Identifying the Common Cell-Free DNA Biomarkers across Seven Major Cancer Types
Blood-based detection of circulating cell-free DNA (cfDNA) is a non-invasive and easily accessible method for early cancer detection. Despite the extensive utility of cfDNA, there are still many challenges to developing clinical biomarkers. For example, cfDNA with genetic alterations often composes...
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| Format: | Article |
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MDPI AG
2023-06-01
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| Series: | Biology |
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| Online Access: | https://www.mdpi.com/2079-7737/12/7/934 |
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| author | Mingyu Luo Yining Liu Min Zhao |
| author_facet | Mingyu Luo Yining Liu Min Zhao |
| author_sort | Mingyu Luo |
| collection | DOAJ |
| description | Blood-based detection of circulating cell-free DNA (cfDNA) is a non-invasive and easily accessible method for early cancer detection. Despite the extensive utility of cfDNA, there are still many challenges to developing clinical biomarkers. For example, cfDNA with genetic alterations often composes 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 healthy populations will be important for cancer-based biomarkers. Additionally, many low-frequency genetic alterations are easily overlooked in a small number of cfDNA-based cancer tests. We hypothesize that the combination of diverse types of cancer studies on cfDNA will provide us with a new perspective on the identification of low-frequency genetic variants across cancer types for promoting early diagnosis. By building a standardized computational pipeline for 1358 cfDNA samples across seven cancer types, we prioritized 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 the membrane, some of which are tumour suppressors, oncogenes, and genes related to cancer initiation. In summary, our integrative analysis revealed the important roles of ribosome proteins as common biomarkers in early cancer diagnosis. |
| first_indexed | 2024-03-11T01:17:49Z |
| format | Article |
| id | doaj.art-9c75df6667f4452aa2fa444c861073be |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-11T01:17:49Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-9c75df6667f4452aa2fa444c861073be2023-11-18T18:23:16ZengMDPI AGBiology2079-77372023-06-0112793410.3390/biology12070934Identifying the Common Cell-Free DNA Biomarkers across Seven Major Cancer TypesMingyu Luo0Yining Liu1Min Zhao2School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4558, AustraliaThe School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 510120, ChinaSchool of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4558, AustraliaBlood-based detection of circulating cell-free DNA (cfDNA) is a non-invasive and easily accessible method for early cancer detection. Despite the extensive utility of cfDNA, there are still many challenges to developing clinical biomarkers. For example, cfDNA with genetic alterations often composes 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 healthy populations will be important for cancer-based biomarkers. Additionally, many low-frequency genetic alterations are easily overlooked in a small number of cfDNA-based cancer tests. We hypothesize that the combination of diverse types of cancer studies on cfDNA will provide us with a new perspective on the identification of low-frequency genetic variants across cancer types for promoting early diagnosis. By building a standardized computational pipeline for 1358 cfDNA samples across seven cancer types, we prioritized 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 the membrane, some of which are tumour suppressors, oncogenes, and genes related to cancer initiation. In summary, our integrative analysis revealed the important roles of ribosome proteins as common biomarkers in early cancer diagnosis.https://www.mdpi.com/2079-7737/12/7/934early cancer diagnosiscell-free DNAbiomarkerintegrative biologypan cancer |
| spellingShingle | Mingyu Luo Yining Liu Min Zhao Identifying the Common Cell-Free DNA Biomarkers across Seven Major Cancer Types Biology early cancer diagnosis cell-free DNA biomarker integrative biology pan cancer |
| title | Identifying the Common Cell-Free DNA Biomarkers across Seven Major Cancer Types |
| title_full | Identifying the Common Cell-Free DNA Biomarkers across Seven Major Cancer Types |
| title_fullStr | Identifying the Common Cell-Free DNA Biomarkers across Seven Major Cancer Types |
| title_full_unstemmed | Identifying the Common Cell-Free DNA Biomarkers across Seven Major Cancer Types |
| title_short | Identifying the Common Cell-Free DNA Biomarkers across Seven Major Cancer Types |
| title_sort | identifying the common cell free dna biomarkers across seven major cancer types |
| topic | early cancer diagnosis cell-free DNA biomarker integrative biology pan cancer |
| url | https://www.mdpi.com/2079-7737/12/7/934 |
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