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A cloud-based resou...
A cloud-based resource for genome coordinate-based exploration and large-scale analysis of chromosome aberrations and gene fusions in cancer
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- Wang, Janet (författare)
- Case Western Reserve University
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- Zheng, Jeanne (författare)
- Brown University
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- Lee, Elaine E. (författare)
- Institute for Systems Biology, Seattle
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visa fler...
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- Aguilar, Boris (författare)
- Institute for Systems Biology, Seattle
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Phan, John (författare)
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Abdilleh, Kawther (författare)
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- Taylor, Ronald C. (författare)
- National Cancer Institute, USA
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- Longabaugh, William (författare)
- Institute for Systems Biology, Seattle
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- Johansson, Bertil (författare)
- Lund University,Lunds universitet,Avdelningen för klinisk genetik,Institutionen för laboratoriemedicin,Medicinska fakulteten,Genetiska och epigenetiska studier av barnleukemi,Forskargrupper vid Lunds universitet,Division of Clinical Genetics,Department of Laboratory Medicine,Faculty of Medicine,Genetic and epigenetic studies of pediatric leukemia,Lund University Research Groups
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- Mertens, Fredrik (författare)
- Lund University,Lunds universitet,Avdelningen för klinisk genetik,Institutionen för laboratoriemedicin,Medicinska fakulteten,Genetiska avvikelser i mjukdelstumörer,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Division of Clinical Genetics,Department of Laboratory Medicine,Faculty of Medicine,The genetics of soft tissue tumors,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments
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- Mitelman, Felix (författare)
- Lund University,Lunds universitet,Avdelningen för klinisk genetik,Institutionen för laboratoriemedicin,Medicinska fakulteten,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Division of Clinical Genetics,Department of Laboratory Medicine,Faculty of Medicine,LUCC: Lund University Cancer Centre,Other Strong Research Environments
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Pot, David (författare)
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- LaFramboise, Thomas (författare)
- Case Western Reserve University
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(creator_code:org_t)
- 2023-02-13
- 2023
- Engelska.
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Ingår i: Genes Chromosomes and Cancer. - : Wiley. - 1045-2257 .- 1098-2264. ; 62:8, s. 441-448
- Relaterad länk:
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http://dx.doi.org/10...
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https://lup.lub.lu.s...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- Cytogenetic analysis provides important information on the genetic mechanisms of cancer. The Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer (Mitelman DB) is the largest catalog of acquired chromosome aberrations, presently comprising >70 000 cases across multiple cancer types. Although this resource has enabled the identification of chromosome abnormalities leading to specific cancers and cancer mechanisms, a large-scale, systematic analysis of these aberrations and their downstream implications has been difficult due to the lack of a standard, automated mapping from aberrations to genomic coordinates. We previously introduced CytoConverter as a tool that automates such conversions. CytoConverter has now been updated with improved interpretation of karyotypes and has been integrated with the Mitelman DB, providing a comprehensive mapping of the 70 000+ cases to genomic coordinates, as well as visualization of the frequencies of chromosomal gains and losses. Importantly, all CytoConverter-generated genomic coordinates are publicly available in Google BigQuery, a cloud-based data warehouse, facilitating data exploration and integration with other datasets hosted by the Institute for Systems Biology Cancer Gateway in the Cloud (ISB-CGC) Resource. We demonstrate the use of BigQuery for integrative analysis of Mitelman DB with other cancer datasets, including a comparison of the frequency of imbalances identified in Mitelman DB cases with those found in The Cancer Genome Atlas (TCGA) copy number datasets. This solution provides opportunities to leverage the power of cloud computing for low-cost, scalable, and integrated analysis of chromosome aberrations and gene fusions in cancer.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Nyckelord
- cloud-based analysis
- cytogenetics
- genomics
- Mitelman database
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- Av författaren/redakt...
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Wang, Janet
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Zheng, Jeanne
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Lee, Elaine E.
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Aguilar, Boris
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Phan, John
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Abdilleh, Kawthe ...
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visa fler...
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Taylor, Ronald C ...
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Longabaugh, Will ...
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Johansson, Berti ...
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Mertens, Fredrik
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Mitelman, Felix
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Pot, David
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LaFramboise, Tho ...
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