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Pediatric Cancer Va...
Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants
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Edmonson, MN (author)
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Patel, AN (author)
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Hedges, DJ (author)
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Wang, ZM (author)
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Rampersaud, E (author)
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Kesserwan, CA (author)
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Zhou, X (author)
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Liu, YL (author)
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Newman, S (author)
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Rusch, MC (author)
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McLeod, CL (author)
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Wilkinson, MR (author)
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Rice, SV (author)
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- Soussi, T (author)
- Karolinska Institutet
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Taylor, JP (author)
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Benatar, M (author)
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Becksfort, JB (author)
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Nichols, KE (author)
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Robison, LL (author)
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Downing, JR (author)
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Zhang, JH (author)
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(creator_code:org_t)
- 2019-08-22
- 2019
- English.
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In: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 29:9, s. 1555-1565
- Related links:
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http://genome.cshlp....
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http://kipublication...
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https://doi.org/10.1...
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Abstract
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- 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.
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- ref (subject category)
- art (subject category)
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To the university's database
- By the author/editor
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Edmonson, MN
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Patel, AN
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Hedges, DJ
-
Wang, ZM
-
Rampersaud, E
-
Kesserwan, CA
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show more...
-
Zhou, X
-
Liu, YL
-
Newman, S
-
Rusch, MC
-
McLeod, CL
-
Wilkinson, MR
-
Rice, SV
-
Soussi, T
-
Taylor, JP
-
Benatar, M
-
Becksfort, JB
-
Nichols, KE
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Robison, LL
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Downing, JR
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Zhang, JH
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show less...
- Articles in the publication
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Genome research
- By the university
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Karolinska Institutet