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Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants

View ORCID ProfileRuibang Luo, View ORCID ProfileTak-Wah Lam, View ORCID ProfileMichael C. Schatz
doi: https://doi.org/10.1101/311985
Ruibang Luo
1Department of Computer Science, The University of Hong Kong, Hong Kong
2Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
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Tak-Wah Lam
1Department of Computer Science, The University of Hong Kong, Hong Kong
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Michael C. Schatz
2Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
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Abstract

Motivation Many rare diseases and cancers are fundamentally diseases of the genome. In the past several years, genome sequencing has become one of the most important tools in clinical practice for rare disease diagnosis and targeted cancer therapy. However, variant interpretation remains the bottleneck as is not yet automated and may take a specialist several hours of work per patient. On average, one-fifth of this time is spent on visually confirming the authenticity of the candidate variants.

Results We developed Skyhawk, an artificial neural network-based discriminator that mimics the process of expert review on clinically significant genomics variants. Skyhawk runs in less than one minute to review ten thousand variants, and among the false positive singletons identified by GATK Haplo-typeCaller, UnifiedGenotyper and 16GT in the HG005 GIAB sample, 79.7% were rejected by Skyhawk.

Availability Skyhawk is easy to use and freely available at https://github.com/aquaskyline/Skyhawk

Contact rbluo{at}cs.hku.hk

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 May 01, 2018.
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Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants
Ruibang Luo, Tak-Wah Lam, Michael C. Schatz
bioRxiv 311985; doi: https://doi.org/10.1101/311985
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Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants
Ruibang Luo, Tak-Wah Lam, Michael C. Schatz
bioRxiv 311985; doi: https://doi.org/10.1101/311985

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