Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease

被引：27

作者：

Sifrim, Alejandro ^{[1
,2
]}

Van Houdt, Jeroen K. J. ^{[3
]}

Tranchevent, Leon-Charles ^{[1
,2
]}

Nowakowska, Beata ^{[3
]}

Sakai, Ryo ^{[1
,2
]}

Pavlopoulos, Georgios A. ^{[1
,2
]}

Devriendt, Koen ^{[3
]}

Vermeesch, Joris R. ^{[3
]}

Moreau, Yves ^{[1
,2
]}

Aerts, Jan ^{[1
,2
]}

机构：

[1] Katholieke Univ Leuven, Dept Elect Engn ESAT, SCD SISTA, B-3001 Louvain, Belgium

[2] IBBT Future Hlth Dept, B-3001 Louvain, Belgium

[3] Katholieke Univ Leuven, Ctr Human Genet, Univ Hosp Gasthuisberg, B-3000 Louvain, Belgium

来源：

GENOME MEDICINE | 2012年 / 4卷

关键词：

NICOLAIDES-BARAITSER SYNDROME; COFFIN-SIRIS SYNDROME; SEQUENCING DATA; FUNCTIONAL ANNOTATION; MENTAL-RETARDATION; MISSENSE MUTATIONS; GENOMIC VARIANTS; HUMAN EXOMES; LARGE-SCALE; DATABASE;

D O I：

10.1186/gm374

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

The increasing size and complexity of exome/genome sequencing data requires new tools for clinical geneticists to discover disease-causing variants. Bottlenecks in identifying the causative variation include poor cross-sample querying, constantly changing functional annotation and not considering existing knowledge concerning the phenotype. We describe a methodology that facilitates exploration of patient sequencing data towards identification of causal variants under different genetic hypotheses. Annotate-it facilitates handling, analysis and interpretation of high-throughput single nucleotide variant data. We demonstrate our strategy using three case studies. Annotate-it is freely available and test data are accessible to all users at http://www.annotate-it.org.

引用

页数：12

共 56 条

[31] The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data [J].

McKenna, Aaron ;

Hanna, Matthew ;

Banks, Eric ;

Sivachenko, Andrey ;

Cibulskis, Kristian ;

Kernytsky, Andrew ;

Garimella, Kiran ;

Altshuler, David ;

Gabriel, Stacey ;

Daly, Mark ;

DePristo, Mark A. .

GENOME RESEARCH, 2010, 20 (09) :1297-1303

[32] Computational tools for prioritizing candidate genes: boosting disease gene discovery [J].

Moreau, Yves ;

Tranchevent, Leon-Charles .

NATURE REVIEWS GENETICS, 2012, 13 (08) :523-536

[33] SIFT: predicting amino acid changes that affect protein function [J].

Ng, PC ;

Henikoff, S .

NUCLEIC ACIDS RESEARCH, 2003, 31 (13) :3812-3814

[34] Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome [J].

Ng, Sarah B. ;

Bigham, Abigail W. ;

Buckingham, Kati J. ;

Hannibal, Mark C. ;

McMillin, Margaret J. ;

Gildersleeve, Heidi I. ;

Beck, Anita E. ;

Tabor, Holly K. ;

Cooper, Gregory M. ;

Mefford, Heather C. ;

Lee, Choli ;

Turner, Emily H. ;

Smith, Joshua D. ;

Rieder, Mark J. ;

Yoshiura, Koh-ichiro ;

Matsumoto, Naomichi ;

Ohta, Tohru ;

Niikawa, Norio ;

Nickerson, Deborah A. ;

Bamshad, Michael J. ;

Shendure, Jay .

NATURE GENETICS, 2010, 42 (09) :790-U85

[35] Exome sequencing identifies the cause of a mendelian disorder [J].

Ng, Sarah B. ;

Buckingham, Kati J. ;

Lee, Choli ;

Bigham, Abigail W. ;

Tabor, Holly K. ;

Dent, Karin M. ;

Huff, Chad D. ;

Shannon, Paul T. ;

Jabs, Ethylin Wang ;

Nickerson, Deborah A. ;

Shendure, Jay ;

Bamshad, Michael J. .

NATURE GENETICS, 2010, 42 (01) :30-U41

[36] Targeted capture and massively parallel sequencing of 12 human exomes [J].

Ng, Sarah B. ;

Turner, Emily H. ;

Robertson, Peggy D. ;

Flygare, Steven D. ;

Bigham, Abigail W. ;

Lee, Choli ;

Shaffer, Tristan ;

Wong, Michelle ;

Bhattacharjee, Arindam ;

Eichler, Evan E. ;

Bamshad, Michael ;

Nickerson, Deborah A. ;

Shendure, Jay .

NATURE, 2009, 461 (7261) :272-U153

[37] Mutations in the Sarcomere Gene MYH7 in Ebstein Anomaly [J].

Postma, Alex V. ;

van Engelen, Klaartje ;

van de Meerakker, Judith ;

Rahman, Thahira ;

Probst, Susanne ;

Baars, Marieke J. H. ;

Bauer, Ulrike ;

Pickardt, Thomas ;

Sperling, Silke R. ;

Berger, Felix ;

Moorman, Antoon F. M. ;

Mulder, Barbara J. M. ;

Thierfelder, Ludwig ;

Keavney, Bernard ;

Goodship, Judith ;

Klaassen, Sabine .

CIRCULATION-CARDIOVASCULAR GENETICS, 2011, 4 (01) :43-50

[38] The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease [J].

Robinson, Peter N. ;

Koehler, Sebastian ;

Bauer, Sebastian ;

Seelow, Dominik ;

Horn, Denise ;

Mundlos, Stefan .

AMERICAN JOURNAL OF HUMAN GENETICS, 2008, 83 (05) :610-615

[39] CORUM: the comprehensive resource of mammalian protein complexes-2009 [J].

Ruepp, Andreas ;

Waegele, Brigitte ;

Lechner, Martin ;

Brauner, Barbara ;

Dunger-Kaltenbach, Irmtraud ;

Fobo, Gisela ;

Frishman, Goar ;

Montrone, Corinna ;

Mewes, H. -Werner .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D497-D501

[40] Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome [J].

Santen, Gijs W. E. ;

Aten, Emmelien ;

Sun, Yu ;

Almomani, Rowida ;

Gilissen, Christian ;

Nielsen, Maartje ;

Kant, Sarina G. ;

Snoeck, Irina N. ;

Peeters, Els A. J. ;

Hilhorst-Hofstee, Yvonne ;

Wessels, Marja W. ;

den Hollander, Nicolette S. ;

Ruivenkamp, Claudia A. L. ;

van Ommen, Gert-Jan B. ;

Breuning, Martijn H. ;

den Dunnen, Johan T. ;

van Haeringen, Arie ;

Kriek, Marjolein .

NATURE GENETICS, 2012, 44 (04) :379-380

← 1 2 3 4 5 6 →