Not logged in Error-corrected flow-based sequencing at whole-genome scale and its application to circulating cell-free DNA profiling Cheng, Alexandre Pellan; Widman, Adam J.; Arora, Anushri; Rusinek, Itai; Sossin, Aaron; Rajagopalan, Srinivas; Midler, Nicholas; Hooper, William F.; Murray, Rebecca M.; Halmos, Daniel; Langanay, Theophile; Chu, Hoyin; Inghirami, Giorgio; Potenski, Catherine; Germer, Soren; Marton, Melissa; Manaa, Dina; Helland, Adrienne; Furatero, Rob; Mcclintock, Jaime; Winterkorn, Lara; Steinsnyder, Zoe; Wang, Yohyoh; Alimohamed, Asrar I.; Malbari, Murtaza S.; Saxena, Ashish; Callahan, Margaret K.; Frederick, Dennie T.; Spain, Lavinia; Sigouros, Michael; Manohar, Jyothi; King, Abigail; Wilkes, David; Otilano, John; Elemento, Olivier; Mosquera, Juan Miguel; Jaimovich, Ariel; Lipson, Doron; Turajlic, Samra; Zody, Michael C.; Altorki, Nasser K.; Wolchok, Jedd D.; Postow, Michael A.; Robine, Nicolas; Faltas, Bishoy M.; Boland, Genevieve; Landau, Dan A. Share Save
Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis Zhu, Yizhou; Lee, Hayan; White, Shannon; Weimer, Annika K.; Monte, Emma; Horning, Aaron; Nevins, Stephanie A.; Esplin, Edward D.; Paul, Kristina; Krieger, Gat; Shipony, Zohar; Chiu, Roxanne; Laquindanum, Rozelle; Karathanos, Thomas V.; Chua, Melissa W. Y.; Mills, Meredith; Ladabaum, Uri; Longacre, Teri; Shen, Jeanne; Jaimovich, Ariel; Lipson, Doron; Kundaje, Anshul; Greenleaf, William J.; Curtis, Christina; Ford, James M.; Snyder, Michael P. Share Save
Cost-effective, comprehensive detection of gene fusions from DNA and RNA using the UG100 sequencer Lithwick-Yanai, Gila; Pollock, Sarah; Lebanony, Danit; Ben Simhon, Keren; Benjamin, Sima; Bogumil, David; Iremadze, Nika; Sexton, Matt; Winer, Peleg; Levy, Maya; Gilad, Shlomit; Haimes, Josh; Corbet, Giulia; Pavlica, Jennifer; Lipson, Doron Share Save
Characterizing the genomic landscapes of breast and lung tumors using cost-effective whole genome sequencing Benjamin, Hila; Soifer, Ilya; Shem-Tov, Doron; Levy, Maya; Tuncay, Islam Oguz; Oh, Baek-Lok; Shin, Jong-Yeon; Ju, Young Seok; Lee, Sangmoon; Barad, Omer; Lipson, Doron Share Save
Microsatellite instability (MSI) detection using flow-based sequencing Lithwick-Yanai, Gila; Benjamin, Hila; Cano-Nistal, Jorge; Geisler, Shir; Jaimovich, Ariel; Iremadze, Nika; Kessler, Dror; Soifer, Ilya; Lebanony, Danit; Ben Simhon, Keren; Gilad, Shlomit; Meiri, Eti; Lipson, Doron; Maruvka, Yosef E. Share Save
Advancements in somatic variant calling from UG100 whole genome and whole exome sequencing data Shem-Tov, Doron; Levy, Maya; Hornung, Gil; Soifer, Ilya; Benjamin, Hila; Jaimovich, Ariel; Blattler, Adam; Brandler, William; Sugar, Robert; Kinde, Isaac; Barad, Omer; Lipson, Doron Share Save
Calling somatic variants from UG100 data using deep learning Levy, Maya; Shem-Tov, Doron; Benjamin, Hila; Benjamin, Sima; Soifer, Ilya; Gilad, Shlomit; Lebanony, Danit; Iremadze, Nika; Meiri, Eti; Lipson, Doron; Barad, Omer Share Save
Whole genome error-corrected sequencing for sensitive circulating tumor DNA cancer monitoring Cheng, Alexandre P.; Widman, Adam J.; Arora, Anushri; Rusinek, Itai; Hooper, William F.; Murray, Rebecca; Halmos, Daniel; Langanay, Theophile; Inghirami, Giorgio; Germer, Soren; Marton, Melissa; Helland, Adrienne; Furatero, Rob; McClintock, Jaime; Winterkorn, Lara; Steinsnyder, Zoe; Wang, Yohyoh; Rajagopalan, Srinivas; Alimohamed, Asrar I.; Malbari, Murtaza S.; Saxena, Ashish; Callahan, Margaret K.; Frederick, Dennie T.; Spain, Lavinia; Jaimovich, Ariel; Lipson, Doron; Turajlic, Samra; Zody, Michael C.; Altorki, Nasser K.; Wolchok, Jedd D.; Postow, Michael A.; Robine, Nicolas; Boland, Genevieve; Landau, Dan A. Share Save
Familial adenomatous polyposis epigenetic landscape as a precancer model of colorectal cancer Lee, Hayan; Krieger, Gat; Clark, Tyson; Zhu, Yizhou; Khan, Aziz; Hanson, Casey R.; Horning, Aaron; Esplin, Edward D.; Badu, Mohan; Paul, Kristina; Chiu, Roxanne; Bahmani, Bahareh; Nevins, Stephanie; Weimer, Annika K.; Jaimovich, Ariel; Curtis, Christina; Greenleaf, William; Ford, James M.; Lipson, Doron; Shipony, Zohar; Snyder, Michael P. Share Save
Phylogenetic reconstruction across 303 metastatic tumor samples using Ultima whole-genome sequencing dramatically increases subclonal resolution Hess, Julian; Martin, Elizabeth; Soifer, Ilya; Benjamin, Hila; Miller, Mendy; Cibulskis, Carrie; Danysh, Brian P.; Coole, Matthew; Gabriel, Stacey; Juric, Dejan; Lipson, Doron; Getz, Gad Share Save
Single-cell analysis of CD34-enriched blood cells reveals early prognostic markers of myelodysplastic syndromes Meiri, Eti; Saar-Furer, Nili; Rappoport, Nimrod; Pollock, Sarah; Lithwick-Yanai, Gila; Shipony, Zohar; Iremadze, Nika; Lipson, Doron; Tanay, Amos; Shlush, Liran Share Save
A longitudinal circulating tumor DNA-based model associated with survival in metastatic non-small-cell lung cancer Assaf, Zoe June F.; Zou, Wei; Fine, Alexander D.; Socinski, Mark A.; Young, Amanda; Lipson, Doron; Freidin, Jonathan F.; Kennedy, Mark; Polisecki, Eliana; Nishio, Makoto; Fabrizio, David; Oxnard, Geoffrey R.; Cummings, Craig; Rode, Anja; Reck, Martin; Patil, Namrata S.; Lee, Mark; Shames, David S.; Schulze, Katja Share Save
Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing Simmons, Sean K.; Lithwick-Yanai, Gila; Adiconis, Xian; Oberstrass, Florian; Iremadze, Nika; Geiger-Schuller, Kathryn; Thakore, Pratiksha, I; Frangieh, Chris J.; Barad, Omer; Almogy, Gilad; Rozenblatt-Rosen, Orit; Regev, Aviv; Lipson, Doron; Levin, Joshua Z. Share Save
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Analytical Validation of a Hybrid Capture-Based Next-Generation Sequencing Clinical Assay for Genomic Profiling of Cell-Free Circulating Tumor DNA Clark, Travis A.; Chung, Jon H.; Kennedy, Mark; Hughes, Jason D.; Chennagiri, Niru; Lieber, Daniel S.; Fendler, Bernard; Young, Lauren; Zhao, Mandy; Coyne, Michael; Breese, Virginia; Young, Geneva; Donahue, Amy; Pavlick, Dean; Tsiros, Alyssa; Brennan, Timothy; Zhong, Shan; Mughal, Tariq; Bailey, Mark; He, Jie; Roels, Steven; Frampton, Garrett M.; Spoerke, Jill M.; Gendreau, Steven; Lackner, Mark; Schleifman, Erica; Peters, Eric; Ross, Jeffrey S.; Ali, Siraj M.; Miller, Vincent A.; Gregg, Jeffrey P.; Stephens, Philip J.; Welsh, Allison; Otto, Geoff A.; Lipson, Doron Share Save
Blood-based tumor mutational burden as a predictor of clinical benefit in non-small-cell lung cancer patients treated with atezolizumab Gandara, David R.; Paul, Sarah M.; Kowanetz, Marcin; Schleifman, Erica; Zou, Wei; Li, Yan; Rittmeyer, Achim; Fehrenbacher, Louis; Otto, Geoff; Malboeuf, Christine; Lieber, Daniel S.; Lipson, Doron; Silterra, Jacob; Amler, Lukas; Riehl, Todd; Cummings, Craig A.; Hegde, Priti S.; Sandler, Alan; Ballinger, Marcus; Fabrizio, David; Mok, Tony; Shames, David S. Share Save
A novel PI3K/Aktpathway activation biomarker using comprehensive genomic profiling (CGP) for clinical trial assay He, Yuting; Wongchenko, Matthew; Skoletsky, Joel; Burns, Christine; Li, Yali; Maness, Paula; Kim, Doris; Lipson, Doron; Stephens, Philip; Miller, Vincent; Ross, Jeffrey; Gendreau, Steven; Sun, James Share Save
An ERBB2 follow-on companion diagnostic for clinical care of patients with breast cancer Yip, Wai-ki; Skoletsky, Joel; Ma, Pei; Luo, Jun; Milbury, Coren; Burns, Christine; Truesdell, John; Elvin, Julia; Otto, Geoff; Lipson, Doron; Ross, Jeffrey; Miller, Vincent; Stephens, Philip; Doherty, Michael; Vietz, Christine; Sun, James X.; Li, Yali Share Save
On-treatment changes in circulating tumor DNA (ctDNA) level as an early predictor of clinical outcome in the LOTUS randomized phase 2 trial of 1st-line ipatasertib (IPAT) plus paclitaxel (PAC) for metastatic triple-negative breast cancer (mTNBC) Wongchenko, Matthew J.; Lipson, Doron; Clark, Travis; Kennedy, Mark; Greene, Mandy; Breese, Virginia; Tsiros, Alyssa; Kim, Sung-Bae; Saura, Cristina; Oliveira, Mafalda; Baselga, Jose; Kapp, Amy V.; Chan, Wai Y.; Singel, Stina M.; Gendreau, Steven; Dent, Rebecca Share Save
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