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Prediction of Primary Tumors in Cancers of Unknown Primary
A cancer of unknown primary (CUP) is a metastatic cancer for which standard diagnostic tests fail to identify the location of the primary tumor. CUPs account for 3–5% of cancer cases. Using molecular data to determine the location of the primary tumor in such cases can help doctors make the right tr...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
De Gruyter
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6042823/ https://www.ncbi.nlm.nih.gov/pubmed/28686574 http://dx.doi.org/10.1515/jib-2017-0013 |
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author | Søndergaard, Dan Nielsen, Svend Pedersen, Christian N.S. Besenbacher, Søren |
author_facet | Søndergaard, Dan Nielsen, Svend Pedersen, Christian N.S. Besenbacher, Søren |
author_sort | Søndergaard, Dan |
collection | PubMed |
description | A cancer of unknown primary (CUP) is a metastatic cancer for which standard diagnostic tests fail to identify the location of the primary tumor. CUPs account for 3–5% of cancer cases. Using molecular data to determine the location of the primary tumor in such cases can help doctors make the right treatment choice and thus improve the clinical outcome. In this paper, we present a new method for predicting the location of the primary tumor using gene expression data: locating cancers of unknown primary (LoCUP). The method models the data as a mixture of normal and tumor cells and thus allows correct classification even in impure samples, where the tumor biopsy is contaminated by a large fraction of normal cells. We find that our method provides a significant increase in classification accuracy (95.8% over 90.8%) on simulated low-purity metastatic samples and shows potential on a small dataset of real metastasis samples with known origin. |
format | Online Article Text |
id | pubmed-6042823 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | De Gruyter |
record_format | MEDLINE/PubMed |
spelling | pubmed-60428232019-01-28 Prediction of Primary Tumors in Cancers of Unknown Primary Søndergaard, Dan Nielsen, Svend Pedersen, Christian N.S. Besenbacher, Søren J Integr Bioinform Research Articles A cancer of unknown primary (CUP) is a metastatic cancer for which standard diagnostic tests fail to identify the location of the primary tumor. CUPs account for 3–5% of cancer cases. Using molecular data to determine the location of the primary tumor in such cases can help doctors make the right treatment choice and thus improve the clinical outcome. In this paper, we present a new method for predicting the location of the primary tumor using gene expression data: locating cancers of unknown primary (LoCUP). The method models the data as a mixture of normal and tumor cells and thus allows correct classification even in impure samples, where the tumor biopsy is contaminated by a large fraction of normal cells. We find that our method provides a significant increase in classification accuracy (95.8% over 90.8%) on simulated low-purity metastatic samples and shows potential on a small dataset of real metastasis samples with known origin. De Gruyter 2017-07-07 /pmc/articles/PMC6042823/ /pubmed/28686574 http://dx.doi.org/10.1515/jib-2017-0013 Text en ©2017, Dan Søndergaard, et al., published by De Gruyter, Berlin/Boston http://creativecommons.org/licenses/by-nc-nd/3.0 This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. |
spellingShingle | Research Articles Søndergaard, Dan Nielsen, Svend Pedersen, Christian N.S. Besenbacher, Søren Prediction of Primary Tumors in Cancers of Unknown Primary |
title | Prediction of Primary Tumors in Cancers of Unknown Primary |
title_full | Prediction of Primary Tumors in Cancers of Unknown Primary |
title_fullStr | Prediction of Primary Tumors in Cancers of Unknown Primary |
title_full_unstemmed | Prediction of Primary Tumors in Cancers of Unknown Primary |
title_short | Prediction of Primary Tumors in Cancers of Unknown Primary |
title_sort | prediction of primary tumors in cancers of unknown primary |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6042823/ https://www.ncbi.nlm.nih.gov/pubmed/28686574 http://dx.doi.org/10.1515/jib-2017-0013 |
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