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

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

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

机译：儿科癌症变异致病性信息交换（Pecanpie）：一种基于云的策划平台，用于治疗种系变体

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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.

机译：大规模平行测序时代的变体解释是具有挑战性的。虽然有许多资源和准则可以协助完成此任务，但存在很少有集成的端到端工具。在这里，我们提出了儿科癌症变异致病性信息交换（PECANPIE），基于网和云的平台用于注释，鉴定和分类已知或推定疾病基因的变异。从一组变体呼叫格式（VCF）的变种开始，通过推定的致病性排列，并根据基于美国医学遗传学和基因组学学院（ACMG）的已发布的指南，使用决策支持界面进行正式分类。。该系统可以接受包含数百万变种的文件并处理单核苷酸变体（SNV），简单的插入/缺失（吲哚），多核苷酸变体（MNV）和复杂的取代。 Pecanpie已被应用于对涉及> 4000名儿科癌症患者的两次大规模调查中的癌症倾向基因的变体致病性，并用作专家审查结果的储存库。 Pecanpie最初是为儿科癌症开发的，但可以很容易地扩展用于非学历癌症和非癌症遗传疾病。虽然Pecanpie的基于Web的界面被设计为无生物信息管理员可以访问，但其后端管道也可以在云上独立运行，促进直接集成和更广泛的采用。 Pecanpie公开可用，免费用于研究使用。

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《Genome research》 |2019年第9期|共11页
作者
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;
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作者单位

St Jude Childrens Res Hosp Dept Computat Biol 332 N Lauderdale St Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Computat Biol 332 N Lauderdale St Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Computat Biol 332 N Lauderdale St Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Computat Biol 332 N Lauderdale St Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Computat Biol 332 N Lauderdale St Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Oncol 332 N Lauderdale St Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Computat Biol 332 N Lauderdale St Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Computat Biol 332 N Lauderdale St Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Computat Biol 332 N Lauderdale St Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Computat Biol 332 N Lauderdale St Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Computat Biol 332 N Lauderdale St Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Computat Biol 332 N Lauderdale St Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Computat Biol 332 N Lauderdale St Memphis TN 38105 USA;

UPMC Univ Paris 06 Sorbonne Univ F-75005 Paris France;

Howard Hughes Med Inst Chevy Chase MD 20815 USA;

Univ Miami Dept Neurol Miami FL 33136 USA;

St Jude Childrens Res Hosp Dept Computat Biol 332 N Lauderdale St Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Oncol 332 N Lauderdale St Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Epidemiol &

Canc Control 332 N Lauderdale Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Pathol 332 N Lauderdale Memphis TN 38105 USA;

St Jude Childrens Res Hosp Dept Computat Biol 332 N Lauderdale St Memphis TN 38105 USA;

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正文语种 eng
中图分类医学遗传学;
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专利

1. Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants [J] . Edmonson Michael N., Patel Aman N., Hedges Dale J., Genome research . 2019,第9期

机译：儿科癌症变异致病性信息交换（Pecanpie）：一种基于云的策划平台，用于治疗种系变体
2. Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline CDH1 CDH1 sequence variants [J] . Lee Kristy, Krempely Kate, Roberts Maegan E., Human mutation . 2018,第11期

机译：用于分析种系CDH1 CDH1序列变体的ACMG / AMP变体策策指南
3. Toward automation of germline variant curation in clinical cancer genetics (vol 21, 2019) [J] . Ravichandran Vignesh, Shameer Zarina, Kemel Yelena, Genetics in medicine . 2019,第7期

机译：朝着临床癌症遗传学中的种系变体策序的自动化（第21,219,219,219）
4. REPURPOSING GERMLINE EXOMES OF THE CANCER GENOME ATLAS DEMANDS A CAUTIOUS APPROACH AND SAMPLE-SPECIFIC VARIANT FILTERING [C] . AMANDA KOIRE, PANAGIOTIS KATSONIS, OLIVIER LICHTARGE Pacific Symposium on Biocomputing . 2016

机译：修复癌症基因组Atlas的种系展示要求谨慎的方法和特定于样的变体过滤
5. Medical Decision Making among Individuals with a Variant of Uncertain Significance in a Hereditary Cancer Gene and those with a CHEK2 Pathogenic Variant [D] . Almanza, Deanna J. 2019

机译：在遗传癌基因中具有不确定意义的个体的医学决策，以及Chek2致病变异的人
6. Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants [O] . Michael N. Edmonson, Aman N. Patel, Dale J. Hedges, 2019

机译：小儿癌症变异病原性信息交换（PeCanPIE）：用于对种系变异进行分类和分类的基于云的平台
7. How I curate: applying American Society of Hematology-Clinical Genome Resource Myeloid Malignancy Variant Curation Expert Panel rules for RUNX1 variant curation for germline predisposition to myeloid malignancies [O] . David Wu, Xi Luo, Simone Feurstein, 2020

机译：我如何策划：应用美国血液学学会 - 临床基因组资源霉菌恶性变异策策专家组规则，用于种系易核对霉菌性病

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

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