Liquid Biopsy: Multi-Analyte and Multi-Omic

• 94 · PDF Liquid biopsy profiling of the tumor microenvironment to determine response to immunotherapy regimens across solid tumors Erin L. Brown, Wubing Zhang, Abul Usmani, Noah Earland, Ayesha Hashmi, Chibuzor Olelewe, Anushka Viswanathan, Pradeep S. Chauhan, Minji Kang, Chloé B. Steen, Hyun Soo Jeon, Susanna Avagyan, Irfan Alahi, Nicholas P. Semenkovich, Matteo Bergsagel, Janella C. Schwab, Chloe M. Sachs, Kaushal Parikh, Faridi Qaium, Peter K. Harris, Antonella Bacchiocchi, Qingyuan Cai, Andrew J. Gentles, Rondell P. Graham, Peter C. Lucas, Ryan C. Fields, Jacob J. Orme, Aaron S. Mansfield, Mario Sznol, Ruth Halaban, David Y. Chen, Aaron M. Newman, Aadel A. Chaudhuri
• 95 · PDF PlasmaCHORD- A machine learning method for identifying clonal hematopoiesis variants in liquid biopsies Daniel J. Rabizadeh, Jenna VanLiere Canzoniero, Ilias Ziakas, Jaime Wehr, Archana Balan, Amna Jamali, Blair V. Landon, Susan Combs Scott, Gavin Pereira, Vincent K. Lam, Christine L. Hann, Christine M. Lovly, Jessica Tao, Patrick M. Forde, Joseph C. Murray, Mark Sausen, Gerrit A. Meijer, Geraldine Vink, Remond J. A. Fijneman, Victor E. Velculescu, Jillian Ayn Phallen, Robert Scharpf, Valsamo Anagnostou
• 96 · PDF Real time multimodal ctDNA and imaging assessment enables adaptive treatment in HPV related oropharyngeal cancer Bill H. Diplas, David N. Brown, Xin Pei, Yingjie Zhu, Achraf Shamseddine, Chiharu Graybill, W. Michael Korn, Emily Westheimer, Luc GT Morris, Richard J. Wong, Sean M. McBride, Alan L. Ho, Heiko Schoder, Eric Sherman, Robert Daber, Nora Katabi, Jorge Reis-Filho, Britta Weigelt, Nancy Lee, Nadeem Riaz
• 98 · PDF Surveillance for recurrent bladder cancer using Oncuria-Monitor, a urine-based multiplex immunoassay Sunao Tanaka, Charles Rosser, Yair Lotan, Menghan Liu, Takashi Kobayashi, Sima P. Porten, Yuki Kita, Yingye Zheng, Zhen Zhang, Hideki Furuya
• 99 · PDF Enhanced detection of EML4-ALK fusions through integration of complex genomic rearrangements in DNA-based assays Aidan C. Manning, Sante Gnerre, Jamie Hutchins
• 100 · PDF Blood-based integration of epigenomic profiles, TMB, and MSI to predict immune checkpoint inhibitor response in advanced non-small cell lung cancer (aNSCLC) Sean Gordon, Jing Wang, Shile Zhang, Marisa Juntilla, Tingting Jiang, Matthew Ellis, Vishnu Ramani, Reagan Barnett, Bernard Herrman, Justin Odegaard, Darya Chudova
• 101 · PDF Fragmentomics-based cancer type and subtype classification in 60,000 cell-free DNA samples Zhenjia Wang, Kevin Cabrera, Yanmei Huang, Daniel S. Lieber, Justin Y. Newberg, Ethan S. Sokol, Zoe Fleischmann
• 102 · PDF TAPS+ enables direct 5mC/5hmC-resolved genomic and methylation profiling of CNS tumors in CSF-derived ctDNA and FFPE Johnathan Rafailov, Eloise Freitag, Aditya Deshpande, Kevin Hadi, Camila Fang, Alexa Oviedo, Emma Hanley, August Kolb, Neha Dhasmana, Hannah Weiss, Chanel Schroff, Yiying Yang, Jonathan Serrano, Kazimierz Wrzeszczynski, Stergios Zacharoulis, Daniel Orringer, Alexandra M. Miller, Marcin Imielinski, Matija Snuderl
• 103 · PDF A multiomic ensemble-based approach for high-specificity detection of clonal hematopoiesis in cfDNA liquid biopsy Patrick C. Fiaux, Mingyang Cai, Jeffrey L. Werbin, Andrew Gross, Che-Yu Lee, Marisa Juntilla, Tingtin Jiang, Reagan Barnett, Errin Lagow, Shile Zhang, Martina Lefterova, Darya Chudova
• 104 · PDF A machine learning approach to predict and mitigate artifact variants for molecular residual disease detection Violeta B. Guthrie, Aamir Shahpurwalla, Daryanaz Dargahi, Onur Sakarya, Spenser Alexander, Tina Wang, Fei Lu, Alexander Hsieh, Ryan Ptashkin, Matthew Rabinowitz, Eser Kirkizlar, Ahmet Zehir
• 105 · PDF Quantification of circulating tumor DNA (ctDNA) in patients using cancer-specific, methylation-based, tissue-free tests for the detection of molecular residual disease (MRD) Princy Parsana, Tzu-Chun Chen, Nathan Liang, Amanda Kennedy, Veronica Rodriguez, Jie Zhang, Boris Gutman, Ehsan Haghshenas, Garima Kushwaha, Breeana L. Mitchell, Minetta Liu, Ehsan Tabari, Joshua Babiarz, Trupti Kawli, Johannes G. Reiter, Matthew Rabinowitz, Alexey Aleshin
• 106 · PDF Integrated plasma multi-omics profiling identifies circulating predictive biomarkers and biological pathways associated with treatment response in NSCLC Laura Heeb, Polina Shichkova, Sandra Schär, Luca Räss, Arthur Viodé, Martin Mehnert, Tobias Treiber, Esther Wortmann, Gordian Adam, Alice Limonciel, Markus Joerger, Jana Musilova, Stefanie Hayoz, Anurag Gupta, Yuehan Feng, Alessandra Curioni-Fontecedro
• 107 · PDF An expanded negative prediction algorithm for actionable mutations utilizing genomic and epigenomic profiling in cfDNA Andrew M. Gross, Hao Wang, Brandy Freschi, Keelia Clemens, Marisa Juntilla, Martina Lefterova, Justin Odegaard, Darya Chudova
• 108 · PDF Fragmentomics powers improved classification of somatic mutations in liquid biopsy Mouses Stamboulian, Anton Valouev, Tingtin Jiang, Jamie Hutchins
• 109 · PDF Integrative analyses of the cfDNA fragmentome and TCR repertoires capture chemo-immunotherapy response in diffuse pleural mesothelioma Jinny Huang, Jennifer Li, James R. White, Shashikant Koul, Gavin Pereira, Nisha Rao, Jennie Yao, Julie R. Brahmer, Robert B. Scharpf, Rachel Karchin, Victor E. Velculescu, Zhouxin Sun, Suresh S. Ramalingam, Patrick M. Forde, Noushin Niknafs, Valsamo (Elsa) K. Anagnostou
• 110 · PDF Clinical utility of landmark ctDNA molecular response as an early indicator of immunotherapy outcomes in lung cancer Jaime Wehr, Noushin Niknafs, Lavanya Sivapalan, Archana Balan, Gavin Pereira, Samira Hosseini-Nami, Iiasha Beadles, Aliyah Pabani, Kristen Marrone, Qing K. Li, Joseph Christopher Murray, Mark Sausen, Bryan Chesnick, Lorenzo Rinaldi, Christine L. Hann, Susan Combs Scott, Josephine Feliciano, Vincent K. Lam, Benjamin Levy, Patrick M. Forde, Julie R. Brahmer, Valsamo (Elsa) Anagnostou
• 111 · PDF Integrated, base-resolution profiling of genetic and epigenetic signatures in cell-free DNA Xingyu Yang, Jing Su, Chen Yang, Xiaoling Li, Si Zhang, Xianrong Chen, Zhihong Zhang, Bingsi Li
• 112 · PDF Analytical performance of an enhanced variant (EV) pipeline for improved circulating tumor DNA (ctDNA) detection in samples with low tumor burden Dina Hafez, Bin Dong, Aamir Shahpurwalla, Bharat Sridhar, Alexander Hsieh, Jordan Feeney, Vu Ngo, Noura Tbeileh, Alexey Aleshin, Matthew Rabinowitz, Himanshu Sethi, Chenlu Hou, Ryan Ptashkin, Eser Kirkizlar, Ahmet Zehir
• 113 · PDF Assessment of sequencing error rates in healthy plasma samples across two whole genome sequencing platforms Aamir Shahpurwalla, Zach Montague, Fei Lu, Spenser Alexander, Garima Goyal, Dina Hafez, Matthew Rabinowitz, Eser Kirkizlar, Ahmet Zehir
• 114 · PDF Unraveling tumor- and tissue-specific gene expression patterns from plasma-derived cfRNA Maria Savchenko, Tatiana Nemchaninova, Alexey Dudakov, Aleksandr Serdiukov, Daria Shafranskaya, Artemiy Nikitin, Anastasia Tarabarova, Desiree Schenk, Alexandr Zaitsev, Anastasia Yudina, Michael F. Goldberg, Alexander Bagaev
• 116 · PDF Comprehensive ctDNA profiling reveals molecular and prognostic landscapes in Korean pan-cancer patients Jiwon Kim, Kyong Hwa Park, Soohyeon Lee, Jwa Hoon Kim, Ju Won Kim, Ji Won Lee, Ji Yoon Lee, You Jin Song, Dayoung Lee, Hyeonmin Jeong, Wooseok Lee, Yoon Ji Choi, Jason K. Sa
• 117 · PDF Single-cell transcriptomic and CNV profiling reveal distinct circulating tumor cell signatures in pancreatic ductal adenocarcinoma Se-Eun Choi, Jihyun Lee, Hyunjung Kee, Moon Jae Chung, Jungwon Kim, Semin Lee
• 118 · PDF Detecting early cancer using cfDNA methylation signatures with nanopore sequencing Yi Yang Hou, Nicholas Cheng, Jared T. Simpson, Philip Awadalla
• 119 · PDF A lightweight self-supervised deep learning framework for automated detection of circulating tumor cells and cancer-associated fibroblasts Hyeongjung Woo, Seonghwan Park, Jungmin Lee, Inkyu Moon, Minseok S. Kim
• 120 · PDF Two integrative molecular subtypes of hepatocellular carcinoma with predictive therapeutic potential: Toward liquid biopsy-guided precision medicine Jiyon Lyu, Woo Young Kwon, Sung Hwan Lee
• 121 · PDF Single stranded ligation enhances the performance of the duet evoC 6-base assay, enhancing value in low DNA input applications including liquid biopsy Tom Charlesworth, Audrey Vandomme, Jens Fullgrabe, Ermira Lleshi, Lidia Prieto-Lafuente, Edyta Bocian-Canepa, Elena Pahiti, Rebecca Ellwood, Mengjie Li, Marjana Lila, Robert Crawford, Robert J. Osborne, Brett Evans
• 122 · PDF Using the 6-base genome for full multiomic analysis of cfDNA through combined methylation and fragmentomic analysis to enhance classification of clinical cancer cfDNA samples Tom Charlesworth, Fabio Puddu, Luke Sarre, Elena Pahiti, Lidia Prieto-Lafuente, Aurelie Modat, Robert Crawford, Simeone Angela, Robert J. Osborne, Steven Ciaramaglia
• 123 · PDF The importance of high analytical sensitivity and specificity of 5 and 6-base assays to enhance the detection of ctDNA in liquid biopsy applications Tom Charlesworth, Luke Sarre, Cillian Nolan, Fabio Puddu, Annelie Johansson, Aurelie Modat, Ermira Lleshi, Simeone Angela, Robert Crawford, Robert J. Osborne, Thao Huynh

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