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Combined burden and...
Combined burden and functional impact tests for cancer driver discovery using DriverPower
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- Shuai, Shimin (författare)
- University of Toronto,Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A8, Canada.;Ontario Inst Canc Res, Computat Biol Program, Toronto, ON M5G 0A3, Canada.
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- Gallinger, Steven (författare)
- Toronto General Hospital,Toronto Gen Hosp, Div Gen Surg, Toronto, ON M5G 2C4, Canada.;Mt Sinai Hosp, Lunenfeld Tanenbaum Res Inst, Toronto, ON M5G 1X5, Canada.
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- Stein, Lincoln D (författare)
- University of Toronto,Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A8, Canada.;Ontario Inst Canc Res, Computat Biol Program, Toronto, ON M5G 0A3, Canada.
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- Borg, Åke (creator_code:cre_t)
- Lund University,Lunds universitet,Bröstcancer-genetik,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Familjär bröstcancer,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Breastcancer-genetics,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine,Familial Breast Cancer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments
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- Ringnér, Markus (creator_code:cre_t)
- Lund University,Lunds universitet,Molekylär cellbiologi,Biologiska institutionen,Naturvetenskapliga fakulteten,Molecular Cell Biology,Department of Biology,Faculty of Science
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- Staaf, Johan (creator_code:cre_t)
- Lund University,Lunds universitet,Forskningsgrupp Lungcancer,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Bröst/lungcancer,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Research Group Lung Cancer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments,Breast/lungcancer,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine
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University of Toronto Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A8, Canada;Ontario Inst Canc Res, Computat Biol Program, Toronto, ON M5G 0A3, Canada. (creator_code:org_t)
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- 2020-02-05
- 2020
- Engelska 12 s.
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11, s. 734-734
- Relaterad länk:
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http://dx.doi.org/10... (free)
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https://www.nature.c...
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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https://lup.lub.lu.s...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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http://kipublication...
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Abstract
Ämnesord
Stäng
- The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower's background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
Nyckelord
- Algorithms
- Genome, Human
- Genomics/methods
- Humans
- MEF2 Transcription Factors/genetics
- Mutation
- Mutation Rate
- Neoplasms/genetics
- Peptide Elongation Factor 1/genetics
- Receptors, G-Protein-Coupled/genetics
- Software
- Whole Genome Sequencing
Publikations- och innehållstyp
- art (ämneskategori)
- ref (ämneskategori)
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