Figure 6 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer
<p>Concordance of 5hmC patterns in 15 matched tissue and cfDNA samples. <b>A,</b> Tissue map scores for 15 cfDNA samples with matched tissue 5hmC-sequencing available. Predicted ct-fraction was determined using a novel 5hmC-classifier. Patients DTB-149 and DTB-216 had two paired sa...
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2025
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| _version_ | 1849927639688544256 |
|---|---|
| author | Martin Sjöström (14845882) |
| author2 | Shuang G. Zhao (12227671) Samuel Levy (14960811) Meng Zhang (14960814) Yuhong Ning (279537) Raunak Shrestha (14949693) Arian Lundberg (14960817) Cameron Herberts (14960820) Adam Foye (14960823) Rahul Aggarwal (14960826) Junjie T. Hua (14960829) Haolong Li (1532230) Anna Bergamaschi (14960832) Corinne Maurice-Dror (14960835) Ashutosh Maheshwari (14960838) Sujun Chen (3553841) Sarah W.S. Ng (14960841) Wenbin Ye (14960844) Jessica Petricca (14960847) Michael Fraser (522709) Lisa Chesner (14960850) Marc D. Perry (14960853) Thaidy Moreno-Rodriguez (14960856) William S. Chen (14960859) Joshi J. Alumkal (14950518) Jonathan Chou (14957015) Alicia K. Morgans (5600567) Tomasz M. Beer (14960862) George V. Thomas (13187926) Martin Gleave (146446) Paul Lloyd (14960865) Tierney Phillips (4664332) Erin McCarthy (14960868) Michael C. Haffner (14960871) Amina Zoubeidi (14960874) Matti Annala (219688) Robert E. Reiter (14960877) Matthew B. Rettig (14960880) Owen N. Witte (14960883) Lawrence Fong (14960886) Rohit Bose (14960889) Franklin W. Huang (10726678) Jianhua Luo (14960892) Anders Bjartell (199682) Joshua M. Lang (12227674) Nupam P. Mahajan (14960895) Primo N. Lara (13009812) Christopher P. Evans (14960898) Phuoc T. Tran (14960901) Edwin M. Posadas (14960904) Chuan He (178952) Xiao-Long Cui (2020402) Jiaoti Huang (88989) Wilbert Zwart (14960907) Luke A. Gilbert (5513207) Christopher A. Maher (14960910) Paul C. Boutros (14954698) Kim N. Chi (14960913) Alan Ashworth (14957030) Eric J. Small (14960916) Housheng H. He (14960919) Alexander W. Wyatt (14960922) David A. Quigley (14957012) Felix Y. Feng (14845891) |
| author2_role | author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| author_facet | Martin Sjöström (14845882) Shuang G. Zhao (12227671) Samuel Levy (14960811) Meng Zhang (14960814) Yuhong Ning (279537) Raunak Shrestha (14949693) Arian Lundberg (14960817) Cameron Herberts (14960820) Adam Foye (14960823) Rahul Aggarwal (14960826) Junjie T. Hua (14960829) Haolong Li (1532230) Anna Bergamaschi (14960832) Corinne Maurice-Dror (14960835) Ashutosh Maheshwari (14960838) Sujun Chen (3553841) Sarah W.S. Ng (14960841) Wenbin Ye (14960844) Jessica Petricca (14960847) Michael Fraser (522709) Lisa Chesner (14960850) Marc D. Perry (14960853) Thaidy Moreno-Rodriguez (14960856) William S. Chen (14960859) Joshi J. Alumkal (14950518) Jonathan Chou (14957015) Alicia K. Morgans (5600567) Tomasz M. Beer (14960862) George V. Thomas (13187926) Martin Gleave (146446) Paul Lloyd (14960865) Tierney Phillips (4664332) Erin McCarthy (14960868) Michael C. Haffner (14960871) Amina Zoubeidi (14960874) Matti Annala (219688) Robert E. Reiter (14960877) Matthew B. Rettig (14960880) Owen N. Witte (14960883) Lawrence Fong (14960886) Rohit Bose (14960889) Franklin W. Huang (10726678) Jianhua Luo (14960892) Anders Bjartell (199682) Joshua M. Lang (12227674) Nupam P. Mahajan (14960895) Primo N. Lara (13009812) Christopher P. Evans (14960898) Phuoc T. Tran (14960901) Edwin M. Posadas (14960904) Chuan He (178952) Xiao-Long Cui (2020402) Jiaoti Huang (88989) Wilbert Zwart (14960907) Luke A. Gilbert (5513207) Christopher A. Maher (14960910) Paul C. Boutros (14954698) Kim N. Chi (14960913) Alan Ashworth (14957030) Eric J. Small (14960916) Housheng H. He (14960919) Alexander W. Wyatt (14960922) David A. Quigley (14957012) Felix Y. Feng (14845891) |
| author_role | author |
| dc.creator.none.fl_str_mv | Martin Sjöström (14845882) Shuang G. Zhao (12227671) Samuel Levy (14960811) Meng Zhang (14960814) Yuhong Ning (279537) Raunak Shrestha (14949693) Arian Lundberg (14960817) Cameron Herberts (14960820) Adam Foye (14960823) Rahul Aggarwal (14960826) Junjie T. Hua (14960829) Haolong Li (1532230) Anna Bergamaschi (14960832) Corinne Maurice-Dror (14960835) Ashutosh Maheshwari (14960838) Sujun Chen (3553841) Sarah W.S. Ng (14960841) Wenbin Ye (14960844) Jessica Petricca (14960847) Michael Fraser (522709) Lisa Chesner (14960850) Marc D. Perry (14960853) Thaidy Moreno-Rodriguez (14960856) William S. Chen (14960859) Joshi J. Alumkal (14950518) Jonathan Chou (14957015) Alicia K. Morgans (5600567) Tomasz M. Beer (14960862) George V. Thomas (13187926) Martin Gleave (146446) Paul Lloyd (14960865) Tierney Phillips (4664332) Erin McCarthy (14960868) Michael C. Haffner (14960871) Amina Zoubeidi (14960874) Matti Annala (219688) Robert E. Reiter (14960877) Matthew B. Rettig (14960880) Owen N. Witte (14960883) Lawrence Fong (14960886) Rohit Bose (14960889) Franklin W. Huang (10726678) Jianhua Luo (14960892) Anders Bjartell (199682) Joshua M. Lang (12227674) Nupam P. Mahajan (14960895) Primo N. Lara (13009812) Christopher P. Evans (14960898) Phuoc T. Tran (14960901) Edwin M. Posadas (14960904) Chuan He (178952) Xiao-Long Cui (2020402) Jiaoti Huang (88989) Wilbert Zwart (14960907) Luke A. Gilbert (5513207) Christopher A. Maher (14960910) Paul C. Boutros (14954698) Kim N. Chi (14960913) Alan Ashworth (14957030) Eric J. Small (14960916) Housheng H. He (14960919) Alexander W. Wyatt (14960922) David A. Quigley (14957012) Felix Y. Feng (14845891) |
| dc.date.none.fl_str_mv | 2025-11-24T22:43:37Z |
| dc.identifier.none.fl_str_mv | 10.1158/0008-5472.30699406 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/figure/Figure_6_from_The_5-Hydroxymethylcytosine_Landscape_of_Prostate_Cancer/30699406 |
| dc.rights.none.fl_str_mv | CC BY info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Cancer Cancer Risk Factors Molecular and Cellular Biology Methods and Technology Epigenetics Epigenomics Genitourinary Cancers Prostate cancer Liquid Biopsy |
| dc.title.none.fl_str_mv | Figure 6 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer |
| dc.type.none.fl_str_mv | Image Figure info:eu-repo/semantics/publishedVersion image |
| description | <p>Concordance of 5hmC patterns in 15 matched tissue and cfDNA samples. <b>A,</b> Tissue map scores for 15 cfDNA samples with matched tissue 5hmC-sequencing available. Predicted ct-fraction was determined using a novel 5hmC-classifier. Patients DTB-149 and DTB-216 had two paired samples at two different time points available with 5hmC sequencing, but not other data modalities and were thus included in this paired analysis but not in integrative analyses. <b>B,</b> Scatterplot for tissue map 5hmC GI-score in tissue and cfDNA for the 15 matched pairs of samples. <b>C,</b> Spearman correlation between tissue 5hmC gene body counts and cfDNA gene body counts. Blue dashed line, median correlation. <b>D,</b> Box and whiskers plot showing correlation for 5hmC gene body counts in tissue and cfDNA for matched pairs (<i>N</i> = 15, blue box) and for average correlation to nonmatched pairs (<i>N</i> = 15, red box). <b>E,</b> Scatterplot for sample similarity of matched tissue and cfDNA samples (<i>N</i> = 15) measured by Spearman correlation for 5hmC gene body counts of protein coding genes and predicted ct-fraction by 5hmC levels. <b>F,</b> Hierarchical clustering of matched 5hmC gene body counts in tissue and cfDNA samples using the top 10% most variable genes. Scaling (z-scores) was performed separately for cfDNA and tissue-derived samples. ct-fraction/purity is estimated from 5hmC-sequencing (cfDNA samples) or from WGS (tissue). Boxplot shows median with hinges at 25th and 75th percentiles and whiskers at largest/smallest value within 1.5 × interquartile range.</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_1e2058761543d2f1de05729bfc140d8e |
| identifier_str_mv | 10.1158/0008-5472.30699406 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/30699406 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY |
| spelling | Figure 6 from The 5-Hydroxymethylcytosine Landscape of Prostate CancerMartin Sjöström (14845882)Shuang G. Zhao (12227671)Samuel Levy (14960811)Meng Zhang (14960814)Yuhong Ning (279537)Raunak Shrestha (14949693)Arian Lundberg (14960817)Cameron Herberts (14960820)Adam Foye (14960823)Rahul Aggarwal (14960826)Junjie T. Hua (14960829)Haolong Li (1532230)Anna Bergamaschi (14960832)Corinne Maurice-Dror (14960835)Ashutosh Maheshwari (14960838)Sujun Chen (3553841)Sarah W.S. Ng (14960841)Wenbin Ye (14960844)Jessica Petricca (14960847)Michael Fraser (522709)Lisa Chesner (14960850)Marc D. Perry (14960853)Thaidy Moreno-Rodriguez (14960856)William S. Chen (14960859)Joshi J. Alumkal (14950518)Jonathan Chou (14957015)Alicia K. Morgans (5600567)Tomasz M. Beer (14960862)George V. Thomas (13187926)Martin Gleave (146446)Paul Lloyd (14960865)Tierney Phillips (4664332)Erin McCarthy (14960868)Michael C. Haffner (14960871)Amina Zoubeidi (14960874)Matti Annala (219688)Robert E. Reiter (14960877)Matthew B. Rettig (14960880)Owen N. Witte (14960883)Lawrence Fong (14960886)Rohit Bose (14960889)Franklin W. Huang (10726678)Jianhua Luo (14960892)Anders Bjartell (199682)Joshua M. Lang (12227674)Nupam P. Mahajan (14960895)Primo N. Lara (13009812)Christopher P. Evans (14960898)Phuoc T. Tran (14960901)Edwin M. Posadas (14960904)Chuan He (178952)Xiao-Long Cui (2020402)Jiaoti Huang (88989)Wilbert Zwart (14960907)Luke A. Gilbert (5513207)Christopher A. Maher (14960910)Paul C. Boutros (14954698)Kim N. Chi (14960913)Alan Ashworth (14957030)Eric J. Small (14960916)Housheng H. He (14960919)Alexander W. Wyatt (14960922)David A. Quigley (14957012)Felix Y. Feng (14845891)CancerCancer Risk FactorsMolecular and Cellular BiologyMethods and TechnologyEpigeneticsEpigenomicsGenitourinary CancersProstate cancerLiquid Biopsy<p>Concordance of 5hmC patterns in 15 matched tissue and cfDNA samples. <b>A,</b> Tissue map scores for 15 cfDNA samples with matched tissue 5hmC-sequencing available. Predicted ct-fraction was determined using a novel 5hmC-classifier. Patients DTB-149 and DTB-216 had two paired samples at two different time points available with 5hmC sequencing, but not other data modalities and were thus included in this paired analysis but not in integrative analyses. <b>B,</b> Scatterplot for tissue map 5hmC GI-score in tissue and cfDNA for the 15 matched pairs of samples. <b>C,</b> Spearman correlation between tissue 5hmC gene body counts and cfDNA gene body counts. Blue dashed line, median correlation. <b>D,</b> Box and whiskers plot showing correlation for 5hmC gene body counts in tissue and cfDNA for matched pairs (<i>N</i> = 15, blue box) and for average correlation to nonmatched pairs (<i>N</i> = 15, red box). <b>E,</b> Scatterplot for sample similarity of matched tissue and cfDNA samples (<i>N</i> = 15) measured by Spearman correlation for 5hmC gene body counts of protein coding genes and predicted ct-fraction by 5hmC levels. <b>F,</b> Hierarchical clustering of matched 5hmC gene body counts in tissue and cfDNA samples using the top 10% most variable genes. Scaling (z-scores) was performed separately for cfDNA and tissue-derived samples. ct-fraction/purity is estimated from 5hmC-sequencing (cfDNA samples) or from WGS (tissue). Boxplot shows median with hinges at 25th and 75th percentiles and whiskers at largest/smallest value within 1.5 × interquartile range.</p>2025-11-24T22:43:37ZImageFigureinfo:eu-repo/semantics/publishedVersionimage10.1158/0008-5472.30699406https://figshare.com/articles/figure/Figure_6_from_The_5-Hydroxymethylcytosine_Landscape_of_Prostate_Cancer/30699406CC BYinfo:eu-repo/semantics/openAccessoai:figshare.com:article/306994062025-11-24T22:43:37Z |
| spellingShingle | Figure 6 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer Martin Sjöström (14845882) Cancer Cancer Risk Factors Molecular and Cellular Biology Methods and Technology Epigenetics Epigenomics Genitourinary Cancers Prostate cancer Liquid Biopsy |
| status_str | publishedVersion |
| title | Figure 6 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer |
| title_full | Figure 6 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer |
| title_fullStr | Figure 6 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer |
| title_full_unstemmed | Figure 6 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer |
| title_short | Figure 6 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer |
| title_sort | Figure 6 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer |
| topic | Cancer Cancer Risk Factors Molecular and Cellular Biology Methods and Technology Epigenetics Epigenomics Genitourinary Cancers Prostate cancer Liquid Biopsy |