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

被引：178

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

页数：18

共 50 条

[1] EXCAVATOR: detecting copy number variants from whole-exome sequencing data
Alberto Magi
Lorenzo Tattini
Ingrid Cifola
Romina D’Aurizio
Matteo Benelli
Eleonora Mangano
Cristina Battaglia
Elena Bonora
Ants Kurg
Marco Seri
Pamela Magini
Betti Giusti
Giovanni Romeo
Tommaso Pippucci
Gianluca De Bellis
Rosanna Abbate
Gian Franco Gensini
Genome Biology, 14
[2] Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2
D'Aurizio, Romina
Pippucci, Tommaso
Tattini, Lorenzo
Giusti, Betti
Pellegrini, Marco
Magi, Alberto
NUCLEIC ACIDS RESEARCH, 2016, 44 (20)
[3] Platform comparison of detecting copy number variants with microarrays and whole-exome sequencing
de Ligt, Joep
Boone, Philip M.
Pfundt, Rolph
Vissers, Lisenka E. L. M.
de Leeuw, Nicole
Shaw, Christine
Brunner, Han G.
Lupski, James R.
Veltman, Joris A.
Hehir-Kwa, Jayne Y.
GENOMICS DATA, 2014, 2 : 144 - 146
[4] CANOES: detecting rare copy number variants from whole exome sequencing data
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Homsy, Jason
Murillo, Laura R.
Glessner, Joe
Lin, Edwin
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[5] Application of whole-exome sequencing for detecting copy number variants in CMT1A/HNPP
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Park, M. -H.
Woo, H. -M.
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CLINICAL GENETICS, 2016, 90 (02) : 177 - 181
[6] Detection of Clinically Relevant Copy Number Variants with Whole-Exome Sequencing
de Ligt, Joep
Boone, Philip M.
Pfundt, Rolph
Vissers, Lisenka E. L. M.
Richmond, Todd
Geoghegan, Joel
O'Moore, Kathleen
de Leeuw, Nicole
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HUMAN MUTATION, 2013, 34 (10) : 1439 - 1448
[7] Copy number estimation from whole-exome sequencing in tumors
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O'Hara, Andrea
Lin, Dong
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CANCER RESEARCH, 2018, 78 (13)
[8] An Evaluation of Copy Number Variation Detection Tools from Whole-Exome Sequencing Data
Tan, Renjie
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HUMAN MUTATION, 2014, 35 (07) : 899 - 907
[9] ExomeHMM: A Hidden Markov Model for Detecting Copy Number Variation Using Whole-Exome Sequencing Data
Guo, Cheng
Yu, Zhenhua
Wang, Minghui
Li, Ao
CURRENT BIOINFORMATICS, 2017, 12 (02) : 147 - 155
[10] CloneCNA: detecting subclonal somatic copy number alterations in heterogeneous tumor samples from whole-exome sequencing data
Yu, Zhenhua
Li, Ao
Wang, Minghui
BMC BIOINFORMATICS, 2016, 17

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