TY  - JOUR
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
Y1  - 2019/09/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1555 
EP  - 1565 
DO  - 10.1101/gr.250357.119 
VL  - 29 
IS  - 9 
UR  - http://genome.cshlp.org/content/29/9/1555.abstract 
N2  - 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. 
ER  -