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

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dc.contributor.authorBae, Mingyunko
dc.contributor.authorKim, Gyuheeko
dc.contributor.authorLee, Tae-Rimko
dc.contributor.authorAhn, Jin Moko
dc.contributor.authorPark, Hyunwookko
dc.contributor.authorPark, Sook Ryunko
dc.contributor.authorSong, Ki Byungko
dc.contributor.authorJun, Eunsungko
dc.contributor.authorOh, Dongryulko
dc.contributor.authorLee, Jeong-Wonko
dc.contributor.authorPark, Young Sikko
dc.contributor.authorSong, Ki-Wonko
dc.contributor.authorByeon, Jeong-Sikko
dc.contributor.authorKim, Bo Hyunko
dc.contributor.authorSohn, Joo Hyukko
dc.contributor.authorKim, Min Hwanko
dc.contributor.authorKim, Gun Minko
dc.contributor.authorChie, Eui Kyuko
dc.contributor.authorKang, Hyun-Cheolko
dc.contributor.authorKong, Sun-Youngko
dc.contributor.authorWoo, Sang Myungko
dc.contributor.authorLee, Jeong Eonko
dc.contributor.authorRyu, Jai Minko
dc.contributor.authorLee, Junnamko
dc.contributor.authorKim, Dasomko
dc.contributor.authorKi, Chang-Seokko
dc.contributor.authorCho, Eun-Haeko
dc.contributor.authorChoi, Jung Kyoonko
dc.identifier.citationNATURE COMMUNICATIONS, v.14, no.1-
dc.description.abstractDespite advances in ctDNA cancer detection, early detection remains difficult. Here, the authors utilise whole genome sequencing of 2,125 patient samples to create a model for early cancer and tissue of origin detection. 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-of-origin 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.-
dc.titleIntegrative modeling of tumor genomes and epigenomes for enhanced cancer diagnosis by cell-free DNA-
dc.citation.publicationnameNATURE COMMUNICATIONS-
dc.contributor.localauthorChoi, Jung Kyoon-
dc.contributor.nonIdAuthorLee, Tae-Rim-
dc.contributor.nonIdAuthorAhn, Jin Mo-
dc.contributor.nonIdAuthorPark, Sook Ryun-
dc.contributor.nonIdAuthorSong, Ki Byung-
dc.contributor.nonIdAuthorJun, Eunsung-
dc.contributor.nonIdAuthorOh, Dongryul-
dc.contributor.nonIdAuthorLee, Jeong-Won-
dc.contributor.nonIdAuthorPark, Young Sik-
dc.contributor.nonIdAuthorSong, Ki-Won-
dc.contributor.nonIdAuthorByeon, Jeong-Sik-
dc.contributor.nonIdAuthorKim, Bo Hyun-
dc.contributor.nonIdAuthorSohn, Joo Hyuk-
dc.contributor.nonIdAuthorKim, Min Hwan-
dc.contributor.nonIdAuthorKim, Gun Min-
dc.contributor.nonIdAuthorChie, Eui Kyu-
dc.contributor.nonIdAuthorKang, Hyun-Cheol-
dc.contributor.nonIdAuthorKong, Sun-Young-
dc.contributor.nonIdAuthorWoo, Sang Myung-
dc.contributor.nonIdAuthorLee, Jeong Eon-
dc.contributor.nonIdAuthorRyu, Jai Min-
dc.contributor.nonIdAuthorLee, Junnam-
dc.contributor.nonIdAuthorKim, Dasom-
dc.contributor.nonIdAuthorKi, Chang-Seok-
dc.contributor.nonIdAuthorCho, Eun-Hae-
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