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For: Benelli M, Romagnoli D, Demichelis F. Tumor purity quantification by clonal DNA methylation signatures. Bioinformatics 2019;34:1642-1649. [PMID: 29325057 DOI: 10.1093/bioinformatics/bty011] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/06/2018] [Indexed: 12/18/2022]  Open
Number Cited by Other Article(s)
1
Jeong Y, Gerhäuser C, Sauter G, Schlomm T, Rohr K, Lutsik P. MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model. Nat Commun 2025;16:788. [PMID: 39824848 PMCID: PMC11742067 DOI: 10.1038/s41467-025-55920-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 01/02/2025] [Indexed: 01/20/2025]  Open
2
Lu Q, Liu Z, Wang X. Inferring tumor purity using multi-omics data based on a uniform machine learning framework MoTP. Brief Bioinform 2024;26:bbaf056. [PMID: 39950745 PMCID: PMC11826339 DOI: 10.1093/bib/bbaf056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Revised: 12/24/2024] [Accepted: 01/27/2025] [Indexed: 02/17/2025]  Open
3
Sasiain I, Nacer D, Aine M, Veerla S, Staaf J. Tumor purity estimated from bulk DNA methylation can be used for adjusting beta values of individual samples to better reflect tumor biology. NAR Genom Bioinform 2024;6:lqae146. [PMID: 39498434 PMCID: PMC11532792 DOI: 10.1093/nargab/lqae146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 10/01/2024] [Accepted: 10/18/2024] [Indexed: 11/07/2024]  Open
4
Franceschini GM, Quaini O, Mizuno K, Orlando F, Ciani Y, Ku SY, Sigouros M, Rothmann E, Alonso A, Benelli M, Nardella C, Auh J, Freeman D, Hanratty B, Adil M, Elemento O, Tagawa ST, Feng FY, Caffo O, Buttigliero C, Basso U, Nelson PS, Corey E, Haffner MC, Attard G, Aparicio A, Demichelis F, Beltran H. Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation. Cancer Discov 2024;14:424-445. [PMID: 38197680 PMCID: PMC10905672 DOI: 10.1158/2159-8290.cd-23-0754] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/31/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024]
5
Kim K, Kim H, Shin I, Noh SJ, Kim JY, Suh KJ, Kim YN, Lee JY, Cho DY, Kim SH, Kim JH, Lee SH, Choi JK. Genomic hypomethylation in cell-free DNA predicts responses to checkpoint blockade in lung and breast cancer. Sci Rep 2023;13:22482. [PMID: 38110532 PMCID: PMC10728099 DOI: 10.1038/s41598-023-49639-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/10/2023] [Indexed: 12/20/2023]  Open
6
Romagnoli D, Nardone A, Galardi F, Paoli M, De Luca F, Biagioni C, Franceschini GM, Pestrin M, Sanna G, Moretti E, Demichelis F, Migliaccio I, Biganzoli L, Malorni L, Benelli M. MIMESIS: minimal DNA-methylation signatures to quantify and classify tumor signals in tissue and cell-free DNA samples. Brief Bioinform 2023;24:6991124. [PMID: 36653909 DOI: 10.1093/bib/bbad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/17/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023]  Open
7
Zhang Z, Wiencke JK, Kelsey KT, Koestler DC, Christensen BC, Salas LA. HiTIMED: hierarchical tumor immune microenvironment epigenetic deconvolution for accurate cell type resolution in the tumor microenvironment using tumor-type-specific DNA methylation data. J Transl Med 2022;20:516. [DOI: 10.1186/s12967-022-03736-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022]  Open
8
Staaf J, Aine M. Tumor purity adjusted beta values improve biological interpretability of high-dimensional DNA methylation data. PLoS One 2022;17:e0265557. [PMID: 36084090 PMCID: PMC9462735 DOI: 10.1371/journal.pone.0265557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/15/2022] [Indexed: 11/19/2022]  Open
9
Intratumor and informatic heterogeneity influence meningioma molecular classification. Acta Neuropathol 2022;144:579-583. [PMID: 35759011 DOI: 10.1007/s00401-022-02455-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 11/01/2022]
10
Choudhury A, Magill ST, Eaton CD, Prager BC, Chen WC, Cady MA, Seo K, Lucas CHG, Casey-Clyde TJ, Vasudevan HN, Liu SJ, Villanueva-Meyer JE, Lam TC, Pu JKS, Li LF, Leung GKK, Swaney DL, Zhang MY, Chan JW, Qiu Z, Martin MV, Susko MS, Braunstein SE, Bush NAO, Schulte JD, Butowski N, Sneed PK, Berger MS, Krogan NJ, Perry A, Phillips JJ, Solomon DA, Costello JF, McDermott MW, Rich JN, Raleigh DR. Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities. Nat Genet 2022;54:649-659. [PMID: 35534562 PMCID: PMC9374001 DOI: 10.1038/s41588-022-01061-8] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 03/22/2022] [Indexed: 02/06/2023]
11
Ferreyra Vega S, Wenger A, Kling T, Olsson Bontell T, Jakola AS, Carén H. Spatial heterogeneity in DNA methylation and chromosomal alterations in diffuse gliomas and meningiomas. Mod Pathol 2022;35:1551-1561. [PMID: 35701666 PMCID: PMC9596370 DOI: 10.1038/s41379-022-01113-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 02/07/2023]
12
Charting differentially methylated regions in cancer with Rocker-meth. Commun Biol 2021;4:1249. [PMID: 34728774 PMCID: PMC8563962 DOI: 10.1038/s42003-021-02761-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022]  Open
13
Verburg N, Barthel FP, Anderson KJ, Johnson KC, Koopman T, Yaqub MM, Hoekstra OS, Lammertsma AA, Barkhof F, Pouwels PJW, Reijneveld JC, Rozemuller AJM, Beliën JAM, Boellaard R, Taylor MD, Das S, Costello JF, Vandertop WP, Wesseling P, de Witt Hamer PC, Verhaak RGW. Spatial concordance of DNA methylation classification in diffuse glioma. Neuro Oncol 2021;23:2054-2065. [PMID: 34049406 PMCID: PMC8643482 DOI: 10.1093/neuonc/noab134] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
14
Koo B, Rhee JK. Prediction of tumor purity from gene expression data using machine learning. Brief Bioinform 2021;22:6265216. [PMID: 33954576 DOI: 10.1093/bib/bbab163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 01/11/2023]  Open
15
Nagaraju GP, Kasa P, Dariya B, Surepalli N, Peela S, Ahmad S. Epigenetics and therapeutic targets in gastrointestinal malignancies. Drug Discov Today 2021;26:2303-2314. [PMID: 33895313 DOI: 10.1016/j.drudis.2021.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/07/2021] [Accepted: 04/11/2021] [Indexed: 12/12/2022]
16
Beltran H, Romanel A, Conteduca V, Casiraghi N, Sigouros M, Franceschini GM, Orlando F, Fedrizzi T, Ku SY, Dann E, Alonso A, Mosquera JM, Sboner A, Xiang J, Elemento O, Nanus DM, Tagawa ST, Benelli M, Demichelis F. Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer. J Clin Invest 2020;130:1653-1668. [PMID: 32091413 DOI: 10.1172/jci131041] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/18/2019] [Indexed: 12/15/2022]  Open
17
Galardi F, De Luca F, Romagnoli D, Biagioni C, Moretti E, Biganzoli L, Di Leo A, Migliaccio I, Malorni L, Benelli M. Cell-Free DNA-Methylation-Based Methods and Applications in Oncology. Biomolecules 2020;10:E1677. [PMID: 33334040 PMCID: PMC7765488 DOI: 10.3390/biom10121677] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022]  Open
18
Lee D, Park Y, Kim S. Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches. Brief Bioinform 2020;22:5896573. [PMID: 34020548 DOI: 10.1093/bib/bbaa188] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/29/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022]  Open
19
Pang S, Wang L, Wang S, Zhang Y, Wang X. PESM: A novel approach of tumor purity estimation based on sample specific methylation sites. J Bioinform Comput Biol 2020;18:2050027. [PMID: 32757807 DOI: 10.1142/s0219720020500274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
20
Azim R, Wang S, Zhou S, Zhong X. Purity estimation from differentially methylated sites using Illumina Infinium methylation microarray data. Cell Cycle 2020;19:2028-2039. [PMID: 32627651 PMCID: PMC7469651 DOI: 10.1080/15384101.2020.1789315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/11/2020] [Accepted: 06/23/2020] [Indexed: 10/23/2022]  Open
21
Liu B, Yang X, Wang T, Lin J, Kang Y, Jia P, Ye K. MEpurity: estimating tumor purity using DNA methylation data. Bioinformatics 2020;35:5298-5300. [PMID: 31297508 DOI: 10.1093/bioinformatics/btz555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 07/04/2019] [Accepted: 07/10/2019] [Indexed: 11/13/2022]  Open
22
Locallo A, Prandi D, Fedrizzi T, Demichelis F. TPES: tumor purity estimation from SNVs. Bioinformatics 2020;35:4433-4435. [PMID: 31099386 DOI: 10.1093/bioinformatics/btz406] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/08/2019] [Accepted: 05/08/2019] [Indexed: 11/12/2022]  Open
23
Fan F, Chen D, Zhao Y, Wang H, Sun H, Sun K. Rapid preliminary purity evaluation of tumor biopsies using deep learning approach. Comput Struct Biotechnol J 2020;18:1746-1753. [PMID: 32695267 PMCID: PMC7352054 DOI: 10.1016/j.csbj.2020.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/18/2020] [Accepted: 06/05/2020] [Indexed: 12/29/2022]  Open
24
McCartney A, Benelli M, Di Leo A. Estimating the magnitude of clinical benefit from (neo)adjuvant chemotherapy in patients with ER-positive/HER2-negative breast cancer. Breast 2020;48 Suppl 1:S81-S84. [PMID: 31839168 DOI: 10.1016/s0960-9776(19)31130-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]  Open
25
Wu A, Cremaschi P, Wetterskog D, Conteduca V, Franceschini GM, Kleftogiannis D, Jayaram A, Sandhu S, Wong SQ, Benelli M, Salvi S, Gurioli G, Feber A, Pereira MB, Wingate AM, Gonzalez-Billalebeitia E, De Giorgi U, Demichelis F, Lise S, Attard G. Genome-wide plasma DNA methylation features of metastatic prostate cancer. J Clin Invest 2020;130:1991-2000. [PMID: 32149736 PMCID: PMC7108919 DOI: 10.1172/jci130887] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 01/08/2020] [Indexed: 12/25/2022]  Open
26
Wang S, Wang L, Zhang Y, Pang S, Wang X. PEIS: a novel approach of tumor purity estimation by identifying information sites through integrating signal based on DNA methylation data. BMC Bioinformatics 2019;20:714. [PMID: 31888435 PMCID: PMC6936156 DOI: 10.1186/s12859-019-3227-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
27
Petralia F, Wang L, Peng J, Yan A, Zhu J, Wang P. A new method for constructing tumor specific gene co-expression networks based on samples with tumor purity heterogeneity. Bioinformatics 2019;34:i528-i536. [PMID: 29949994 PMCID: PMC6022554 DOI: 10.1093/bioinformatics/bty280] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
28
Johann PD, Jäger N, Pfister SM, Sill M. RF_Purify: a novel tool for comprehensive analysis of tumor-purity in methylation array data based on random forest regression. BMC Bioinformatics 2019;20:428. [PMID: 31419933 PMCID: PMC6697926 DOI: 10.1186/s12859-019-3014-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/30/2019] [Indexed: 11/17/2022]  Open
29
Morigi C. Highlights of the 16th St Gallen International Breast Cancer Conference, Vienna, Austria, 20-23 March 2019: personalised treatments for patients with early breast cancer. Ecancermedicalscience 2019;13:924. [PMID: 31281421 PMCID: PMC6546258 DOI: 10.3332/ecancer.2019.924] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Indexed: 12/15/2022]  Open
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