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

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

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

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.

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

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: BMC bioinformatics

VOLUME: 9

Page Numbers: 261

Journal Abbreviation: BMC Bioinformatics

ISSN: 1471-2105

DAY: 4

MONTH: 06

YEAR: 2008

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

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LANGUAGE: eng

NlmUniqueID: 100965194

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AFFILIATION: Center for research in environmental epidemiology (CREAL), Barcelona, Spain. jrgonzalez@imim.es

Country: England

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MEDLINETA: BMC Bioinformatics

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