Deep learning improves pancreatic cancer diagnosis using rna-based variants

Al-Fatlawi A, Malekian N, García S, Henschel A, Kim I, Dahl A, Jahnke B, Bailey P, Bolz SN, Poetsch AR, Mahler S, Grützmann R, Pilarsky C, Schroeder M (2021)

Publication Type: Journal article

Publication year: 2021

Journal

Cancers MDPI

Book Volume: 13

Article Number: 2654

Journal Issue: 11

DOI: 10.3390/cancers13112654

Abstract

For optimal pancreatic cancer treatment, early and accurate diagnosis is vital. Blood-derived biomarkers and genetic predispositions can contribute to early diagnosis, but they often have limited accuracy or applicability. Here, we seek to exploit the synergy between them by combining the biomarker CA19-9 with RNA-based variants. We use deep sequencing and deep learning to improve differentiating pancreatic cancer and chronic pancreatitis. We obtained samples of nucleated cells found in peripheral blood from 268 patients suffering from resectable, non-resectable pancreatic cancer, and chronic pancreatitis. We sequenced RNA with high coverage and obtained millions of variants. The high-quality variants served as input together with CA19-9 values to deep learning models. Our model achieved an area under the curve (AUC) of 96% in differentiating resectable cancer from pancreatitis using a test cohort. Moreover, we identified variants to estimate survival in resectable cancer. We show that the blood transcriptome harbours variants, which can substantially improve noninvasive clinical diagnosis.

Authors with CRIS profile

Robert Grützmann Lehrstuhl für Allgemein- und Viszeralchirurgie Christian Pilarsky Professur für Chirurgische Forschung

Involved external institutions

Universitätsklinikum Carl Gustav Carus Dresden DE Germany (DE) Technische Universität Dresden DE Germany (DE) Khalifa University of Science, Technology & Research (KUSTAR) / جامعة خليفة AE United Arab Emirates (AE)

How to cite

APA:

Al-Fatlawi, A., Malekian, N., García, S., Henschel, A., Kim, I., Dahl, A.,... Schroeder, M. (2021). Deep learning improves pancreatic cancer diagnosis using rna-based variants. Cancers, 13(11). https://doi.org/10.3390/cancers13112654

MLA:

Al-Fatlawi, Ali, et al. "Deep learning improves pancreatic cancer diagnosis using rna-based variants." Cancers 13.11 (2021).

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