cnvCapSeq: detecting copy number variation in long-range targeted resequencing data.
Nucleic Acids Res
; 42(20): e158, 2014 Nov 10.
Article
em En
| MEDLINE
| ID: mdl-25228465
ABSTRACT
Targeted resequencing technologies have allowed for efficient and cost-effective detection of genomic variants in specific regions of interest. Although capture sequencing has been primarily used for investigating single nucleotide variants and indels, it has the potential to elucidate a broader spectrum of genetic variation, including copy number variants (CNVs). Various methods exist for detecting CNV in whole-genome and exome sequencing datasets. However, no algorithms have been specifically designed for contiguous target sequencing, despite its increasing importance in clinical and research applications. We have developed cnvCapSeq, a novel method for accurate and sensitive CNV discovery and genotyping in long-range targeted resequencing. cnvCapSeq was benchmarked using a simulated contiguous capture sequencing dataset comprising 21 genomic loci of various lengths. cnvCapSeq was shown to outperform the best existing exome CNV method by a wide margin both in terms of sensitivity (92.0 versus 48.3%) and specificity (99.8 versus 70.5%). We also applied cnvCapSeq to a real capture sequencing cohort comprising a contiguous 358 kb region that contains the Complement Factor H gene cluster. In this dataset, cnvCapSeq identified 41 samples with CNV, including two with duplications, with a genotyping accuracy of 99%, as ascertained by quantitative real-time PCR.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
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Análise de Sequência de DNA
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Variações do Número de Cópias de DNA
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Sequenciamento de Nucleotídeos em Larga Escala
Idioma:
En
Ano de publicação:
2014
Tipo de documento:
Article
País de afiliação:
Reino Unido