title: Interactive Exploration, Analysis, and Visualization of Complex Phenome-Genome Datasets with ASPIREdb.
abstract: Identifying variants causal for complex genetic disorders is challenging. With the advent of whole-exome and whole-genome sequencing, computational tools are needed to explore and analyze the list of variants for further validation. Correlating genetic variants with subject phenotype is crucial for the interpretation of the disease-causing mutations. Often such work is done by teams of researchers who need to share information and coordinate activities. To this end, we have developed a powerful, easy to use Web application, ASPIREdb, which allows researchers to search, organize, analyze, and visualize variants and phenotypes associated with a set of human subjects. Investigators can annotate variants using publicly available reference databases and build powerful queries to identify subjects or variants of interest. Functional information and phenotypic associations of these genes are made accessible as well. Burden analysis and additional reporting tools allow investigation of variant properties and phenotype characteristics. Projects can be shared, allowing researchers to work collaboratively to build queries and annotate the data. We demonstrate ASPIREdb's functionality using publicly available data sets, showing how the software can be used to accomplish goals that might otherwise require specialized bioinformatics expertise. ASPIREdb is available at http://aspiredb.chibi.ubc.ca.
authors.affiliation: Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Powell Patrick Cheng
authors.initials: PP
authors.lastname: Tan
authors.affiliation: Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Sanja
authors.initials: S
authors.lastname: Rogic
authors.affiliation: Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Anton
authors.initials: A
authors.lastname: Zoubarev
authors.affiliation: Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Cameron
authors.initials: C
authors.lastname: McDonald
authors.affiliation: Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Frances
authors.initials: F
authors.lastname: Lui
authors.affiliation: Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Gayathiri
authors.initials: G
authors.lastname: Charathsandran
authors.affiliation: Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Matthew
authors.initials: M
authors.lastname: Jacobson
authors.affiliation: Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Manuel
authors.initials: M
authors.lastname: Belmadani
authors.affiliation: Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Justin
authors.initials: J
authors.lastname: Leong
authors.affiliation: Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Thea
authors.initials: T
authors.lastname: Van Rossum
authors.affiliation: Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Elodie
authors.initials: E
authors.lastname: Portales-Casamar
authors.affiliation: Department of Pathology, BC Child and Family Research Institute, University of British Columbia (UBC), Vancouver, British Columbia V5Z 4H4, Canada.|Department of Medical Genetics, BC Child and Family Research Institute, UBC, Vancouver, British Columbia V6H 3N1, Canada.
authors.forename: Ying
authors.initials: Y
authors.lastname: Qiao
authors.affiliation: Department of Medical Genetics, BC Child and Family Research Institute, UBC, Vancouver, British Columbia V6H 3N1, Canada.
authors.forename: Kristina
authors.initials: K
authors.lastname: Calli
authors.affiliation: Department of Psychiatry, Queen's University, Kingston, Ontario, K7L 3N6, Canada.|Ongwanada Resource Centre, Kingston, Ontario, K7L 3N6, Canada.
authors.forename: Xudong
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Psychiatry, Queen's University, Kingston, Ontario, K7L 3N6, Canada.
authors.forename: Melissa
authors.initials: M
authors.lastname: Hudson
authors.affiliation: Department of Pathology, BC Child and Family Research Institute, University of British Columbia (UBC), Vancouver, British Columbia V5Z 4H4, Canada.
authors.forename: Evica
authors.initials: E
authors.lastname: Rajcan-Separovic
authors.affiliation: Department of Medical Genetics, BC Child and Family Research Institute, UBC, Vancouver, British Columbia V6H 3N1, Canada.
authors.forename: Me Suzanne
authors.initials: MS
authors.lastname: Lewis
authors.affiliation: Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Paul
authors.initials: P
authors.lastname: Pavlidis
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D059472:Exome; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D010641:Phenotype; D064878:Web Browser
keywords: WES; WGS; computational biology; genotype-phenotype; visualization; whole-exome sequencing; whole-genome sequencing