title: Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease.
abstract: 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.
authors.affiliation: KU Leuven, Department of Electrical Engineering-ESAT, SCD-SISTA, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium ; IBBT Future Health Department, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Sifrim
authors.affiliation: KU Leuven, Centre for Human Genetics, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium.
authors.forename: Jeroen Kj
authors.initials: JK
authors.lastname: Van Houdt
authors.affiliation: KU Leuven, Department of Electrical Engineering-ESAT, SCD-SISTA, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium ; IBBT Future Health Department, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium.
authors.forename: Leon-Charles
authors.initials: LC
authors.lastname: Tranchevent
authors.affiliation: KU Leuven, Centre for Human Genetics, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium.
authors.forename: Beata
authors.initials: B
authors.lastname: Nowakowska
authors.affiliation: KU Leuven, Department of Electrical Engineering-ESAT, SCD-SISTA, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium ; IBBT Future Health Department, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium.
authors.forename: Ryo
authors.initials: R
authors.lastname: Sakai
authors.affiliation: KU Leuven, Department of Electrical Engineering-ESAT, SCD-SISTA, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium ; IBBT Future Health Department, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium.
authors.forename: Georgios A
authors.initials: GA
authors.lastname: Pavlopoulos
authors.affiliation: KU Leuven, Centre for Human Genetics, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium.
authors.forename: Koen
authors.initials: K
authors.lastname: Devriendt
authors.affiliation: KU Leuven, Centre for Human Genetics, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium.
authors.forename: Joris R
authors.initials: JR
authors.lastname: Vermeesch
authors.affiliation: KU Leuven, Department of Electrical Engineering-ESAT, SCD-SISTA, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium ; IBBT Future Health Department, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium.
authors.forename: Yves
authors.initials: Y
authors.lastname: Moreau
authors.affiliation: KU Leuven, Department of Electrical Engineering-ESAT, SCD-SISTA, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium ; IBBT Future Health Department, Kasteelpark Arenberg 10, B-3001, Leuven, Belgium.
authors.forename: Jan
authors.initials: J
authors.lastname: Aerts