EXCAVATOR: detecting copy number variants from whole-exome sequencing data

被引：180

作者：

Magi, Alberto ^{[1
]}

Tattini, Lorenzo ^{[1
,2
]}

Cifola, Ingrid ^{[3
]}

D'Aurizio, Romina ^{[4
,5
]}

Benelli, Matteo ^{[6
]}

Mangano, Eleonora ^{[3
]}

Battaglia, Cristina ^{[3
,7
]}

Bonora, Elena ^{[8
]}

Kurg, Ants ^{[9
]}

Seri, Marco ^{[8
]}

Magini, Pamela ^{[8
]}

Giusti, Betti ^{[1
]}

Romeo, Giovanni ^{[8
]}

Pippucci, Tommaso ^{[8
]}

De Bellis, Gianluca ^{[3
]}

Abbate, Rosanna ^{[1
]}

Gensini, Gian Franco ^{[1
]}

机构：

[1] Univ Florence, Dept Clin & Expt Med, Florence, Italy

[2] G Gaslini Inst Children, Mol Genet Lab, Genoa, Italy

[3] CNR, Inst Biomed Technol, Milan, Italy

[4] CNR, Inst Informat & Telemat, LISM, Pisa, Italy

[5] CNR, Inst Clin Physiol, Pisa, Italy

[6] Careggi Hosp, Diagnost Genet Unit, Florence, Italy

[7] Univ Milan, Dipartimento Biotecnol Med & Med Traslaz BIOMETRA, Milan, Italy

[8] Univ Bologna, Dept Med & Surg Sci, Med Genet Unit, Bologna, Italy

[9] Univ Tartu, Inst Mol & Cell Biol, EE-50090 Tartu, Estonia

来源：

GENOME BIOLOGY | 2013年 / 14卷 / 10期

关键词：

STRUCTURAL VARIATION; SHORT-READ; GENOME; DISCOVERY; HETEROZYGOSITY; POLYMORPHISM; ABERRATIONS; ALGORITHMS; FRAMEWORK; DELETIONS;

D O I：

10.1186/gb-2013-14-10-r120

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

We developed a novel software tool, EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states. We validate EXCAVATOR on three datasets and compare the results with three other methods. These analyses show that EXCAVATOR outperforms the other methods and is therefore a valuable tool for the investigation of CNVs in largescale projects, as well as in clinical research and diagnostics. EXCAVATOR is freely available at http://sourceforge.net/projects/excavatortool/.

引用

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