Open Access Research

Multiple samples aCGH analysis for rare CNVs detection

Maciej Sykulski1, Tomasz Gambin24, Magdalena Bartnik3, Katarzyna Derwińska3, Barbara Wiśniowiecka-Kowalnik3, Paweł Stankiewicz34 and Anna Gambin15*

Author Affiliations

1 Institute of Informatics, University of Warsaw, Warsaw, Poland

2 Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland

3 Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland

4 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA

5 Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland

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Journal of Clinical Bioinformatics 2013, 3:12  doi:10.1186/2043-9113-3-12

Published: 11 June 2013

Abstract

Background

DNA copy number variations (CNV) constitute an important source of genetic variability. The standard method used for CNV detection is array comparative genomic hybridization (aCGH).

Results

We propose a novel multiple sample aCGH analysis methodology aiming in rare CNVs detection. In contrast to the majority of previous approaches, which deal with cancer datasets, we focus on constitutional genomic abnormalities identified in a diverse spectrum of diseases in human. Our method is tested on exon targeted aCGH array of 366 patients affected with developmental delay/intellectual disability, epilepsy, or autism. The proposed algorithms can be applied as a post–processing filtering to any given segmentation method.

Conclusions

Thanks to the additional information obtained from multiple samples, we could efficiently detect significant segments corresponding to rare CNVs responsible for pathogenic changes. The robust statistical framework applied in our method enables to eliminate the influence of widespread technical artifact termed ‘waves’.