumor tissue. Recurrent aberrations, occurring in the same region across multiple subjects, are of interest because they may highlight genes associated with tumor development or progression. A number of tools have been proposed to assess the statistical significance of recurrent DNA copy number aberrations, but their statistical properties have not been carefully studied. Cyclic shift testing, a permutation procedure using independent random shifts of genomic marker observations on the genome, has been proposed to identify recurrent aberrations, and is potentially useful for a wider variety of purposes, including identifying regions with methylation aberrations or overrepresented in disease association studies. For data following a countable-state Markov model, we prove the asymptotic validity of cyclic shift $p$-values under a fixed sample size regime as the number of observed markers tends to infinity. We illustrate cyclic shift testing for a variety of data types, producing biologically relevant findings for three publicly available datasets.

Full work available at URL: https://arxiv.org/abs/1403.1876

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zbMATH Keywords

consistencyDNA copy numberDNA methylationgenome-wide association studyhypothesis testing

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Markov processes: hypothesis testing (62M02) Genetics and epigenetics (92D10)

Cited In (2)

• DiNAMIC.Duo
• A note on cyclic shift permutation testing for large eigenvalues

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