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Prioritization of enhancer mutations by combining allele-specific chromatin accessibility with deep learning

View ORCID ProfileZeynep Kalender Atak, View ORCID ProfileIbrahim Ihsan Taskiran, Christopher Flerin, David Mauduit, Liesbeth Minnoye, Gert Hulsemans, Valerie Christiaens, Ghanem-Elias Ghanem, Jasper Wouters, View ORCID ProfileStein Aerts
doi: https://doi.org/10.1101/2019.12.21.885806
Zeynep Kalender Atak
1VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
2KU Leuven, Department of Human Genetics KU Leuven, Leuven, Belgium
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  • ORCID record for Zeynep Kalender Atak
Ibrahim Ihsan Taskiran
1VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
2KU Leuven, Department of Human Genetics KU Leuven, Leuven, Belgium
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  • ORCID record for Ibrahim Ihsan Taskiran
Christopher Flerin
1VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
2KU Leuven, Department of Human Genetics KU Leuven, Leuven, Belgium
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David Mauduit
1VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
2KU Leuven, Department of Human Genetics KU Leuven, Leuven, Belgium
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Liesbeth Minnoye
1VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
2KU Leuven, Department of Human Genetics KU Leuven, Leuven, Belgium
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Gert Hulsemans
1VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
2KU Leuven, Department of Human Genetics KU Leuven, Leuven, Belgium
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Valerie Christiaens
1VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
2KU Leuven, Department of Human Genetics KU Leuven, Leuven, Belgium
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Ghanem-Elias Ghanem
3Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
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Jasper Wouters
1VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
2KU Leuven, Department of Human Genetics KU Leuven, Leuven, Belgium
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Stein Aerts
1VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
2KU Leuven, Department of Human Genetics KU Leuven, Leuven, Belgium
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  • ORCID record for Stein Aerts
  • For correspondence: stein.aerts@kuleuven.vib.be
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Brief Abstract

Prioritization of non-coding genome variation benefits from explainable AI to predict and interpret the impact of a mutation on gene regulation. Here we apply a specialized deep learning model to phased melanoma genomes and identify functional enhancer mutations with allelic imbalance of chromatin accessibility and gene expression.

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Posted December 23, 2019.
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Prioritization of enhancer mutations by combining allele-specific chromatin accessibility with deep learning
Zeynep Kalender Atak, Ibrahim Ihsan Taskiran, Christopher Flerin, David Mauduit, Liesbeth Minnoye, Gert Hulsemans, Valerie Christiaens, Ghanem-Elias Ghanem, Jasper Wouters, Stein Aerts
bioRxiv 2019.12.21.885806; doi: https://doi.org/10.1101/2019.12.21.885806
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Prioritization of enhancer mutations by combining allele-specific chromatin accessibility with deep learning
Zeynep Kalender Atak, Ibrahim Ihsan Taskiran, Christopher Flerin, David Mauduit, Liesbeth Minnoye, Gert Hulsemans, Valerie Christiaens, Ghanem-Elias Ghanem, Jasper Wouters, Stein Aerts
bioRxiv 2019.12.21.885806; doi: https://doi.org/10.1101/2019.12.21.885806

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