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Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): A Cloud-based Platform for Curating and Classifying Germline Variants

View ORCID ProfileMichael N. Edmonson, Aman N. Patel, Dale J. Hedges, Zhaoming Wang, Evadnie Rampersaud, Chimene A. Kesserwan, Xin Zhou, Yanling Liu, Scott Newman, Michael C. Rusch, Clay L. McLeod, Mark R. Wilkinson, Stephen V. Rice, Jared B. Becksfort, Kim E. Nichols, Leslie L. Robison, James R. Downing, Jinghui Zhang
doi: https://doi.org/10.1101/340901
Michael N. Edmonson
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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  • ORCID record for Michael N. Edmonson
Aman N. Patel
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Dale J. Hedges
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Zhaoming Wang
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Evadnie Rampersaud
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Chimene A. Kesserwan
2Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Xin Zhou
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Yanling Liu
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Scott Newman
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Michael C. Rusch
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Clay L. McLeod
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Mark R. Wilkinson
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Stephen V. Rice
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Jared B. Becksfort
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Kim E. Nichols
2Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Leslie L. Robison
3Department of Epidemiology & Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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James R. Downing
4Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Jinghui Zhang
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Abstract

Variant interpretation in the era of next-generation sequencing (NGS) is challenging. While many resources and guidelines are available to assist with this task, few integrated end-to-end tools exist. Here we present “PeCanPIE” – the Pediatric Cancer Variant Pathogenicity Information Exchange, a web- and cloud-based platform for annotation, identification, and classification of variations in known or putative disease genes. Starting from a set of variants in Variant Call Format (VCF), variants are annotated, ranked by putative pathogenicity, and presented for formal classification using a decision-support interface based on published guidelines from the American College of Medical Genetics and Genomics (ACMG). The system can accept files containing millions of variants and handle single-nucleotide variants (SNVs), simple insertions/deletions (indels), multiple-nucleotide variants (MNVs), and complex substitutions. PeCanPIE has been applied to classify variant pathogenicity in cancer predisposition genes in two large-scale investigations involving >4,000 pediatric cancer patients, and serves as a repository for the expert-reviewed results. While PeCanPIE’s web-based interface was designed to be accessible to non-bioinformaticians, its back end pipelines may also be run independently on the cloud, facilitating direct integration and broader adoption. PeCanPIE is publicly available and free for research use.

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 June 06, 2018.
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Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): A Cloud-based Platform for Curating and Classifying Germline Variants
Michael N. Edmonson, Aman N. Patel, Dale J. Hedges, Zhaoming Wang, Evadnie Rampersaud, Chimene A. Kesserwan, Xin Zhou, Yanling Liu, Scott Newman, Michael C. Rusch, Clay L. McLeod, Mark R. Wilkinson, Stephen V. Rice, Jared B. Becksfort, Kim E. Nichols, Leslie L. Robison, James R. Downing, Jinghui Zhang
bioRxiv 340901; doi: https://doi.org/10.1101/340901
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Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): A Cloud-based Platform for Curating and Classifying Germline Variants
Michael N. Edmonson, Aman N. Patel, Dale J. Hedges, Zhaoming Wang, Evadnie Rampersaud, Chimene A. Kesserwan, Xin Zhou, Yanling Liu, Scott Newman, Michael C. Rusch, Clay L. McLeod, Mark R. Wilkinson, Stephen V. Rice, Jared B. Becksfort, Kim E. Nichols, Leslie L. Robison, James R. Downing, Jinghui Zhang
bioRxiv 340901; doi: https://doi.org/10.1101/340901

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