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Stratified time-course gene preselection shows a pre-diagnostic transcriptomic signal for metastasis in blood cells: a proof of concept from the NOWAC study

Einar Holsbø, Vittorio Perduca, Lars Ailo Bongo, Eiliv Lund, Etienne Birmelé
doi: https://doi.org/10.1101/141325
Einar Holsbø
1Department of Computer Science, UiT The Arctic University of Norway, Norway.
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Vittorio Perduca
2Laboratoire MAP5, Université Paris Descartes, France.
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Lars Ailo Bongo
1Department of Computer Science, UiT The Arctic University of Norway, Norway.
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Eiliv Lund
3Department of Community Medicine, UiT The Arctic University of Norway, Norway.
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Etienne Birmelé
2Laboratoire MAP5, Université Paris Descartes, France.
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Abstract

We investigate whether there is information in gene expression levels in blood that predicts breast cancer metastasis. Our data comes from the NOWAC epidemiological cohort study where blood samples were provided at enrollment. This could be anywhere from years to weeks before any cancer diagnosis. When and if a cancer is diagnosed, it could be so in different ways: at a screening, between screenings, or in the clinic, outside of the screening program. To build predictive models we propose that variable selection should include followup time and stratify by detection method. We show by simulations that this improves the probability of selecting relevant predictor genes. We also demonstrate that it leads to improved predictions and more stable gene signatures in our data. There is some indication that blood gene expression levels hold predictive information about metastasis. With further development such information could be used for early detection of metastatic potential and as such aid in cancer treatment.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 25, 2018.
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Stratified time-course gene preselection shows a pre-diagnostic transcriptomic signal for metastasis in blood cells: a proof of concept from the NOWAC study
Einar Holsbø, Vittorio Perduca, Lars Ailo Bongo, Eiliv Lund, Etienne Birmelé
bioRxiv 141325; doi: https://doi.org/10.1101/141325
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Stratified time-course gene preselection shows a pre-diagnostic transcriptomic signal for metastasis in blood cells: a proof of concept from the NOWAC study
Einar Holsbø, Vittorio Perduca, Lars Ailo Bongo, Eiliv Lund, Etienne Birmelé
bioRxiv 141325; doi: https://doi.org/10.1101/141325

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