MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model
DNA methylation (DNAm) is a key epigenetic mark that shows profound alterations in cancer. Read-level methylomes enable more in-depth analyses, due to their broad genomic coverage and preservation of rare cell-type signals, compared to summarized data such as 450K/EPIC microarrays. Here, we propose...
Gespeichert in:
| Hauptverfasser: | , , , , , |
|---|---|
| Dokumenttyp: | Article (Journal) |
| Sprache: | Englisch |
| Veröffentlicht: |
17 January 2025
|
| In: |
Nature Communications
Year: 2025, Jahrgang: 16, Pages: 1-14 |
| ISSN: | 2041-1723 |
| DOI: | 10.1038/s41467-025-55920-z |
| Online-Zugang: | Verlag, kostenfrei, Volltext: https://doi.org/10.1038/s41467-025-55920-z Verlag, kostenfrei, Volltext: https://www.nature.com/articles/s41467-025-55920-z 
|
| Verfasserangaben: | Yunhee Jeong, Clarissa Gerhäuser, Guido Sauter, Thorsten Schlomm, Karl Rohr, and Pavlo Lutsik |
MARC
| LEADER | 00000caa a2200000 c 4500 | ||
|---|---|---|---|
| 001 | 193344603X | ||
| 003 | DE-627 | ||
| 005 | 20250913141853.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 250818s2025 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1038/s41467-025-55920-z |2 doi | |
| 035 | |a (DE-627)193344603X | ||
| 035 | |a (DE-599)KXP193344603X | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rda | ||
| 041 | |a eng | ||
| 084 | |a 33 |2 sdnb | ||
| 100 | 1 | |a Jeong, Yunhee |d 1995- |e VerfasserIn |0 (DE-588)1324464143 |0 (DE-627)188432908X |4 aut | |
| 245 | 1 | 0 | |a MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model |c Yunhee Jeong, Clarissa Gerhäuser, Guido Sauter, Thorsten Schlomm, Karl Rohr, and Pavlo Lutsik |
| 264 | 1 | |c 17 January 2025 | |
| 300 | |b Illustrationen | ||
| 300 | |a 14 | ||
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a Computermedien |b c |2 rdamedia | ||
| 338 | |a Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Gesehen am 18.08.2025 | ||
| 520 | |a DNA methylation (DNAm) is a key epigenetic mark that shows profound alterations in cancer. Read-level methylomes enable more in-depth analyses, due to their broad genomic coverage and preservation of rare cell-type signals, compared to summarized data such as 450K/EPIC microarrays. Here, we propose MethylBERT, a Transformer-based model for read-level methylation pattern classification. MethylBERT identifies tumour-derived sequence reads based on their methylation patterns and local genomic sequence, and estimates tumour cell fractions within bulk samples. In our evaluation, MethylBERT outperforms existing deconvolution methods and demonstrates high accuracy regardless of methylation pattern complexity, read length and read coverage. Moreover, we show its applicability to cell-type deconvolution as well as non-invasive early cancer diagnostics using liquid biopsy samples. MethylBERT represents a significant advancement in read-level methylome analysis and enables accurate tumour purity estimation. The broad applicability of MethylBERT will enhance studies on both tumour and non-cancerous bulk methylomes. | ||
| 650 | 4 | |a DNA methylation | |
| 650 | 4 | |a Machine learning | |
| 650 | 4 | |a Tumour biomarkers | |
| 700 | 1 | |a Gerhäuser, Clarissa |d 1964- |e VerfasserIn |0 (DE-588)17267123X |0 (DE-627)697604470 |0 (DE-576)133529568 |4 aut | |
| 700 | 1 | |a Sauter, Guido |e VerfasserIn |4 aut | |
| 700 | 1 | |a Schlomm, Thorsten |e VerfasserIn |4 aut | |
| 700 | 1 | |a Rohr, Karl |e VerfasserIn |0 (DE-588)137474466 |0 (DE-627)695829440 |0 (DE-576)303788593 |4 aut | |
| 700 | 1 | |a Lutsik, Pavlo |e VerfasserIn |0 (DE-588)1176218166 |0 (DE-627)1047372894 |0 (DE-576)516581988 |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Nature Communications |d [London] : Springer Nature, 2010 |g 16(2025), Artikel-ID 788, Seite 1-14 |h Online-Ressource |w (DE-627)626457688 |w (DE-600)2553671-0 |w (DE-576)331555905 |x 2041-1723 |7 nnas |a MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model |
| 773 | 1 | 8 | |g volume:16 |g year:2025 |g elocationid:788 |g pages:1-14 |g extent:14 |a MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model |
| 856 | 4 | 0 | |u https://doi.org/10.1038/s41467-025-55920-z |x Verlag |x Resolving-System |z kostenfrei |3 Volltext |
| 856 | 4 | 0 | |u https://www.nature.com/articles/s41467-025-55920-z |x Verlag |z kostenfrei |3 Volltext |
| 951 | |a AR | ||
| 992 | |a 20250818 | ||
| 993 | |a Article | ||
| 994 | |a 2025 | ||
| 998 | |g 1176218166 |a Lutsik, Pavlo |m 1176218166:Lutsik, Pavlo |d 50000 |e 50000PL1176218166 |k 0/50000/ |p 6 |y j | ||
| 998 | |g 137474466 |a Rohr, Karl |m 137474466:Rohr, Karl |d 160000 |d 160000 |d 160100 |e 160000PR137474466 |e 160000PR137474466 |e 160100PR137474466 |k 0/160000/ |k 0/160000/ |k 1/160000/160100/ |p 5 | ||
| 998 | |g 17267123X |a Gerhäuser, Clarissa |m 17267123X:Gerhäuser, Clarissa |d 50000 |e 50000PG17267123X |k 0/50000/ |p 2 | ||
| 999 | |a KXP-PPN193344603X |e 475873965X | ||
| BIB | |a Y | ||
| SER | |a journal | ||
| JSO | |a {"physDesc":[{"extent":"14 S.","noteIll":"Illustrationen"}],"id":{"doi":["10.1038/s41467-025-55920-z"],"eki":["193344603X"]},"type":{"media":"Online-Ressource","bibl":"article-journal"},"title":[{"title_sort":"MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model","title":"MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model"}],"relHost":[{"pubHistory":["2010-"],"part":{"pages":"1-14","text":"16(2025), Artikel-ID 788, Seite 1-14","volume":"16","extent":"14","year":"2025"},"id":{"issn":["2041-1723"],"zdb":["2553671-0"],"eki":["626457688"]},"type":{"bibl":"periodical","media":"Online-Ressource"},"origin":[{"dateIssuedDisp":"[2010]-","publisher":"Springer Nature ; Nature Publishing Group UK","publisherPlace":"[London] ; [London]"}],"recId":"626457688","title":[{"title_sort":"Nature Communications","title":"Nature Communications"}],"physDesc":[{"extent":"Online-Ressource"}],"language":["eng"],"note":["Gesehen am 13.06.24"],"disp":"MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based modelNature Communications"}],"language":["eng"],"person":[{"family":"Jeong","given":"Yunhee","display":"Jeong, Yunhee","role":"aut"},{"given":"Clarissa","family":"Gerhäuser","role":"aut","display":"Gerhäuser, Clarissa"},{"given":"Guido","family":"Sauter","role":"aut","display":"Sauter, Guido"},{"display":"Schlomm, Thorsten","role":"aut","family":"Schlomm","given":"Thorsten"},{"given":"Karl","family":"Rohr","role":"aut","display":"Rohr, Karl"},{"role":"aut","display":"Lutsik, Pavlo","given":"Pavlo","family":"Lutsik"}],"origin":[{"dateIssuedKey":"2025","dateIssuedDisp":"17 January 2025"}],"recId":"193344603X","name":{"displayForm":["Yunhee Jeong, Clarissa Gerhäuser, Guido Sauter, Thorsten Schlomm, Karl Rohr, and Pavlo Lutsik"]},"note":["Gesehen am 18.08.2025"]} | ||
| SRT | |a JEONGYUNHEMETHYLBERT1720 | ||