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A harmonized meta-k...
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer
- Article/chapterEnglish2020
Publisher, publication year, extent ...
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2020-04-03
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Springer Science and Business Media LLC,2020
Numbers
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LIBRIS-ID:oai:prod.swepub.kib.ki.se:143356701
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http://kipublications.ki.se/Default.aspx?queryparsed=id:143356701URI
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https://doi.org/10.1038/s41588-020-0603-8DOI
Supplementary language notes
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Language:English
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Summary in:English
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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Precision oncology relies on accurate discovery and interpretation of genomic variants, enabling individualized diagnosis, prognosis and therapy selection. We found that six prominent somatic cancer variant knowledgebases were highly disparate in content, structure and supporting primary literature, impeding consensus when evaluating variants and their relevance in a clinical setting. We developed a framework for harmonizing variant interpretations to produce a meta-knowledgebase of 12,856 aggregate interpretations. We demonstrated large gains in overlap between resources across variants, diseases and drugs as a result of this harmonization. We subsequently demonstrated improved matching between a patient cohort and harmonized interpretations of potential clinical significance, observing an increase from an average of 33% per individual knowledgebase to 57% in aggregate. Our analyses illuminate the need for open, interoperable sharing of variant interpretation data. We also provide a freely available web interface (search.cancervariants.org) for exploring the harmonized interpretations from these six knowledgebases.
Added entries (persons, corporate bodies, meetings, titles ...)
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Walsh, B
(author)
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Mayfield, G
(author)
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Tamborero, DKarolinska Institutet
(author)
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Sonkin, D
(author)
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Krysiak, K
(author)
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Deu-Pons, J
(author)
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Duren, RP
(author)
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Gao, JJ
(author)
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McMurry, J
(author)
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Patterson, S
(author)
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Fitz, CD
(author)
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Pitel, BA
(author)
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Sezerman, OU
(author)
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Ellrott, K
(author)
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Warner, JL
(author)
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Rieke, DT
(author)
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Aittokallio, T
(author)
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Cerami, E
(author)
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Ritter, DI
(author)
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Schriml, LM
(author)
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Freimuth, RR
(author)
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Haendel, M
(author)
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Raca, G
(author)
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Madhavan, S
(author)
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Baudis, M
(author)
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Beckmann, JS
(author)
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Dienstmann, R
(author)
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Chakravarty, D
(author)
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Li, XS
(author)
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Mockus, S
(author)
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Elemento, O
(author)
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Schultz, N
(author)
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Lopez-Bigas, N
(author)
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Lawler, M
(author)
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Goecks, J
(author)
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Griffith, M
(author)
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Griffith, OL
(author)
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Margolin, AA
(author)
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Karolinska Institutet
(creator_code:org_t)
Related titles
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In:Nature genetics: Springer Science and Business Media LLC52:4, s. 448-+1546-17181061-4036
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Wagner, AH
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Walsh, B
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Mayfield, G
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Tamborero, D
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Sonkin, D
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Krysiak, K
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show more...
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Deu-Pons, J
-
Duren, RP
-
Gao, JJ
-
McMurry, J
-
Patterson, S
-
Fitz, CD
-
Pitel, BA
-
Sezerman, OU
-
Ellrott, K
-
Warner, JL
-
Rieke, DT
-
Aittokallio, T
-
Cerami, E
-
Ritter, DI
-
Schriml, LM
-
Freimuth, RR
-
Haendel, M
-
Raca, G
-
Madhavan, S
-
Baudis, M
-
Beckmann, JS
-
Dienstmann, R
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Chakravarty, D
-
Li, XS
-
Mockus, S
-
Elemento, O
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Schultz, N
-
Lopez-Bigas, N
-
Lawler, M
-
Goecks, J
-
Griffith, M
-
Griffith, OL
-
Margolin, AA
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Nature genetics
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Karolinska Institutet