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Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors

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  1. Aleix Prat & Fara Brasó-Maristany & Olga Martínez-Sáez & Esther Sanfeliu & Youli Xia & Meritxell Bellet & Patricia Galván & Débora Martínez & Tomás Pascual & Mercedes Marín-Aguilera & Anna Rodríguez &, 2023. "Circulating tumor DNA reveals complex biological features with clinical relevance in metastatic breast cancer," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  2. Francesc Muyas & Manuel José Gómez Rodriguez & Rita Cascão & Angela Afonso & Carolin M. Sauer & Claudia C. Faria & Isidro Cortés-Ciriano & Ignacio Flores, 2024. "The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  3. Elena Denisenko & Leanne Kock & Adeline Tan & Aaron B. Beasley & Maria Beilin & Matthew E. Jones & Rui Hou & Dáithí Ó Muirí & Sanela Bilic & G. Raj K. A. Mohan & Stuart Salfinger & Simon Fox & Khaing , 2024. "Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  4. Maria Pouyiourou & Bianca N. Kraft & Timothy Wohlfromm & Michael Stahl & Boris Kubuschok & Harald Löffler & Ulrich T. Hacker & Gerdt Hübner & Lena Weiss & Michael Bitzer & Thomas Ernst & Philipp Schüt, 2023. "Nivolumab and ipilimumab in recurrent or refractory cancer of unknown primary: a phase II trial," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  5. Todd P. Knutson & Bin Luo & Anna Kobilka & Jacqueline Lyman & Siyuan Guo & Sarah A. Munro & Yingming Li & Rakesh Heer & Luke Gaughan & Michael J. Morris & Himisha Beltran & Charles J. Ryan & Emmanuel , 2024. "AR alterations inform circulating tumor DNA detection in metastatic castration resistant prostate cancer patients," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  6. Iris van ’t Erve & Bahar Alipanahi & Keith Lumbard & Zachary L. Skidmore & Lorenzo Rinaldi & Laurel K. Millberg & Jacob Carey & Bryan Chesnick & Stephen Cristiano & Carter Portwood & Tony Wu & Erica P, 2024. "Cancer treatment monitoring using cell-free DNA fragmentomes," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  7. Nicolette M. Fonseca & Corinne Maurice-Dror & Cameron Herberts & Wilson Tu & William Fan & Andrew J. Murtha & Catarina Kollmannsberger & Edmond M. Kwan & Karan Parekh & Elena Schönlau & Cecily Q. Bern, 2024. "Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  8. Mireia Crispin-Ortuzar & Ramona Woitek & Marika A. V. Reinius & Elizabeth Moore & Lucian Beer & Vlad Bura & Leonardo Rundo & Cathal McCague & Stephan Ursprung & Lorena Escudero Sanchez & Paula Martin-, 2023. "Integrated radiogenomics models predict response to neoadjuvant chemotherapy in high grade serous ovarian cancer," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  9. Alicia-Marie Conway & Simon P. Pearce & Alexandra Clipson & Steven M. Hill & Francesca Chemi & Dan Slane-Tan & Saba Ferdous & A. S. Md Mukarram Hossain & Katarzyna Kamieniecka & Daniel J. White & Clai, 2024. "A cfDNA methylation-based tissue-of-origin classifier for cancers of unknown primary," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  10. Udit Singhal & Srinivas Nallandhighal & Jeffrey J. Tosoian & Kevin Hu & Trinh M. Pham & Judith Stangl-Kremser & Chia-Jen Liu & Razeen Karim & Komal R. Plouffe & Todd M. Morgan & Marcin Cieslik & Rober, 2024. "Integrative multi-region molecular profiling of primary prostate cancer in men with synchronous lymph node metastasis," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
  11. Anna-Lisa Doebley & Minjeong Ko & Hanna Liao & A. Eden Cruikshank & Katheryn Santos & Caroline Kikawa & Joseph B. Hiatt & Robert D. Patton & Navonil De Sarkar & Katharine A. Collier & Anna C. H. Hoge , 2022. "A framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  12. Mingyun Bae & Gyuhee Kim & Tae-Rim Lee & Jin Mo Ahn & Hyunwook Park & Sook Ryun Park & Ki Byung Song & Eunsung Jun & Dongryul Oh & Jeong-Won Lee & Young Sik Park & Ki-Won Song & Jeong-Sik Byeon & Bo H, 2023. "Integrative modeling of tumor genomes and epigenomes for enhanced cancer diagnosis by cell-free DNA," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  13. Xiao Zhou & Zhen Cheng & Mingyu Dong & Qi Liu & Weiyang Yang & Min Liu & Junzhang Tian & Weibin Cheng, 2022. "Tumor fractions deciphered from circulating cell-free DNA methylation for cancer early diagnosis," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  14. Jonathan C. M. Wan & Dennis Stephens & Lingqi Luo & James R. White & Caitlin M. Stewart & Benoît Rousseau & Dana W. Y. Tsui & Luis A. Diaz, 2022. "Genome-wide mutational signatures in low-coverage whole genome sequencing of cell-free DNA," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  15. Dimitrios V. Vavoulis & Anthony Cutts & Nishita Thota & Jordan Brown & Robert Sugar & Antonio Rueda & Arman Ardalan & Kieran Howard & Flavia Matos Santo & Thippesh Sannasiddappa & Bronwen Miller & Ste, 2025. "Multimodal cell-free DNA whole-genome TAPS is sensitive and reveals specific cancer signals," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
  16. Jorge Gómez Tejeda Zañudo & Romualdo Barroso-Sousa & Esha Jain & Qingchun Jin & Tianyu Li & Jorge E. Buendia-Buendia & Alyssa Pereslete & Daniel L. Abravanel & Arlindo R. Ferreira & Eileen Wrabel & Ka, 2024. "Exemestane plus everolimus and palbociclib in metastatic breast cancer: clinical response and genomic/transcriptomic determinants of resistance in a phase I/II trial," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  17. Naser Ansari-Pour & Yonglan Zheng & Toshio F. Yoshimatsu & Ayodele Sanni & Mustapha Ajani & Jean-Baptiste Reynier & Avraam Tapinos & Jason J. Pitt & Stefan Dentro & Anna Woodard & Padma Sheila Rajagop, 2021. "Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
  18. Hitomi Hosoya & Mia Carleton & Kailee Tanaka & Brian Sworder & Shriya Syal & Bita Sahaf & Alisha M. Maltos & Oscar Silva & Henning Stehr & Vanna Hovanky & George Duran & Tian Zhang & Michaela Liedtke , 2025. "Deciphering response dynamics and treatment resistance from circulating tumor DNA after CAR T-cells in multiple myeloma," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
  19. Jiaqi Liu & Lijun Dai & Qiang Wang & Chenghao Li & Zhichao Liu & Tongyang Gong & Hengyi Xu & Ziqi Jia & Wanyuan Sun & Xinyu Wang & Minyi Lu & Tongxuan Shang & Ning Zhao & Jiahui Cai & Zhigang Li & Hon, 2024. "Multimodal analysis of cfDNA methylomes for early detecting esophageal squamous cell carcinoma and precancerous lesions," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  20. Maksymilian Prondzynski & Paul Berkson & Michael A. Trembley & Yashasvi Tharani & Kevin Shani & Raul H. Bortolin & Mason E. Sweat & Joshua Mayourian & Dogacan Yucel & Albert M. Cordoves & Beatrice Gab, 2024. "Efficient and reproducible generation of human iPSC-derived cardiomyocytes and cardiac organoids in stirred suspension systems," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  21. Kate E. Stanley & Tatjana Jatsenko & Stefania Tuveri & Dhanya Sudhakaran & Lore Lannoo & Kristel Calsteren & Marie Borre & Ilse Parijs & Leen Coillie & Kris Bogaert & Rodrigo Almeida Toledo & Liesbeth, 2024. "Cell type signatures in cell-free DNA fragmentation profiles reveal disease biology," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  22. Harshabad Singh & Kristen E. Lowder & Kevin Kapner & Ronan J. Kelly & Hui Zheng & Nadine Jackson McCleary & Thomas A. Abrams & Jennifer A. Chan & Eileen M. Regan & Samuel J. Klempner & Alison M. Hanni, 2024. "Clinical outcomes and ctDNA correlates for CAPOX BETR: a phase II trial of capecitabine, oxaliplatin, bevacizumab, trastuzumab in previously untreated advanced HER2+ gastroesophageal adenocarcinoma," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  23. Yaping Liu & Sarah C. Reed & Christopher Lo & Atish D. Choudhury & Heather A. Parsons & Daniel G. Stover & Gavin Ha & Gregory Gydush & Justin Rhoades & Denisse Rotem & Samuel Freeman & David W. Katz &, 2024. "FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
  24. Thomas C. Westbrook & Xiangnan Guan & Eva Rodansky & Diana Flores & Chia Jen Liu & Aaron M. Udager & Radhika A. Patel & Michael C. Haffner & Ya-Mei Hu & Duanchen Sun & Tomasz M. Beer & Adam Foye & Rah, 2022. "Transcriptional profiling of matched patient biopsies clarifies molecular determinants of enzalutamide-induced lineage plasticity," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  25. Sebastian Hollizeck & Ning Wang & Stephen Q. Wong & Cassandra Litchfield & Jerick Guinto & Sarah Ftouni & Richard Rebello & Sehrish Kanwal & Ruining Dong & Sean Grimmond & Shahneen Sandhu & Linda Mile, 2024. "Unravelling mutational signatures with plasma circulating tumour DNA," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
  26. Yunyun An & Xin Zhao & Ziteng Zhang & Zhaohua Xia & Mengqi Yang & Li Ma & Yu Zhao & Gang Xu & Shunda Du & Xiang’an Wu & Shuowen Zhang & Xin Hong & Xin Jin & Kun Sun, 2023. "DNA methylation analysis explores the molecular basis of plasma cell-free DNA fragmentation," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
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