title: Outlier-based identification of copy number variations using targeted resequencing in a small cohort of patients with Tetralogy of Fallot.
abstract: Copy number variations (CNVs) are one of the main sources of variability in the human genome. Many CNVs are associated with various diseases including cardiovascular disease. In addition to hybridization-based methods, next-generation sequencing (NGS) technologies are increasingly used for CNV discovery. However, respective computational methods applicable to NGS data are still limited. We developed a novel CNV calling method based on outlier detection applicable to small cohorts, which is of particular interest for the discovery of individual CNVs within families, de novo CNVs in trios and/or small cohorts of specific phenotypes like rare diseases. Approximately 7,000 rare diseases are currently known, which collectively affect ∼6% of the population. For our method, we applied the Dixon's Q test to detect outliers and used a Hidden Markov Model for their assessment. The method can be used for data obtained by exome and targeted resequencing. We evaluated our outlier-based method in comparison to the CNV calling tool CoNIFER using eight HapMap exome samples and subsequently applied both methods to targeted resequencing data of patients with Tetralogy of Fallot (TOF), the most common cyanotic congenital heart disease. In both the HapMap samples and the TOF cases, our method is superior to CoNIFER, such that it identifies more true positive CNVs. Called CNVs in TOF cases were validated by qPCR and HapMap CNVs were confirmed with available array-CGH data. In the TOF patients, we found four copy number gains affecting three genes, of which two are important regulators of heart development (NOTCH1, ISL1) and one is located in a region associated with cardiac malformations (PRODH at 22q11). In summary, we present a novel CNV calling method based on outlier detection, which will be of particular interest for the analysis of de novo or individual CNVs in trios or cohorts up to 30 individuals, respectively.
authors.affiliation: Department of Cardiovascular Genetics, Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin and Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany ; Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany.
authors.forename: Vikas
authors.initials: V
authors.lastname: Bansal
authors.affiliation: Department of Cardiovascular Genetics, Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin and Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany ; Department of Biology, Chemistry, and Pharmacy, Free University of Berlin, Berlin, Germany.
authors.forename: Cornelia
authors.initials: C
authors.lastname: Dorn
authors.affiliation: Department of Cardiovascular Genetics, Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin and Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany.
authors.forename: Marcel
authors.initials: M
authors.lastname: Grunert
authors.affiliation: For the National Register for Congenital Heart Defects, Berlin, Germany ; Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin and Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany ; Department of Pediatric Cardiology, Charité - Universitätsmedizin Berlin, Berlin, Germany.
authors.forename: Sabine
authors.initials: S
authors.lastname: Klaassen
authors.affiliation: Department of Cardiac Surgery, German Heart Institute Berlin, Berlin, Germany.
authors.forename: Roland
authors.initials: R
authors.lastname: Hetzer
authors.affiliation: Department of Pediatric Cardiology, Charité - Universitätsmedizin Berlin, Berlin, Germany ; Department of Pediatric Cardiology, German Heart Institute Berlin, Berlin, Germany.
authors.forename: Felix
authors.initials: F
authors.lastname: Berger
authors.affiliation: Department of Cardiovascular Genetics, Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin and Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany ; Department of Biology, Chemistry, and Pharmacy, Free University of Berlin, Berlin, Germany.
authors.forename: Silke R
authors.initials: SR
authors.lastname: Sperling
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D056915:DNA Copy Number Variations; D059472:Exome; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008390:Markov Chains; D017422:Sequence Analysis, DNA / Q000379:methods*; D013771:Tetralogy of Fallot / Q000235:genetics*