Accounting for uncertainty when assessing association between copy number and disease

A latent class model

Juan R. González, Isaac Subirana, Geòrgia Escaramís, Solymar Peraza, Alejandro Cáceres, Xavier P. Estivill, Lluís Armengol

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

Background: Copy number variations (CNVs) may play an important role in disease risk by altering dosage of genes and other regulatory elements, which may have functional and, ultimately, phenotypic consequences. Therefore, determining whether a CNV is associated or not with a given disease might be relevant in understanding the genesis and progression of human diseases. Current stage technology give CNV probe signal from which copy number status is inferred. Incorporating uncertainty of CNV calling in the statistical analysis is therefore a highly important aspect. In this paper, we present a framework for assessing association between CNVs and disease in case-control studies where uncertainty is taken into account. We also indicate how to use the model to analyze continuous traits and adjust for confounding covariates. Results: Through simulation studies, we show that our method outperforms other simple methods based on inferring the underlying CNV and assessing association using regular tests that do not propagate call uncertainty. We apply the method to a real data set in a controlled MLPA experiment showing good results. The methodology is also extended to illustrate how to analyze aCGH data. Conclusion: We demonstrate that our method is robust and achieves maximal theoretical power since it accommodates uncertainty when copy number status are inferred. We have made R functions freely available.

Original languageEnglish
Article number172
JournalBMC Bioinformatics
Volume10
DOIs
Publication statusPublished - 6 Jun 2009
Externally publishedYes

Fingerprint

Latent Class Model
Uncertainty
Gene Dosage
Regulator Genes
Disease Progression
Case-Control Studies
Statistical methods
Genes
Technology
Case-control Study
Confounding
Progression
Statistical Analysis
Covariates
Probe
Experiments
Simulation Study
Gene
Methodology

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Structural Biology
  • Applied Mathematics

Cite this

Accounting for uncertainty when assessing association between copy number and disease : A latent class model. / González, Juan R.; Subirana, Isaac; Escaramís, Geòrgia; Peraza, Solymar; Cáceres, Alejandro; Estivill, Xavier P.; Armengol, Lluís.

In: BMC Bioinformatics, Vol. 10, 172, 06.06.2009.

Research output: Contribution to journalArticle

González, Juan R. ; Subirana, Isaac ; Escaramís, Geòrgia ; Peraza, Solymar ; Cáceres, Alejandro ; Estivill, Xavier P. ; Armengol, Lluís. / Accounting for uncertainty when assessing association between copy number and disease : A latent class model. In: BMC Bioinformatics. 2009 ; Vol. 10.
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