Genomic Approaches to Define Tumor Biology and Clinical Stratification

• 7261 Comprehensive multi-omics profiling reveals molecular heterogeneity and developmental signatures in solid pseudopapillary neoplasm of the pancreas Dong-Ju Shin, Jin Ho Choi, Sang Hyub Lee, In Rae Cho, Kyung-Min Lee, Ji Kon Ryu, Woo Hyun Paik, Jin-Ku Lee
• 7262 A fully automated walkaway system programmed with a novel library prep target enrichment protocol for detection of ultra-low frequency mutations in liquid biopsy and tumor samples Saharnaz Bigdeli, Jan Godoski, Bernd Buehler, Bahram Arezi, Brandyn Clark, Denise Rhodes, schryl castaneda, Bonita Lam, Yun Bao, ji zhu, Gilbert Amparo, Neelima Mehendale, Khine Win, Karen Chapman
• 7263 Identification of molecular alterations in soft tissue sarcoma patients with combined pan-cancer CGP and bespoke sarcoma fusion detection testing Chaugiang Duong, Ryan Bender, Nathan Montgomery, Fernando J. Lopez-Diaz
• 7264 · PDF Molecular differences between ovarian and uterine carcinosarcomas Kwong-Kwok Wong, Yvonne Tsang
• 7265 · PDF MBCproject: multi-omic profiling of metastatic breast cancer evolution through patient-partnered research Diana Garcia-Cortes, Esha Jain, Mary McGillicuddy, Beena S. Thomas, Dewey Kim, Sara Balch, John Navarro, Jakob H. Weiss, Tania G. Hernandez, Michael Dunphy, Brett N. Tomson, Colleen M. Nguyen, Jeremy Johnson, Parker S. Chastain, Sarah Winnicki, Elana Anastasio, Diane M. Diehl, Todd R. Golub, Corrie A. Painter, Nikhil Wagle, Daniel L. Abravanel, Jorge Gomez Tejeda Zanudo
• 7266 Advancing insights into disease biology of non-muscle invasive bladder cancer (NMIBC) through comprehensive multi-omics analysis Siew Kee Low, Yoshiyuki Nagumo, Xuesong Lyu, Jiarui Zhang, Jie Zhao, Kozaburo Tanuma, Satoka Kinase, Karen Urtishak, Neil Beeharry, Shibu THOMAS, Longen Zhou, Hiroyuki Nishiyama
• 7267 · PDF Genomic architecture of prostate cancer in BRCA1/2 germline carriers Taylor B. Crawford, Heena Desai, Jiannong Li, Ryan Hausler, Candace L. Haroldsen, Martin W. Schoen, Timothy R. Rebbeck, Brent S. Rose, Michael J. Kelley, Bruce Montgomery, Nicholas G. Nickols, Matthew B. Rettig, Kosj Yamoah, Isla P. Garraway, Kara N. Maxwell
• 7268 · PDF AI-Driven stratification of cancer patients using The Cancer Genome Atlas whole-genome sequencing data Jonghoon Lee, Chunyang Bao, Hansol Park, Gang-Hee Lee, Yoonsuh Lee, Beomki Lee, David Lehotzky, Ron Solan, Antonia Kowalewski, Xavi Loinaz, Vasuki Narasimha Swamy, David I. Heiman, Samantha Van Seters, Saveliy Belkin, Sam Wiseman, Andrew D. Cherniack, Luis Antonio Corchete Sanchez, Brian P Danysh, Zachary Everton, Chip Stewart, Haruna Tomono, Gengchao Wang, Esther Rheinbay, Gad Getz, Young Seok Ju, Won-Chul Lee, Ryul Kim
• 7269 Development and validation of an optimized, bead-based dual nucleic acid extraction method for high-yield genomic profiling of scarce FFPE tumor specimens Nripesh Prasad, Rebecca Beatty, Rachel Marshall, Chan-Ho Lee, Elizabeth Coffey, Annamaria Szanto
• 7270 · PDF Comprehensive mutation profiling from The Cancer Genome Atlas (TCGA) whole-genome sequencing datasets Chunyang Bao, Hansol Park, Gang-Hee Lee, Ryul Kim, Won-Chul Lee, Jonghoon Lee, Yoonsuh Lee, Beomki Lee, David Lehotzky, Ron Solan, Antonia Kowalewski, Xavi Loinaz, Vasuki Narasimha Swamy, David I. Heiman, Samantha Van Seters, Saveliy Belkin, Sam Wiseman, Andrew D. Cherniack, Luis Antonio Corchete Sanchez, Brian P. Danysh, Zachary Everton, Chip Stewart, Haruna Tomono, Gengchao Wang, Esther Rheinbay, Gad Getz, Young Seok Ju
• 7271 Clinical genomic and functional genomic support for a role of ARID1A loss in progression of desmoplastic small round cell tumor Tom Zhang, Andrea Gazzo, Christopher A. Febres-Aldana, Juan Luis Gomez Martis, Lee Spraggon, Romel Somwar, Marc Ladanyi
• 7273 · PDF Genomic Concordance Patterns Distinguish Multiple Primary Tumors from Metastatic Recurrences Brandie Taylor, Samuel Rivero-Hinojosa, Sandro Satta, Nicole Scott, Faraz Salmasi, Kevin Manage, Stephanie Woods, Charuta C. Palsuledesai, Ekaterina Kalashnikova, Angel Augusto Rodriguez, Minetta C. Liu
• 7274 · PDF Structural variant signature discovery across >8,000 TCGA whole genomes using QuantHDP Gregory Raskind, Youyun Zheng, Anthony Zhao, Julia Sun, Simona Dalin, Siyun Lee, Chunyang Bao, Antonia Kowalewski, Ron Solan, Sam Wiseman, Samantha Van Seters, Saveliy Belkin, David I. Heiman, Chip Stewart, David Lehotzky, Vasuki Narasimha Swamy, Brian P. Danysh, Luis Antonio Corchete Sanchez, Andrew D. Cherniack, Haruna Tomono, Gengchao Wang, Xavi Loinaz, Zachary Everton, Gang-Hee Lee, Won-Chul Lee, Hansol Park, Ryul Kim, Young Seok Ju, Gad Getz, Esther Rheinbay, Rameen Beroukhim
• 7275 Molecular characterization of Latino gastric adenocarcinomas identifies homologous recombination deficiency and TGF-beta pathways as targets for aggressive genomically stable tumors Dennis J. Montoya, Ana Patricia Estrada-Florez, Paul Lott, Katherine Chiu, Javi Villalpando, Shriveda Reddy, Jasmine Diaz Sezati, Fabian Castro, Guadalupe M Polanco-Echeverry, Magdalena Echeverry de Polanco, Javier Torres, Mabel Bohorquez, Luis G. Carvajal-Carmona
• 7276 · PDF Understanding cutaneous immune-related adverse events at single-cell resolution Olivia J. Cheng, Nabeela Khan, Terri Clister, Rebecca Nichols, Khanh Doan, Connor Hall, Rajan Kulkarni, Aik Choon Tan
• 7278 Single-cell RNA-seq analysis reveals distinct tumor and immunosuppressive T-cell phenotypes in CLL patients treated with ibrutinib. Shanmugapriya Thangavadivel, Jami Shaffer, Shrilekha Misra, Samon Benrashid, Britten Gordon, Alexander He, Wantong Li, Konur Oyman, Annika Chura, Shelby Cabrera, Altan Turkoglu, Tzung-Huei Lai, Kerry Rogers, Seema Bhat, John C. Byrd, James S. Blachly, Jennifer A. Woyach, Bradley Blaser
• 7279 · PDF Beyond HLA LOH: Alternative modes of HLA loss are common and vary by cancer type Qidi Yang, Michael Brodie Mumphrey, Wenjin Gu, Taylor Harding, Ariane Lozac'hmeur
• 7280 · PDF Pan-cancer single-cell RNA sequencing analysis refines multiorigin monocyte and macrophage lineages Truc Do Thanh Nguyen, Andrew J. Lee, Hyun Jung Park, Nameeta Shah, Bayrta Mandzhieva, Dong-Sup Lee, Inkyung Jung, Woong-Yang Park
• 7281 Immune senescence and antigen presentation defects define a pre-existing state of BCG unresponsiveness in bladder cancer KyounJun Lee, Jee Soo Park, Myung Eun Lee, Jongchan Kim, Hyoung-oh Jeong, Minseo Kim, Won Sik Ham, Semin Lee
• 7282 A comprehensive multiomics atlas of treatment-naïve breast cancer uncovers co-occurring tumor-immune ecosystems driving immune hot and cold phenotypes Hani Jieun Kim, Beata Kiedik, Kate Harvey, Sehrish Kanwal, James Douglas, John Reeves, Alexander Lobanov, Daniel L. Roden, Sophie Van Der Leij, Mun N. Hui, Aziz Al’Khafaji, Elgene Lim, Sean M. Grimmond, Joakim Lundeberg, Charles M. Perou, Alexander Swarbrick
• 7283 Genomic landscape of IDH-wild-type glioblastoma in a patient treated with TNF-alpha inhibitor: Implications for risk stratification and therapeutic decision-making Suryanarayan Mohapatra, Natarajan Ganesan
• 7284 · PDF Clinically significant cancer variants detected by comprehensive genomic profiling test PGDx elio tissue complete Kenneth C. Valkenburg, Jesse Fox, Jennifer Jackson, Robert Auber, Ann L. Carr, Eric Severson, Taylor Jensen, Shakti Ramkissoon, Marcia Eisenberg, Brian Caveney, Christopher Coldren

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