RT Journal
A1 Edmonson, Michael N.
A1 Patel, Aman N.
A1 Hedges, Dale J.
A1 Wang, Zhaoming
A1 Rampersaud, Evadnie
A1 Kesserwan, Chimene A.
A1 Zhou, Xin
A1 Liu, Yanling
A1 Newman, Scott
A1 Rusch, Michael C.
A1 McLeod, Clay L.
A1 Wilkinson, Mark R.
A1 Rice, Stephen V.
A1 Soussi, Thierry
A1 Taylor, J. Paul
A1 Benatar, Michael
A1 Becksfort, Jared B.
A1 Nichols, Kim E.
A1 Robison, Leslie L.
A1 Downing, James R.
A1 Zhang, Jinghui
T1 Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants
JF Genome Research 
JO Genome Research 
YR 2019 
FD September 01 
VO 29 
IS 9 
SP 1555 
OP 1565 
DO 10.1101/gr.250357.119 
UL http://genome.cshlp.org/content/29/9/1555.abstract 
AB 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 Pediatric Cancer Variant Pathogenicity Information Exchange (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.