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VariCarta: a comprehensive database of harmonized genomic variants found in ASD sequencing studies

View ORCID ProfileManuel Belmadani, Matthew Jacobson, Nathan Holmes, Minh Phan, View ORCID ProfilePaul Pavlidis, View ORCID ProfileSanja Rogic
doi: https://doi.org/10.1101/608356
Manuel Belmadani
1Michael Smith Laboratories, UBC, Vancouver, BC
2Department of Psychiatry, UBC, Vancouver, BC
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  • ORCID record for Manuel Belmadani
Matthew Jacobson
1Michael Smith Laboratories, UBC, Vancouver, BC
2Department of Psychiatry, UBC, Vancouver, BC
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Nathan Holmes
1Michael Smith Laboratories, UBC, Vancouver, BC
2Department of Psychiatry, UBC, Vancouver, BC
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Minh Phan
1Michael Smith Laboratories, UBC, Vancouver, BC
2Department of Psychiatry, UBC, Vancouver, BC
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Paul Pavlidis
1Michael Smith Laboratories, UBC, Vancouver, BC
2Department of Psychiatry, UBC, Vancouver, BC
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Sanja Rogic
1Michael Smith Laboratories, UBC, Vancouver, BC
2Department of Psychiatry, UBC, Vancouver, BC
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  • For correspondence: rogic@msl.ubc.ca
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Abstract

Background Recent years has seen a boom in the application of the next-generation sequencing technology to the study of human diseases, including Autism Spectrum Disorder (ASD), where the focus has been on identifying rare, possibly causative genomic variants in ASD individuals. Because of the high genetic heterogeneity of ASD, a large number of subjects is needed to establish evidence for a variant or gene ASD-association, thus aggregating data across cohorts and studies is necessary. However, methodological inconsistencies and subject overlap across studies complicate data aggregation.

Description Here we present VariCarta, a web-based database developed to address these challenges by collecting, reconciling and consistently cataloguing literature-derived genomic variants found in ASD subjects using ongoing semi-manual curation. The careful manual curation combined with a robust data import pipeline rectifies errors, converts variants into a standardized format, identifies and harmonizes cohort overlaps and documents data provenance. The harmonization aspect is especially important since it prevents the potential double-counting of variants which can lead to inflation of gene-based evidence for ASD-association.

Conclusion VariCarta is the largest collection of systematically curated, harmonized and comprehensively annotated literature-derived ASD-associated variants. The database currently contains 35,615 variant events from 8,044 subjects, collected across 50 publications, and reconciles 6,057 variants that have been reported in literature multiple times. VariCarta is freely accessible at http://varicarta.msl.ubc.ca.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 15, 2019.
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VariCarta: a comprehensive database of harmonized genomic variants found in ASD sequencing studies
Manuel Belmadani, Matthew Jacobson, Nathan Holmes, Minh Phan, Paul Pavlidis, Sanja Rogic
bioRxiv 608356; doi: https://doi.org/10.1101/608356
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VariCarta: a comprehensive database of harmonized genomic variants found in ASD sequencing studies
Manuel Belmadani, Matthew Jacobson, Nathan Holmes, Minh Phan, Paul Pavlidis, Sanja Rogic
bioRxiv 608356; doi: https://doi.org/10.1101/608356

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