Exploring genomic alteration in pediatric cancer using ProteinPaint

The pediatric data set consists of 27,188 validated somatic coding lesions acquired at diagnosis or relapse from 17 subtypes of pediatric cancer, 252 pathogenic or loss-of-function germline lesions detected in >1,000 pediatric patients with cancer of 21 subtypes6 and RNA sequencing (RNA-seq) data...

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Published in:	Nature genetics Vol. 48; no. 1; pp. 4 - 6
Main Authors:	Zhou, Xin, Edmonson, Michael N, Wilkinson, Mark R, Patel, Aman, Wu, Gang, Liu, Yu, Li, Yongjin, Zhang, Zhaojie, Rusch, Michael C, Parker, Matthew, Becksfort, Jared, Downing, James R, Zhang, Jinghui
Format:	Journal Article
Language:	English
Published:	New York Nature Publishing Group US 01.01.2016 Nature Publishing Group
Subjects:	45 45/23 631/114/794 692/699/67 Agriculture Animal Genetics and Genomics Biomedicine Cancer Cancer Research Cancer treatment Child Children & youth correspondence Databases, Genetic Gene expression Gene Expression Regulation, Neoplastic Gene Function Genome, Human Genomes Human Genetics Humans Kinases Lesions Medical research Mutation Neoplasms - genetics Pediatrics Proteins Proteins - genetics Software Studies Tumors User-Computer Interface Visualization
ISSN:	1061-4036, 1546-1718, 1546-1718
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Abstract	The pediatric data set consists of 27,188 validated somatic coding lesions acquired at diagnosis or relapse from 17 subtypes of pediatric cancer, 252 pathogenic or loss-of-function germline lesions detected in >1,000 pediatric patients with cancer of 21 subtypes6 and RNA sequencing (RNA-seq) data for 928 pediatric tumors from 36 subtypes (Supplementary Note). Data in mutation annotation format (MAF) generated by studies such as The Cancer Genome Atlas (TCGA) or individual research laboratories can be uploaded to ProteinPaint to enable data visualization and cross-study comparison for the broad genetic research community (Supplementary Fig. 8 and Supplementary Tutorial).
AbstractList	The pediatric data set consists of 27,188 validated somatic coding lesions acquired at diagnosis or relapse from 17 subtypes of pediatric cancer, 252 pathogenic or loss-of-function germline lesions detected in >1,000 pediatric patients with cancer of 21 subtypes6 and RNA sequencing (RNA-seq) data for 928 pediatric tumors from 36 subtypes (Supplementary Note). Data in mutation annotation format (MAF) generated by studies such as The Cancer Genome Atlas (TCGA) or individual research laboratories can be uploaded to ProteinPaint to enable data visualization and cross-study comparison for the broad genetic research community (Supplementary Fig. 8 and Supplementary Tutorial).
Audience	Academic
Author	Edmonson, Michael N Wilkinson, Mark R Liu, Yu Downing, James R Zhou, Xin Patel, Aman Rusch, Michael C Li, Yongjin Parker, Matthew Zhang, Jinghui Zhang, Zhaojie Becksfort, Jared Wu, Gang
Author_xml	– sequence: 1 givenname: Xin surname: Zhou fullname: Zhou, Xin organization: Department of Computational Biology, St. Jude Children's Research Hospital – sequence: 2 givenname: Michael N surname: Edmonson fullname: Edmonson, Michael N organization: Department of Computational Biology, St. Jude Children's Research Hospital – sequence: 3 givenname: Mark R surname: Wilkinson fullname: Wilkinson, Mark R organization: Department of Computational Biology, St. Jude Children's Research Hospital – sequence: 4 givenname: Aman surname: Patel fullname: Patel, Aman organization: Department of Computational Biology, St. Jude Children's Research Hospital – sequence: 5 givenname: Gang orcidid: 0000-0002-1678-5864 surname: Wu fullname: Wu, Gang organization: Department of Computational Biology, St. Jude Children's Research Hospital – sequence: 6 givenname: Yu surname: Liu fullname: Liu, Yu organization: Department of Computational Biology, St. Jude Children's Research Hospital – sequence: 7 givenname: Yongjin surname: Li fullname: Li, Yongjin organization: Department of Computational Biology, St. Jude Children's Research Hospital – sequence: 8 givenname: Zhaojie surname: Zhang fullname: Zhang, Zhaojie organization: Department of Computational Biology, St. Jude Children's Research Hospital – sequence: 9 givenname: Michael C surname: Rusch fullname: Rusch, Michael C organization: Department of Computational Biology, St. Jude Children's Research Hospital – sequence: 10 givenname: Matthew surname: Parker fullname: Parker, Matthew organization: Department of Computational Biology, St. Jude Children's Research Hospital – sequence: 11 givenname: Jared surname: Becksfort fullname: Becksfort, Jared organization: Department of Computational Biology, St. Jude Children's Research Hospital – sequence: 12 givenname: James R surname: Downing fullname: Downing, James R organization: Department of Computational Biology, St. Jude Children's Research Hospital, Department of Pathology, St. Jude Children's Research Hospital – sequence: 13 givenname: Jinghui surname: Zhang fullname: Zhang, Jinghui email: jinghui.zhang@stjude.org organization: Department of Computational Biology, St. Jude Children's Research Hospital
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/26711108$$D View this record in MEDLINE/PubMed
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SubjectTerms	45 45/23 631/114/794 692/699/67 Agriculture Animal Genetics and Genomics Biomedicine Cancer Cancer Research Cancer treatment Child Children & youth correspondence Databases, Genetic Gene expression Gene Expression Regulation, Neoplastic Gene Function Genome, Human Genomes Human Genetics Humans Kinases Lesions Medical research Mutation Neoplasms - genetics Pediatrics Proteins Proteins - genetics Software Studies Tumors User-Computer Interface Visualization
Title	Exploring genomic alteration in pediatric cancer using ProteinPaint
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