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A robust model for read count data in exome sequencing experiments and implications for copy number variant calling

Plagnol, V; Curtis, J; Epstein, M; Mok, KY; Stebbings, E; Grigoriadou, S; Wood, NW; (2012) A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics , 28 (21) 2747 - 2754. 10.1093/bioinformatics/bts526. Gold open access

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Abstract

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.

Type: Article
Title: A robust model for read count data in exome sequencing experiments and implications for copy number variant calling
Location: England
Open access status: An open access publication
DOI: 10.1093/bioinformatics/bts526
Language: English
Additional information: PMCID: PMC3476336
Keywords: Algorithms, Exome, False Negative Reactions, GATA2 Transcription Factor, Gene Deletion, Gene Dosage, Genetic Variation, Guanine Nucleotide Exchange Factors, Humans, Immunologic Deficiency Syndromes, Markov Chains, Models, Molecular, Models, Statistical, Molecular Sequence Data, Sequence Analysis, Protein
UCL classification: UCL > School of Life and Medical Sciences > Faculty of Brain Sciences > Institute of Neurology > Molecular Neuroscience
UCL > School of Life and Medical Sciences > Faculty of Life Sciences > Biosciences (Division of) > Genetics, Evolution and Environment > UCL Genetics Institute
UCL > School of Life and Medical Sciences > Faculty of Medical Sciences > Infection and Immunity (Division of)
URI: http://discovery.ucl.ac.uk/id/eprint/1361141
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