Details

Autor(en) / Beteiligte

• 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

Titel

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

Ist Teil von

• Genome research, 2019-09, Vol.29 (9), p.1555

Ort / Verlag

United States

Erscheinungsjahr

2019

Link zum Volltext

Quelle

MEDLINE

Beschreibungen/Notizen

• 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.