title: A robust model for read count data in exome sequencing experiments and implications for copy number variant calling.
abstract: BACKGROUND
  Exome sequencing has proven to be an effective tool to discover the genetic basis of Mendelian disorders. It is well established that copy number variants (CNVs) contribute to the etiology of these disorders. However, calling CNVs from exome sequence data is challenging. A typical read depth strategy consists of using another sample (or a combination of samples) as a reference to control for the variability at the capture and sequencing steps. However, technical variability between samples complicates the analysis and can create spurious CNV calls.
  
  
  RESULTS
  Here, we introduce ExomeDepth, a new CNV calling algorithm designed to control for this technical variability. ExomeDepth uses a robust model for the read count data and uses this model to build an optimized reference set in order to maximize the power to detect CNVs. As a result, ExomeDepth is effective across a wider range of exome datasets than the previously existing tools, even for small (e.g. one to two exons) and heterozygous deletions. We used this new approach to analyse exome data from 24 patients with primary immunodeficiencies. Depending on data quality and the exact target region, we find between 170 and 250 exonic CNV calls per sample. Our analysis identified two novel causative deletions in the genes GATA2 and DOCK8.
  
  
  BACKGROUND
  The code used in this analysis has been implemented into an R package called ExomeDepth and is available at the Comprehensive R Archive Network (CRAN).
authors.affiliation: UCL Genetics Institute, UCL, London, UK. v.plagnol@ucl.ac.uk
authors.forename: Vincent
authors.initials: V
authors.lastname: Plagnol
authors.forename: James
authors.initials: J
authors.lastname: Curtis
authors.forename: Michael
authors.initials: M
authors.lastname: Epstein
authors.forename: Kin Y
authors.initials: KY
authors.lastname: Mok
authors.forename: Emma
authors.initials: E
authors.lastname: Stebbings
authors.forename: Sofia
authors.initials: S
authors.lastname: Grigoriadou
authors.forename: Nicholas W
authors.initials: NW
authors.lastname: Wood
authors.forename: Sophie
authors.initials: S
authors.lastname: Hambleton
authors.forename: Siobhan O
authors.initials: SO
authors.lastname: Burns
authors.forename: Adrian J
authors.initials: AJ
authors.lastname: Thrasher
authors.forename: Dinakantha
authors.initials: D
authors.lastname: Kumararatne
authors.forename: Rainer
authors.initials: R
authors.lastname: Doffinger
authors.forename: Sergey
authors.initials: S
authors.lastname: Nejentsev
mesh_terms: D000465:Algorithms; D059472:Exome / Q000235:genetics*; D005188:False Negative Reactions; D050989:GATA2 Transcription Factor / Q000235:genetics*; D017353:Gene Deletion; D018628:Gene Dosage / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics; D020662:Guanine Nucleotide Exchange Factors / Q000235:genetics*; D006801:Humans; D007153:Immunologic Deficiency Syndromes / Q000235:genetics*; D008390:Markov Chains; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D020539:Sequence Analysis, Protein / Q000379:methods
chemical_list: C516591:DOCK8 protein, human; D050989:GATA2 Transcription Factor; C494711:GATA2 protein, human; D020662:Guanine Nucleotide Exchange Factors