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Identifying the Common Cell-Free DNA Biomarkers across Seven Major Cancer Types
Version 1
: Received: 5 June 2023 / Approved: 5 June 2023 / Online: 5 June 2023 (09:20:14 CEST)
A peer-reviewed article of this Preprint also exists.
Luo, M.; Liu, Y.; Zhao, M. Identifying the Common Cell-Free DNA Biomarkers across Seven Major Cancer Types. Biology 2023, 12, 934. Luo, M.; Liu, Y.; Zhao, M. Identifying the Common Cell-Free DNA Biomarkers across Seven Major Cancer Types. Biology 2023, 12, 934.
Abstract
Blood-based circulating cell free DNA(cfDNA) detection offers a non-invasive and easily accessible way for early cancer detection. Despite the extensive utility of cfDNA, there are still many challenges to develop the clinical biomarkers. For example, cfDNA with genetic alterations often compose a small portion of the DNA circulating in plasma, which can be confounded by cfDNA contributed by normal cells. Therefore, filtering out the potential false-positive cfDNA mutations from health population will be important for the cancer-based biomarkers. Additionally, many low-frequency genetic alterations are easily overlooked in small amount of cfDNA-based cancer test. We hypothesize that, the combination of diverse types of cancer studies on cfDNA can provide us a new insight to identify low-frequency genetic variant across cancer types for early clinical detection of cancers. By building a standardized computational pipeline for 1358 cfDNA samples across seven cancer types, we prioritize 129 shard genetic variants in the major cancer types. Further functional analysis of the 129 variants found that they are mainly enriched in ribosome pathways such as cotranslational protein targeting to membrane, some of which are tumor suppressor, oncogene and related to cancer initiation. In summary, our integrative analysis revealed the important roles of ribosome proteins as the common biomarkers in early cancer diagnosis.
Keywords
Early cancer diagnosis; cell free DNA; biomarker; integrative biology; pan cancer
Subject
Biology and Life Sciences, Biology and Biotechnology
Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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