Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA)

Juan R. González, Josep L. Carrasco, Lluís Armengol, Sergi Villatoro, Lluís Jover, Yutaka Yasui, Xavier P. Estivill

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Background: MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes based on linear mixed-model. This method establishes a threshold by using different tolerance intervals that accommodates the specific random error variability observed in each test sample. Results: Through simulation studies we have shown that our proposed method outperforms two existing methods that are based on simple threshold rules or iterative regression. We have illustrated the method using a controlled MLPA assay in which targeted regions are variable in copy number in individuals suffering from different disorders such as Prader-Willi, DiGeorge or Autism showing the best performace. Conclusion: Using the proposed mixed-model, we are able to determine thresholds to decide whether a region is altered. These threholds are specific for each individual, incorporating experimental variability, resulting in improved sensitivity and specificity as the examples with real data have revealed.

Original languageEnglish
Article number261
JournalBMC Bioinformatics
Volume9
DOIs
Publication statusPublished - 4 Jun 2008
Externally publishedYes

Fingerprint

Multiplex Polymerase Chain Reaction
Mixed Model
Amplification
Probe
Dependent
Random errors
Assays
Nonlinear Mixed Model
Tolerance Interval
Linear Mixed Model
Random Error
Statistical Significance
Nonlinear Dynamics
Autistic Disorder
Normalization
Specificity
Disorder
Regression
Linear Models
Simulation Study

ASJC Scopus subject areas

  • Medicine(all)
  • Structural Biology
  • Applied Mathematics

Cite this

Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA). / González, Juan R.; Carrasco, Josep L.; Armengol, Lluís; Villatoro, Sergi; Jover, Lluís; Yasui, Yutaka; Estivill, Xavier P.

In: BMC Bioinformatics, Vol. 9, 261, 04.06.2008.

Research output: Contribution to journalArticle

González, Juan R. ; Carrasco, Josep L. ; Armengol, Lluís ; Villatoro, Sergi ; Jover, Lluís ; Yasui, Yutaka ; Estivill, Xavier P. / Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA). In: BMC Bioinformatics. 2008 ; Vol. 9.
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