Genomic Profiling to Understand Cancer Biology

• 3236 · PDF Genomic landscape of bladder cancer in a turkish cohort: Unveiling the unique mutational spectrum with clinical insights Burcu Yucel, Fatma Zehra Sarı, Dine Guner Mercan, Hüseyin Özgür Kazan, Ceren Sumer, Melike Akman, Demet Akdeniz Ödemiş, Mehmet Baysan, Asıf Yıldırım, Mahmut Gümüş
• 3237 · PDF A multimodal sequencing framework to define viral and host genomic heterogeneity in HPV associated head and neck cancer Ella P. Jackert, Shu-Yun Cheng, Swar Vimawala, Liyang Tang, Daniel Kwon, Niels C. Kokot, Uttam Sinha, Albert Y. Han
• 3238 · PDF Integrity of high-molecular-weight DNA is essential for accurate long-read sequencing and comprehensive cancer genomics Susan M. Magdaleno, Juili Kelvekar, Monica K. Campbell, Alexis Tapanes-Castillo, Hannah E. Saunders
• 3239 · PDF Single assay, tumor-only, somatic SNVs, SVs, and CNVs profiling using nanopore adaptive sampling Sergey Aganezov, Philipp Rescheneder, Rory Sinnott, Sissel Juul
• 3241 · PDF High-fidelity whole genome sequencing from low-input FFPE samples: Enabling accurate tumor-informed MRD assay design through superior variant detection and uniform coverage Vanessa Process, Sushant Khanal, Madan Ambavaram, Sameer Vasantgadkar, Luca Beker, Alaina Villarreal, Jose Gil, Andrew Laneville, Martina Werner, Greg Endress, Ulrich Thomann, Eugenio Daviso
• 3242 · PDF Integrated long-read target enrichment and comprehensive genomic profiling for hematologic malignancies using the SureSelect Cancer Pan Heme assay Brandyn Clark, Adam Janssen, Jeff Fox, Nedda Saremi, Kristi Stephenson, Kelle Hammock, Bahram Arezi
• 3243 · PDF Investigating the value of testing for actionable alterations and circulating tumor DNA in breast and colorectal cancers Gargi D. Basu, Nick Johnson, Angela Deem, Judith Frederick, Terence Wong, Janine R. LoBello, Szabolcs Szelinger, Nishitha Therala, Mark Evans, Miriam Walker, Jean-Paul De La O
• 3244 · PDF Rapid, one-tube sub 10-minute whole genome library prep for cfDNA Ben Krajacich, Seana Lymer, Kevin Green, Xiaodong Qi, Kyle Donohoe, June (Junhua) Zhao, Michael Previte
• 3245 · PDF Scaling liquid biopsy biomarker discovery: Multi-center, analytical validation of high resolution ctDNA profiling using TSO500 v2 on NovaSeq X Plus Gabriela Edwards Faret, Emmanuel Rivière, Silvie Franck, Bart Tegenbos, Lisa Van den Bossche, Joke Verbist, Lien Heyrman, Magdalena Lesnicki, Rachel Raz, Brian Chapman, Eric Harness, Jan Van de Velde, Dirk Goossens, Jurgen Del Favero
• 3246 · PDF SeqF™: evaluation of an affordable nanopore-based assay for decentralized tumor profiling Kimberly A. Holden, Roi Feingersch, Dvir Dahary, Margalit Feiger, Tal Havkin-Solomon, Benjamin M. Cohen, George Way, Shakti Ramkissoon, Marcia Eisenberg, Brian Caveney, Eric Severson, Taylor J. Jensen, Jonathan Williams
• 3247 · PDF Origins of structural variant junctional insertions across >8,000 TCGA whole genomes Youyun Zheng, Gregory Raskind, Sophie Webster, Narmen Azazmeh, Haruna Tomono, Andrew Cherniack, David Lehotzky, Ron Solan, Antonia Kowalewski, Xavi Loinaz, Hansol Park, Vasuki N. Swamy, David Heiman, Samantha Van Seters, Saveliy Belkin, Sam Wiseman, Chunyang Bao, Luis A. Corchete Sanchez, Zachary Everton, Ryul Kim, Beomki Lee, Won-Chul Lee, Chip Stewart, Gengchao Wang, Brian P. Danysh, Young Seok Ju, Esther Rheinbay, Gad Getz, Rameen Beroukhim
• 3248 · PDF Characterization of multiple myeloma genomes with LinkPrep assay enables detection of somatic variation and SV-driven interactions of the 3D genome Lisa Munding, Nathan Becker, Enze Liu, Alexander Fortuna, Jonathan Torchia, Aneta Mikulasova, J. Zachary Sanborn, Brian Walker
• 3249 · PDF Extending a cfDNA-optimized library preparation workflow to mechanically sheared FFPE DNA for high-quality NGS data Sean Tighe, Owen Smith, Tiffany Truong, Tong Liu, Elian Lee, Esteban Toro, Siyuan Chen
• 3250 · PDF Comparative study of human and canine nerve sheath tumors in terms of morphology, prognosis, treatment, epigenetics, transcriptomics, and genomics Jace P. Landry, Angela D. Bhalla, Sharon M. Landers, Rossana Lazcano, Lindsay A. Parker, Tasha M. Miller, Noelle Niemi, Heather G. Lyu, Heather A. Lillemoe, Emily Z. Keung, Christopher P. Scally, Christina L. Roland, Kelly K. Hunt, John M. Slopis, Ian E. McCutcheon, Beth Boudreau, Heather Wilson-Robles, Alexander J. Lazar, Kunal Rai, Dominique J. Wiener, Brian W. Davis, Brandan Wustefeld-Janssens, Keila E. Torres
• 3252 · PDF Simplified genomic profiling using Aspyre Lung solves real-life challenges with limited and poor-quality tissue Elizabeth Gillon-Zhang, Eleanor Gray, Candace King, Ethan Clark, Cory Kiser, Mary Beth Rossi, Julia Brown, Ryan Evans, Katherine Knudsen, James Schaffernoth, Tatiana Yuen, Magdalena Stolarek-Januszkiewicz, Sophie Hackinger, Amanda Green, Kelly Pitts, Honey V. Reddi, Shari Brown, Barnaby Balmforth
• 3253 · PDF A new workflow for FFPE tumor samples enables a streamlined solution for structural variant detection and phasing of somatic mutations through long read sequencing Camille Conner, Ian McLaughlin, Juniper Lake, Davy Lee, Heather Ferrao, Greg Endress, Ulrich Thomann, Martina Werner, Luca Beker
• 3254 · PDF Gene profiling using whole genome analysis of bile tract cancer and its association with clinical factors Toshio Kokuryo, Masaki Sunagawa, Junpei Yamaguchi, Taisuke Baba, Takashi Mizuno, Shunsuke Onoe, Nobuyuki Watanabe, Mihoko Yamada, Shoji Kawakatsu, Tomoki Ebata
• 3255 · PDF Long-read hybrid-capture based targeting of 95 known cancer genes detects large structural and complex variants with a simple bioinformatics workflow and an AI-based clinical interpretation solution. Nathan H. Blewett, Megan Zais, Jingxiao Zhang, Jixin Deng, John DiCarlo, Jamie Hill, Christa Haldrup, Matthew Fosbrink, Jonathan Shaffer
• 3256 · PDF Identification of germline variants associated with somatic mutational profiles in triple-negative breast cancer among African American women Guochong Jia, Jie Ping, Christine B. Ambrosone, John D. Carpten, Julie R. Palmer, Song Yao, Wei Zheng
• 3257 · PDF Improved Variantplex workflow reduces assay time and enhances sensitivity for acute myeloid leukemia targets David Knupp, Michael Washburn
• 3258 · PDF Metatranscriptomic signatures in triple negative breast cancer Roshan Kumar, Golya Shahrokhi, Shafiq Shaikh, Sunday Negedu, Nicole He, Clayton C. Yates, Upender Manne, Akinyemi I. Ojesina
• 3259 · PDF Detection and functional assessment of extrachromosomal DNA amplifications in FFPE lung tumor specimens using Hi-C sequencing Kristin Sikkink, Blake Skrable, Alex Hastie, Anthony Schmitt
• 3260 · PDF Development of multimodal comprehensive genomic profiling panel with on-flow cell hybrid capture Mariam Ashraf, Michelle Baird, Markus Storbeck, Xiaodong Qi, June (Junhua) Zhao, Helene Bauby, Zhong Wu, Jonathan M. Shaffer
• 3261 · PDF Evaluation of FFPE-extracted nucleic acid quality and performance from various commercial extraction kits using contrived multiplexed reference materials Dana J. Ruminski Lowe, Richard Howard, Serene Roque, Praveena Kamineni, Edward S. Davis, Andrew Anfora, Yves Konigshofer, Catherine Huang, Russell K. Garlick
• 3262 · PDF Characterization of NGS reference standards for genetic and epigenetic content Jayanthi Ramprakash, Matthew G. Butler, Ojaswee Dahal, Colt W. Nash, Andrew T. Anfora, Yves Konigshofer
• 3263 · PDF Where sensitivity meets complexity: Electrophoretic assessment of genomic DNA integrity at low concentrations and for FFPE samples using DIN-based analysis Solange Borg, Isabell Priester, Annika Dorn, Tim Butler
• 3264 · PDF Epidemiology meets novel transcriptomics in poorly differentiated endometrial carcinomas Thulo Molefi, Motshedisi Sebitloane, Zodwa Dlamini
• 3265 · PDF An optimized WGS workflow for FFPE samples: Enabling high-confidence variant detection for MRD surveillance Bella Pfeiffer, Gabrie l Lipof, Alaina Villareal, Kristopher Amirault, Sameer Vasantgadkar, Madan Ambavaram, Vanessa Process, Sushant Khanal, Martina Werner, Greg Endress, Ulrich Thomann, Eugenio Daviso

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