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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 (författare)
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Patel, AN (författare)
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Hedges, DJ (författare)
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visa fler...
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Wang, ZM (författare)
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Rampersaud, E (författare)
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Kesserwan, CA (författare)
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Zhou, X (författare)
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Liu, YL (författare)
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Newman, S (författare)
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Rusch, MC (författare)
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McLeod, CL (författare)
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Wilkinson, MR (författare)
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Rice, SV (författare)
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- Soussi, T (författare)
- Karolinska Institutet
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Taylor, JP (författare)
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Benatar, M (författare)
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Becksfort, JB (författare)
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Nichols, KE (författare)
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Robison, LL (författare)
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Downing, JR (författare)
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Zhang, JH (författare)
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(creator_code:org_t)
- 2019-08-22
- 2019
- Engelska.
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Ingår i: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 29:9, s. 1555-1565
- Relaterad länk:
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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
Ämnesord
Stäng
- 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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- art (ämneskategori)
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Till lärosätets databas
- Av författaren/redakt...
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Edmonson, MN
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Patel, AN
-
Hedges, DJ
-
Wang, ZM
-
Rampersaud, E
-
Kesserwan, CA
-
visa fler...
-
Zhou, X
-
Liu, YL
-
Newman, S
-
Rusch, MC
-
McLeod, CL
-
Wilkinson, MR
-
Rice, SV
-
Soussi, T
-
Taylor, JP
-
Benatar, M
-
Becksfort, JB
-
Nichols, KE
-
Robison, LL
-
Downing, JR
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Zhang, JH
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visa färre...
- Artiklar i publikationen
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Genome research
- Av lärosätet
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Karolinska Institutet