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Integrative modeling of tumor genomes and epigenomes for enhanced cancer diagnosis by cell-free DNA

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Abstract
Multi-cancer early detection remains a key challenge in cell-free DNA (cfDNA)-based liquid biopsy. Here, we perform cfDNA whole-genome sequencing to generate two test datasets covering 2125 patient samples of 9 cancer types and 1241 normal control samples, and also a reference dataset for background variant filtering based on 20,529 low-depth healthy samples. An external cfDNA dataset consisting of 208 cancer and 214 normal control samples is used for additional evaluation. Accuracy for cancer detection and tissue-oforigin localization is achieved using our algorithm, which incorporates cancer type-specific profiles of mutation distribution and chromatin organization in tumor tissues as model references. Our integrative model detects early-stage cancers, including those of pancreatic origin, with high sensitivity that is comparable to that of late-stage detection. Model interpretation reveals the contribution of cancer type-specific genomic and epigenomic features. Our methodologies may lay the groundwork for accurate cfDNA-based cancer diagnosis, especially at early stages.
Author(s)
Mingyun BaeGyuhee KimTae-Rim LeeJin Mo AhnHyunwook ParkSook Ryun ParkKi Byung SongEunsung JunDongryul OhJeong-Won LeeYoung Sik ParkKi-Won SongJeong-Sik ByeonBo Hyun KimJoo Hyuk SohnMin Hwan KimGun Min KimEui Kyu ChieHyun-Cheol KangSun-Young KongSang Myung WooJeong Eon LeeJai Min RyuJunnam LeeDasom KimChang-Seok KiEun-Hae ChoJung Kyoon Choi
Issued Date
2023
Type
Article
Keyword
AlgorithmsBiopsyCancerChromatinDiagnosisDNAEpigenomeGenomesHuman beingsMutationScienceTumorsWhole Genome Sequencing
DOI
10.1038/s41467-023-37768-3
URI
https://oak.ulsan.ac.kr/handle/2021.oak/16677
Publisher
Nature Communications
Language
영어
ISSN
2041-1723
Citation Volume
14
Citation Number
1
Citation Start Page
1
Citation End Page
15
Appears in Collections:
Medicine > Nursing
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