Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants

Variant interpretation in the era of massively parallel sequencing is challenging. Although many resources and guidelines are available to assist with this task, few integrated end-to-end tools exist. Here, we present the diatric cer Variant athogenicity nformation xchange (PeCanPIE), a web- and clo...

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Veröffentlicht in:	Genome research Jg. 29; H. 9; S. 1555
Hauptverfasser:	Edmonson, Michael N, Patel, Aman N, Hedges, Dale J, Wang, Zhaoming, Rampersaud, Evadnie, Kesserwan, Chimene A, Zhou, Xin, Liu, Yanling, Newman, Scott, Rusch, Michael C, McLeod, Clay L, Wilkinson, Mark R, Rice, Stephen V, Soussi, Thierry, Taylor, J Paul, Benatar, Michael, Becksfort, Jared B, Nichols, Kim E, Robison, Leslie L, Downing, James R, Zhang, Jinghui
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	United States 01.09.2019
Schlagworte:	Child Cloud Computing Computational Biology - methods Databases, Genetic Genetic Predisposition to Disease Germ-Line Mutation High-Throughput Nucleotide Sequencing Humans Neoplasms - genetics User-Computer Interface
ISSN:	1549-5469, 1549-5469
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Zusammenfassung:	Variant interpretation in the era of massively parallel sequencing is challenging. Although many resources and guidelines are available to assist with this task, few integrated end-to-end tools exist. Here, we present the diatric cer Variant athogenicity nformation xchange (PeCanPIE), 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 >4000 pediatric cancer patients and serves as a repository for the expert-reviewed results. PeCanPIE was originally developed for pediatric cancer but can be easily extended for use for nonpediatric cancers and noncancer genetic diseases. Although 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.
Bibliographie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1549-5469 1549-5469
DOI:	10.1101/gr.250357.119