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,
Chimene A. Kesserwan,
Michael C. Rusch,
Clay L. McLeod,
Mark R. Wilkinson,
Stephen V. Rice,
Jared B. Becksfort,
Kim E. Nichols,
Leslie L. Robison,
James R. Downing,
Posted 06 Jun 2018
bioRxiv DOI: 10.1101/340901 (published DOI: 10.1101/gr.250357.119)
Posted 06 Jun 2018
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.
- Downloaded 447 times
- Download rankings, all-time:
- Site-wide: 67,238
- In bioinformatics: 6,452
- Year to date:
- Site-wide: 129,817
- Since beginning of last month:
- Site-wide: 134,914
Downloads over time
Distribution of downloads per paper, site-wide
- 27 Nov 2020: The website and API now include results pulled from medRxiv as well as bioRxiv.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!