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1,864 results on '"Schultz, Nikolaus"'

1. Autonomous Artificial Intelligence Agents for Clinical Decision Making in Oncology

Author

Ferber, Dyke, Nahhas, Omar S. M. El, Wölflein, Georg, Wiest, Isabella C., Clusmann, Jan, Leßman, Marie-Elisabeth, Foersch, Sebastian, Lammert, Jacqueline, Tschochohei, Maximilian, Jäger, Dirk, Salto-Tellez, Manuel, Schultz, Nikolaus, Truhn, Daniel, and Kather, Jakob Nikolas

Subjects
Computer Science - Artificial Intelligence, Quantitative Biology - Tissues and Organs
Abstract

Multimodal artificial intelligence (AI) systems have the potential to enhance clinical decision-making by interpreting various types of medical data. However, the effectiveness of these models across all medical fields is uncertain. Each discipline presents unique challenges that need to be addressed for optimal performance. This complexity is further increased when attempting to integrate different fields into a single model. Here, we introduce an alternative approach to multimodal medical AI that utilizes the generalist capabilities of a large language model (LLM) as a central reasoning engine. This engine autonomously coordinates and deploys a set of specialized medical AI tools. These tools include text, radiology and histopathology image interpretation, genomic data processing, web searches, and document retrieval from medical guidelines. We validate our system across a series of clinical oncology scenarios that closely resemble typical patient care workflows. We show that the system has a high capability in employing appropriate tools (97%), drawing correct conclusions (93.6%), and providing complete (94%), and helpful (89.2%) recommendations for individual patient cases while consistently referencing relevant literature (82.5%) upon instruction. This work provides evidence that LLMs can effectively plan and execute domain-specific models to retrieve or synthesize new information when used as autonomous agents. This enables them to function as specialist, patient-tailored clinical assistants. It also simplifies regulatory compliance by allowing each component tool to be individually validated and approved. We believe, that our work can serve as a proof-of-concept for more advanced LLM-agents in the medical domain., Comment: 91 pages, 2 Figures

Published
2024

2. Automated real-world data integration improves cancer outcome prediction

Author

Jee, Justin, Fong, Christopher, Pichotta, Karl, Tran, Thinh Ngoc, Luthra, Anisha, Waters, Michele, Fu, Chenlian, Altoe, Mirella, Liu, Si-Yang, Maron, Steven B., Ahmed, Mehnaj, Kim, Susie, Pirun, Mono, Chatila, Walid K., de Bruijn, Ino, Pasha, Arfath, Kundra, Ritika, Gross, Benjamin, Mastrogiacomo, Brooke, Aprati, Tyler J., Liu, David, Gao, JianJiong, Capelletti, Marzia, Pekala, Kelly, Loudon, Lisa, Perry, Maria, Bandlamudi, Chaitanya, Donoghue, Mark, Satravada, Baby Anusha, Martin, Axel, Shen, Ronglai, Chen, Yuan, Brannon, A. Rose, Chang, Jason, Braunstein, Lior, Li, Anyi, Safonov, Anton, Stonestrom, Aaron, Sanchez-Vela, Pablo, Wilhelm, Clare, Robson, Mark, Scher, Howard, Ladanyi, Marc, Reis-Filho, Jorge S., Solit, David B., Jones, David R., Gomez, Daniel, Yu, Helena, Chakravarty, Debyani, Yaeger, Rona, Abida, Wassim, Park, Wungki, O’Reilly, Eileen M., Garcia-Aguilar, Julio, Socci, Nicholas, Sanchez-Vega, Francisco, Carrot-Zhang, Jian, Stetson, Peter D., Levine, Ross, Rudin, Charles M., Berger, Michael F., Shah, Sohrab P., Schrag, Deborah, Razavi, Pedram, Kehl, Kenneth L., Li, Bob T., Riely, Gregory J., and Schultz, Nikolaus

Published
2024
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5. DNA liquid biopsy-based prediction of cancer-associated venous thromboembolism

Author

Jee, Justin, Brannon, A. Rose, Singh, Rohan, Derkach, Andriy, Fong, Christopher, Lee, Adrian, Gray, Lauren, Pichotta, Karl, Luthra, Anisha, Diosdado, Monica, Haque, Mohammad, Guo, Jiannan, Hernandez, Jennifer, Garg, Kavita, Wilhelm, Clare, Arcila, Maria E., Pavlakis, Nick, Clarke, Stephen, Shah, Sohrab P., Razavi, Pedram, Reis-Filho, Jorge S., Ladanyi, Marc, Schultz, Nikolaus, Zwicker, Jeffrey, Berger, Michael F., Li, Bob T., and Mantha, Simon

Published
2024
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7. The DACH1 gene is frequently deleted in prostate cancer, restrains prostatic intraepithelial neoplasia, decreases DNA damage repair, and predicts therapy responses.

Author

Li, Zhiping, Jiao, Xuanmao, Robertson, A, Di Sante, Gabriele, Ashton, Anthony, DiRocco, Agnese, Wang, Min, Zhao, Jun, Addya, Sankar, Wang, Chenguang, McCue, Peter, South, Andrew, Cordon-Cardo, Carlos, Liu, Runzhi, Patel, Kishan, Hamid, Rasha, Parmar, Jorim, DuHadaway, James, Jones, Steven, Casimiro, Mathew, Schultz, Nikolaus, Kossenkov, Andrew, Phoon, Lai, Chen, Hao, Lan, Li, Sun, Yunguang, Iczkowski, Kenneth, Rui, Hallgeir, and Pestell, Richard

Subjects
Male, Humans, Prostatic Intraepithelial Neoplasia, Prostatic Neoplasms, Prostate, DNA Damage, Transforming Growth Factor beta, Eye Proteins, Transcription Factors
Abstract

Prostate cancer (PCa), the second leading cause of death in American men, includes distinct genetic subtypes with distinct therapeutic vulnerabilities. The DACH1 gene encodes a winged helix/Forkhead DNA-binding protein that competes for binding to FOXM1 sites. Herein, DACH1 gene deletion within the 13q21.31-q21.33 region occurs in up to 18% of human PCa and was associated with increased AR activity and poor prognosis. In prostate OncoMice, prostate-specific deletion of the Dach1 gene enhanced prostatic intraepithelial neoplasia (PIN), and was associated with increased TGFβ activity and DNA damage. Reduced Dach1 increased DNA damage in response to genotoxic stresses. DACH1 was recruited to sites of DNA damage, augmenting recruitment of Ku70/Ku80. Reduced Dach1 expression was associated with increased homology directed repair and resistance to PARP inhibitors and TGFβ kinase inhibitors. Reduced Dach1 expression may define a subclass of PCa that warrants specific therapies.

Published
2023

10. Distinct tumor architectures and microenvironments for the initiation of breast cancer metastasis in the brain

Author

Gan, Siting, Macalinao, Danilo G., Shahoei, Sayyed Hamed, Tian, Lin, Jin, Xin, Basnet, Harihar, Bibby, Catherine, Muller, James T., Atri, Pranita, Seffar, Evan, Chatila, Walid, Karacay, Ali, Chanda, Pharto, Hadjantonakis, Anna-Katerina, Schultz, Nikolaus, Brogi, Edi, Bale, Tejus A., Moss, Nelson S., Murali, Rajmohan, Pe’er, Dana, and Massagué, Joan

Published
2024
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11. Distinct clinical outcomes and biological features of specific KRAS mutants in human pancreatic cancer

Author

McIntyre, Caitlin A., Grimont, Adrien, Park, Jiwoon, Meng, Yinuo, Sisso, Whitney J., Seier, Kenneth, Jang, Gun Ho, Walch, Henry, Aveson, Victoria G., Falvo, David J., Fall, William B., Chan, Christopher W., Wenger, Andrew, Ecker, Brett L., Pulvirenti, Alessandra, Gelfer, Rebecca, Zafra, Maria Paz, Schultz, Nikolaus, Park, Wungki, O’Reilly, Eileen M., Houlihan, Shauna L., Alonso, Alicia, Hissong, Erika, Church, George M., Mason, Christopher E., Siolas, Despina, Notta, Faiyaz, Gonen, Mithat, Dow, Lukas E., Jarnagin, William R., and Chandwani, Rohit

Published
2024
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13. Integrated clinical and genomic analysis identifies driver events and molecular evolution of colitis-associated cancers

Author

Chatila, Walid K., Walch, Henry, Hechtman, Jaclyn F., Moyer, Sydney M., Sgambati, Valeria, Faleck, David M., Srivastava, Amitabh, Tang, Laura, Benhamida, Jamal, Ismailgeci, Dorina, Campos, Carl, Wu, Fan, Chang, Qing, Vakiani, Efsevia, de Stanchina, Elisa, Weiser, Martin R., Widmar, Maria, Yantiss, Rhonda K., Shah, Manish A., Bass, Adam J., Stadler, Zsofia K., Katz, Lior H., Mellinghoff, Ingo K., Sethi, Nilay S., Schultz, Nikolaus, Ganesh, Karuna, Kelsen, David, and Yaeger, Rona

Published
2023
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14. MITI Minimum Information guidelines for highly multiplexed tissue images

Author

Schapiro, Denis, Yapp, Clarence, Sokolov, Artem, Reynolds, Sheila M., Chen, Yu-An, Sudar, Damir, Xie, Yubin, Muhlich, Jeremy L., Arias-Camison, Raquel, Arena, Sarah, Taylor, Adam J., Nikolov, Milen, Tyler, Madison, Lin, Jia-Ren, Burlingame, Erik A., Network, Human Tumor Atlas, Chang, Young H., Farhi, Samouil L, Thorsson, Vésteinn, Venkatamohan, Nithya, Drewes, Julia L., Pe'er, Dana, Gutman, David A., Herrmann, Markus D., Gehlenborg, Nils, Bankhead, Peter, Roland, Joseph T., Herndon, John M., Snyder, Michael P., Angelo, Michael, Nolan, Garry, Swedlow, Jason R., Schultz, Nikolaus, Merrick, Daniel T., Mazzilli, Sarah A., Cerami, Ethan, Rodig, Scott J., Santagata, Sandro, and Sorger, Peter K.

Subjects
Quantitative Biology - Other Quantitative Biology, Electrical Engineering and Systems Science - Image and Video Processing
Abstract

The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that guide data deposition, curation and release. We describe a Minimum Information about highly multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology.

Published
2021

15. Natural History and Genomic Landscape of Chemotherapy-Resistant Muscle-Invasive Bladder Cancer

Author

Lenis, Andrew T., Whiting, Karissa, Ravichandran, Vignesh, Tallman, Jacob E., Alam, Syed M., Chu, Carissa E., Jesus Escano, Manual De, Bochner, Emily, Katims, Andrew, Reisz, Peter A., Truong, Hong, Clinton, Timothy N., Telis, Leon, Dason, Shawn, McPherson, Victor, Teo, Min Yuen, Funt, Samuel, Aggen, David, Goh, Alvin C., Donahue, Timothy F., Cha, Eugene K., Donat, S. Machele, Herr, Harry W., Dalbagni, Guido, Schultz, Nikolaus, Berger, Michael F., Bajorin, Dean F., Rosenberg, Jonathan E., Bochner, Bernard H., Ostrovnaya, Irina, Al-Ahmadie, Hikmat, Solit, David B., Iyer, Gopa, and Pietzak, Eugene J.

Published
2024
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16. The context-specific role of germline pathogenicity in tumorigenesis

Author

Srinivasan, Preethi, Bandlamudi, Chaitanya, Jonsson, Philip, Kemel, Yelena, Chavan, Shweta S, Richards, Allison L, Penson, Alexander V, Bielski, Craig M, Fong, Christopher, Syed, Aijazuddin, Jayakumaran, Gowtham, Prasad, Meera, Hwee, Jason, Sumer, Selcuk Onur, de Bruijn, Ino, Li, Xiang, Gao, JianJiong, Schultz, Nikolaus, Cambria, Roy, Galle, Jesse, Mukherjee, Semanti, Vijai, Joseph, Cadoo, Karen A, Carlo, Maria I, Walsh, Michael F, Mandelker, Diana, Ceyhan-Birsoy, Ozge, Shia, Jinru, Zehir, Ahmet, Ladanyi, Marc, Hyman, David M, Zhang, Liying, Offit, Kenneth, Robson, Mark E, Solit, David B, Stadler, Zsofia K, Berger, Michael F, and Taylor, Barry S

Subjects
Biological Sciences, Genetics, Human Genome, Rare Diseases, Cancer, Clinical Research, 2.1 Biological and endogenous factors, Aetiology, Carcinogenesis, DNA Copy Number Variations, DNA Mismatch Repair, Genetic Predisposition to Disease, Germ-Line Mutation, Heterozygote, Humans, Neoplasms, Phenotype, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Human cancers arise from environmental, heritable and somatic factors, but how these mechanisms interact in tumorigenesis is poorly understood. Studying 17,152 prospectively sequenced patients with cancer, we identified pathogenic germline variants in cancer predisposition genes, and assessed their zygosity and co-occurring somatic alterations in the concomitant tumors. Two major routes to tumorigenesis were apparent. In carriers of pathogenic germline variants in high-penetrance genes (5.1% overall), lineage-dependent patterns of biallelic inactivation led to tumors exhibiting mechanism-specific somatic phenotypes and fewer additional somatic oncogenic drivers. Nevertheless, 27% of cancers in these patients, and most tumors in patients with pathogenic germline variants in lower-penetrance genes, lacked particular hallmarks of tumorigenesis associated with the germline allele. The dependence of tumors on pathogenic germline variants is variable and often dictated by both penetrance and lineage, a finding with implications for clinical management.

Published
2021

17. Pathogenic germline variants in non-BRCA1/2 homologous recombination genes in ovarian cancer: Analysis of tumor phenotype and survival

Author

Kahn, Ryan M., Selenica, Pier, Boerner, Thomas, Long Roche, Kara, Xiao, Yonghong, Sia, Tiffany Y., Maio, Anna, Kemel, Yelena, Sheehan, Margaret, Salo-Mullen, Erin, Breen, Kelsey E., Zhou, Qin, Iasonos, Alexia, Grisham, Rachel N., O’Cearbhaill, Roisin E., Chi, Dennis S., Berger, Michael F., Kundra, Ritika, Schultz, Nikolaus, Ellenson, Lora H., Stadler, Zsofia K., Offit, Kenneth, Mandelker, Diana, Aghajanian, Carol, Zamarin, Dmitriy, Sabbatini, Paul, Weigelt, Britta, and Liu, Ying L.

Published
2024
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18. Prospective pan-cancer germline testing using MSK-IMPACT informs clinical translation in 751 patients with pediatric solid tumors

Author

Fiala, Elise M, Jayakumaran, Gowtham, Mauguen, Audrey, Kennedy, Jennifer A, Bouvier, Nancy, Kemel, Yelena, Fleischut, Megan Harlan, Maio, Anna, Salo-Mullen, Erin E, Sheehan, Margaret, Arnold, Angela G, Latham, Alicia, Carlo, Maria I, Cadoo, Karen, Murkherjee, Semanti, Slotkin, Emily K, Trippett, Tanya, Glade Bender, Julia, Meyers, Paul A, Wexler, Leonard, Dela Cruz, Filemon S, Cheung, Nai-Kong, Basu, Ellen, Kentsis, Alex, Ortiz, Michael, Francis, Jasmine H, Dunkel, Ira J, Khakoo, Yasmin, Gilheeney, Stephen, Farouk Sait, Sameer, Forlenza, Christopher J, Sulis, Maria, Karajannis, Matthias, Modak, Shakeel, Gerstle, Justin T, Heaton, Todd E, Roberts, Stephen, Yang, Ciyu, Jairam, Sowmya, Vijai, Joseph, Topka, Sabine, Friedman, Danielle N, Stadler, Zsofia K, Robson, Mark, Berger, Michael F, Schultz, Nikolaus, Ladanyi, Marc, O’Reilly, Richard J, Abramson, David H, Ceyhan-Birsoy, Ozge, Zhang, Liying, Mandelker, Diana, Shukla, Neerav N, Kung, Andrew L, Offit, Kenneth, Zehir, Ahmet, and Walsh, Michael F

Subjects
Rare Diseases, Genetic Testing, Genetics, Pediatric, Human Genome, Clinical Research, Pediatric Cancer, Cancer, Aetiology, 2.1 Biological and endogenous factors, Detection, screening and diagnosis, 4.2 Evaluation of markers and technologies, Good Health and Well Being, Child, Genetic Predisposition to Disease, Germ Cells, Germ-Line Mutation, Humans, Neoplasms, Prospective Studies
Abstract

The spectrum of germline predisposition in pediatric cancer continues to be realized. Here we report 751 solid tumor patients who underwent prospective matched tumor-normal DNA sequencing and downstream clinical use (clinicaltrials.gov NCT01775072). Germline pathogenic and likely pathogenic (P/LP) variants were reported. One or more P/LP variants were found in 18% (138/751) of individuals when including variants in low, moderate, and high penetrance dominant or recessive genes, or 13% (99/751) in moderate and high penetrance dominant genes. 34% of high or moderate penetrance variants were unexpected based on the patient's diagnosis and previous history. 76% of patients with positive results completed a clinical genetics visit, and 21% had at least one relative undergo cascade testing as a result of this testing. Clinical actionability additionally included screening, risk reduction in relatives, reproductive use, and use of targeted therapies. Germline testing should be considered for all children with cancer.

Published
2021

19. Tumor sequencing of African ancestry reveals differences in clinically relevant alterations across common cancers

Author

Jiagge, Evelyn, Jin, Dexter X., Newberg, Justin Y., Perea-Chamblee, Tomin, Pekala, Kelly R., Fong, Christopher, Waters, Michele, Ma, David, Dei-Adomakoh, Yvonne, Erb, Gilles, Arora, Kanika S., Maund, Sophia L., Njiraini, Njoki, Ntekim, Atara, Kim, Susie, Bai, Xuechun, Thomas, Marlene, van Eeden, Ronwyn, Hegde, Priti, Jee, Justin, Chakravarty, Debyani, Schultz, Nikolaus, Berger, Michael F., Frampton, Garrett M., Sokol, Ethan S., and Carrot-Zhang, Jian

Published
2023
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20. TP53 mutations identify high-risk events for peripheral T-cell lymphoma treated with CHOP-based chemotherapy

Author

Johnson, William T., Ganesan, Nivetha, Epstein-Peterson, Zachary D., Moskowitz, Alison J., Stuver, Robert N., Maccaro, Catherine R., Galasso, Natasha, Chang, Tiffany, Khan, Niloufer, Aypar, Umut, Lewis, Natasha E., Zelenetz, Andrew D., Palomba, M. Lia, Matasar, Matthew J., Noy, Ariela, Hamilton, Audrey M., Hamlin, Paul, Caron, Philip C., Straus, David J., Intlekofer, Andrew M., Lee Batlevi, Connie, Kumar, Anita, Owens, Colette N., Sauter, Craig S., Falchi, Lorenzo, Lue, Jennifer K., Vardhana, Santosha A., Salles, Gilles, Dogan, Ahmet, Schultz, Nikolaus D., Arcila, Maria E., and Horwitz, Steven M.

Published
2023
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23. Undifferentiated and Dedifferentiated Metastatic Melanomas Masquerading as Soft Tissue Sarcomas: Mutational Signature Analysis and Immunotherapy Response

Author

Kasago, Israel S., Chatila, Walid K., Lezcano, Cecilia M., Febres-Aldana, Christopher A., Schultz, Nikolaus, Vanderbilt, Chad, Dogan, Snjezana, Bartlett, Edmund K., D’Angelo, Sandra P., Tap, William D., Singer, Samuel, Ladanyi, Marc, Shoushtari, Alexander N., Busam, Klaus J., and Hameed, Meera

Published
2023
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24. Accelerating precision medicine in metastatic prostate cancer

Author

Mateo, Joaquin, McKay, Rana, Abida, Wassim, Aggarwal, Rahul, Alumkal, Joshi, Alva, Ajjai, Feng, Felix, Gao, Xin, Graff, Julie, Hussain, Maha, Karzai, Fatima, Montgomery, Bruce, Oh, William, Patel, Vaibhav, Rathkopf, Dana, Rettig, Matthew, Schultz, Nikolaus, Smith, Matthew, Solit, David, Sternberg, Cora, Van Allen, Eliezer, VanderWeele, David, Vinson, Jake, Soule, Howard R, Chinnaiyan, Arul, Small, Eric, Simons, Jonathan W, Dahut, William, Miyahira, Andrea K, and Beltran, Himisha

Subjects
Clinical Research, Human Genome, Genetics, Cancer, Biotechnology, Urologic Diseases, Aging, Health Services, Prostate Cancer, Good Health and Well Being, Early Detection of Cancer, Humans, Male, Medical Oncology, Precision Medicine, Prostate-Specific Antigen, Prostatic Neoplasms
Abstract

Despite advances in prostate cancer screening and treatment, available therapy options, particularly in later stages of the disease, remain limited and the treatment-resistant setting represents a serious unmet medical need. Moreover, disease heterogeneity and disparities in patient access to medical advances result in significant variability in outcomes across patients. Disease classification based on genomic sequencing is a promising approach to identify patients whose tumors exhibit actionable targets and make more informed treatment decisions. Here we discuss how we can accelerate precision oncology to inform broader genomically-driven clinical decisions for men with advanced prostate cancer, drug development and ultimately contribute to new treatment paradigms.

Published
2020

25. Recent Advances in Systems and Network Medicine: Meeting Report from the First International Conference in Systems and Network Medicine

Author

Kurnat-Thoma, Emma, Baranova, Ancha, Baird, Pat, Brodsky, Elia, Butte, Atul J, Cheema, Amrita K, Cheng, Feixiong, Dutta, Shuchismita, Grant, Christina, Giordano, James, Maitland-van der Zee, Anke H, Fridsma, Douglas B, Jarrin, Robert, Kann, Maricel G, Keeney, Jonathon, Loscalzo, Joseph, Madhavan, Guru, Maron, Bradley A, McBride, Dennis K, McKean, Maeve, Mun, Seong K, Palmer, James C, Patel, Bakul, Parakh, Kapil, Pariser, Anne R, Pristipino, Christian, Radstake, Timothy RDJ, Rajasimha, Harsha K, Rouse, William B, Rozman, Damjana, Saleh, Alif, Schmidt, Harald HHW, Schultz, Nikolaus, Sethi, Tavpritesh, Silverman, Edwin K, Skopac, Jessica, Svab, Igor, Trujillo, Sylvia, Valentine, James E, Verma, Dinesh, West, Bruce J, and Vasudevan, Sona

Subjects
Biomedical and Clinical Sciences, Philosophy and Religious Studies, History and Philosophy Of Specific Fields, Generic health relevance, Good Health and Well Being, artificial intelligence, big data, ethical legal social implications, international conference, network medicine, regulatory and health policy, systems
Abstract

The First International Conference in Systems and Network Medicine gathered together 200 global thought leaders, scientists, clinicians, academicians, industry and government experts, medical and graduate students, postdoctoral scholars and policymakers. Held at Georgetown University Conference Center in Washington D.C. on September 11-13, 2019, the event featured a day of pre-conference lectures and hands-on bioinformatic computational workshops followed by two days of deep and diverse scientific talks, panel discussions with eminent thought leaders, and scientific poster presentations. Topics ranged from: Systems and Network Medicine in Clinical Practice; the role of -omics technologies in Health Care; the role of Education and Ethics in Clinical Practice, Systems Thinking, and Rare Diseases; and the role of Artificial Intelligence in Medicine. The conference served as a unique nexus for interdisciplinary discovery and dialogue and fostered formation of new insights and possibilities for health care systems advances.

Published
2020

26. Genomic mapping of metastatic organotropism in lung adenocarcinoma

Author

Lengel, Harry B., Mastrogiacomo, Brooke, Connolly, James G., Tan, Kay See, Liu, Yuan, Fick, Cameron N., Dunne, Elizabeth G., He, Di, Lankadasari, Manendra B., Satravada, Baby Anusha, Sun, Yichao, Kundra, Ritika, Fong, Chris, Smith, Shaleigh, Riely, Gregory J., Rudin, Charles M., Gomez, Daniel R., Solit, David B., Berger, Michael F., Li, Bob T., Mayo, Marty W., Matei, Irina, Lyden, David C., Adusumilli, Prasad S., Schultz, Nikolaus, Sanchez-Vega, Francisco, and Jones, David R.

Published
2023
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27. Characterization of Central Nervous System Clinico-Genomic Outcomes in ALK-Positive Non-Small Cell Lung Cancer Patients with Brain Metastases Treated with Alectinib

Author

Miao, Emily, Eichholz, Jordan E., Lebow, Emily S., Flynn, Jessica, Zhang, Zhigang, Walch, Henry, Hubbeling, Harper, Beal, Kathryn, Moss, Nelson S., Yu, Kenny K., Meng, Alicia, Kelly, Daniel W., Gomez, Daniel R., Li, Bob T., Rimner, Andreas, Schultz, Nikolaus, Drilon, Alexander, Imber, Brandon S., and Pike, Luke R.G.

Published
2023
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28. Overall survival with circulating tumor DNA-guided therapy in advanced non-small-cell lung cancer

Author

Jee, Justin, Lebow, Emily S., Yeh, Randy, Das, Jeeban P., Namakydoust, Azadeh, Paik, Paul K., Chaft, Jamie E., Jayakumaran, Gowtham, Rose Brannon, A., Benayed, Ryma, Zehir, Ahmet, Donoghue, Mark, Schultz, Nikolaus, Chakravarty, Debyani, Kundra, Ritika, Madupuri, Ramyasree, Murciano-Goroff, Yonina R., Tu, Hai-Yan, Xu, Chong-Rui, Martinez, Andrés, Wilhelm, Clare, Galle, Jesse, Daly, Bobby, Yu, Helena A., Offin, Michael, Hellmann, Matthew D., Lito, Piro, Arbour, Kathryn C., Zauderer, Marjorie G., Kris, Mark G., Ng, Kenneth K., Eng, Juliana, Preeshagul, Isabel, Victoria Lai, W., Fiore, John J., Iqbal, Afsheen, Molena, Daniela, Rocco, Gaetano, Park, Bernard J., Lim, Lee P., Li, Mark, Tong-Li, Candace, De Silva, Madhawa, Chan, David L., Diakos, Connie I., Itchins, Malinda, Clarke, Stephen, Pavlakis, Nick, Lee, Adrian, Rekhtman, Natasha, Chang, Jason, Travis, William D., Riely, Gregory J., Solit, David B., Gonen, Mithat, Rusch, Valerie W., Rimner, Andreas, Gomez, Daniel, Drilon, Alexander, Scher, Howard I., Shah, Sohrab P., Berger, Michael F., Arcila, Maria E., Ladanyi, Marc, Levine, Ross L., Shen, Ronglai, Razavi, Pedram, Reis-Filho, Jorge S., Jones, David R., Rudin, Charles M., Isbell, James M., and Li, Bob T.

Published
2022
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29. Genomic Predictors of Recurrence Patterns After Complete Resection of Colorectal Liver Metastases and Adjuvant Hepatic Artery Infusion Chemotherapy

Author

Narayan, Raja R., Datta, Jashodeep, Goldman, Debra A., Aveson, Victoria G., Walch, Henry S., Sanchez-Vega, Francisco, Gönen, Mithat, Balachandran, Vinod P., Drebin, Jeffrey A., Jarnagin, William R., Kingham, T. Peter, Wei, Alice C., Schultz, Nikolaus, Kemeny, Nancy E., and D’Angelica, Michael I.

Published
2022
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31. Unique Genomic Alterations and Microbial Profiles Identified in Patients With Gastric Cancer of African, European, and Asian Ancestry: A Novel Path for Precision Oncology

Author

Abate, Miseker, Walch, Henry, Arora, Kanika, Vanderbilt, Chad M., Fei, Teng, Drebin, Harrison, Shimada, Shoji, Maio, Anna, Kemel, Yelena, Stadler, Zsofia K., Schmeltz, Joseph, Sihag, Smita, Ku, Geoffrey Y., Gu, Ping, Tang, Laura, Vardhana, Santosha, Berger, Michael F., Brennan, Murray F., Schultz, Nikolaus D., and Strong, Vivian E.

Published
2023
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33. Table S15 from Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data

Author

Darmofal, Madison, primary, Suman, Shalabh, primary, Atwal, Gurnit, primary, Toomey, Michael, primary, Chen, Jie-Fu, primary, Chang, Jason C., primary, Vakiani, Efsevia, primary, Varghese, Anna M., primary, Balakrishnan Rema, Anoop, primary, Syed, Aijazuddin, primary, Schultz, Nikolaus, primary, Berger, Michael F., primary, and Morris, Quaid, primary

Published
2024
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34. Figure S5: GDD-ENS Performance Across Purity Values from Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data

Author

Darmofal, Madison, primary, Suman, Shalabh, primary, Atwal, Gurnit, primary, Toomey, Michael, primary, Chen, Jie-Fu, primary, Chang, Jason C., primary, Vakiani, Efsevia, primary, Varghese, Anna M., primary, Balakrishnan Rema, Anoop, primary, Syed, Aijazuddin, primary, Schultz, Nikolaus, primary, Berger, Michael F., primary, and Morris, Quaid, primary

Published
2024
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35. Figure S3: Confusion Matrix Across All Confidence Predictions from Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data

Author

Darmofal, Madison, primary, Suman, Shalabh, primary, Atwal, Gurnit, primary, Toomey, Michael, primary, Chen, Jie-Fu, primary, Chang, Jason C., primary, Vakiani, Efsevia, primary, Varghese, Anna M., primary, Balakrishnan Rema, Anoop, primary, Syed, Aijazuddin, primary, Schultz, Nikolaus, primary, Berger, Michael F., primary, and Morris, Quaid, primary

Published
2024
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36. Figure S4: Ancestry Accuracy Differentials from Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data

Author

Darmofal, Madison, primary, Suman, Shalabh, primary, Atwal, Gurnit, primary, Toomey, Michael, primary, Chen, Jie-Fu, primary, Chang, Jason C., primary, Vakiani, Efsevia, primary, Varghese, Anna M., primary, Balakrishnan Rema, Anoop, primary, Syed, Aijazuddin, primary, Schultz, Nikolaus, primary, Berger, Michael F., primary, and Morris, Quaid, primary

Published
2024
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37. Figure S6: Individual Type Shapley Values from Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data

Author

Darmofal, Madison, primary, Suman, Shalabh, primary, Atwal, Gurnit, primary, Toomey, Michael, primary, Chen, Jie-Fu, primary, Chang, Jason C., primary, Vakiani, Efsevia, primary, Varghese, Anna M., primary, Balakrishnan Rema, Anoop, primary, Syed, Aijazuddin, primary, Schultz, Nikolaus, primary, Berger, Michael F., primary, and Morris, Quaid, primary

Published
2024
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38. Figure S1: Accuracy of Feature-Specific Classifiers from Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data

Author

Darmofal, Madison, primary, Suman, Shalabh, primary, Atwal, Gurnit, primary, Toomey, Michael, primary, Chen, Jie-Fu, primary, Chang, Jason C., primary, Vakiani, Efsevia, primary, Varghese, Anna M., primary, Balakrishnan Rema, Anoop, primary, Syed, Aijazuddin, primary, Schultz, Nikolaus, primary, Berger, Michael F., primary, and Morris, Quaid, primary

Published
2024
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39. Figure S2: GDD-ENS Precision Recall Curves from Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data

Author

Darmofal, Madison, primary, Suman, Shalabh, primary, Atwal, Gurnit, primary, Toomey, Michael, primary, Chen, Jie-Fu, primary, Chang, Jason C., primary, Vakiani, Efsevia, primary, Varghese, Anna M., primary, Balakrishnan Rema, Anoop, primary, Syed, Aijazuddin, primary, Schultz, Nikolaus, primary, Berger, Michael F., primary, and Morris, Quaid, primary

Published
2024
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40. Figure S7: Individual Type Shapley Values - Broad Categories from Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data

Author

Darmofal, Madison, primary, Suman, Shalabh, primary, Atwal, Gurnit, primary, Toomey, Michael, primary, Chen, Jie-Fu, primary, Chang, Jason C., primary, Vakiani, Efsevia, primary, Varghese, Anna M., primary, Balakrishnan Rema, Anoop, primary, Syed, Aijazuddin, primary, Schultz, Nikolaus, primary, Berger, Michael F., primary, and Morris, Quaid, primary

Published
2024
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41. Supplementary Methods from Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data

Author

Darmofal, Madison, primary, Suman, Shalabh, primary, Atwal, Gurnit, primary, Toomey, Michael, primary, Chen, Jie-Fu, primary, Chang, Jason C., primary, Vakiani, Efsevia, primary, Varghese, Anna M., primary, Balakrishnan Rema, Anoop, primary, Syed, Aijazuddin, primary, Schultz, Nikolaus, primary, Berger, Michael F., primary, and Morris, Quaid, primary

Published
2024
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42. A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: the Hidden-Genome Classifier

Author

Song, Yi, primary, Boerner, Thomas, additional, Drill, Esther, additional, Shin, Paul, additional, Kumar, Sandeep, additional, Sigel, Carlie, additional, Cercek, Andrea, additional, Kemeny, Nancy, additional, Abou-Alfa, Ghassan, additional, Iacobuzio-Donahue, Christine, additional, Cowzer, Darren, additional, Schultz, Nikolaus, additional, Walch, Henry, additional, Balachandran, Vinod, additional, Groot Koerkamp, Bas, additional, Kingham, T. Peter., additional, Soares, Kevin, additional, Wei, Alice, additional, D'Angelica, Michael, additional, Drebin, Jeffrey, additional, Chandwani, Rohit, additional, Harding, James, additional, and Jarnagin, William R., additional

Published
2024
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43. Figure S8: Organ Shapley Value Distributions from Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data

Author

Darmofal, Madison, primary, Suman, Shalabh, primary, Atwal, Gurnit, primary, Toomey, Michael, primary, Chen, Jie-Fu, primary, Chang, Jason C., primary, Vakiani, Efsevia, primary, Varghese, Anna M., primary, Balakrishnan Rema, Anoop, primary, Syed, Aijazuddin, primary, Schultz, Nikolaus, primary, Berger, Michael F., primary, and Morris, Quaid, primary

Published
2024
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44. Figure S11: Heatmap of Labels Mapped for Adaptable Prior Distributions from Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data

Author

Darmofal, Madison, primary, Suman, Shalabh, primary, Atwal, Gurnit, primary, Toomey, Michael, primary, Chen, Jie-Fu, primary, Chang, Jason C., primary, Vakiani, Efsevia, primary, Varghese, Anna M., primary, Balakrishnan Rema, Anoop, primary, Syed, Aijazuddin, primary, Schultz, Nikolaus, primary, Berger, Michael F., primary, and Morris, Quaid, primary

Published
2024
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45. Figure S12: Results flow for Met Site, Histology Prior from Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data

Author

Darmofal, Madison, primary, Suman, Shalabh, primary, Atwal, Gurnit, primary, Toomey, Michael, primary, Chen, Jie-Fu, primary, Chang, Jason C., primary, Vakiani, Efsevia, primary, Varghese, Anna M., primary, Balakrishnan Rema, Anoop, primary, Syed, Aijazuddin, primary, Schultz, Nikolaus, primary, Berger, Michael F., primary, and Morris, Quaid, primary

Published
2024
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46. Figure S10: KRAS Shapley Values across typesSupplementary Data from Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data

Author

Darmofal, Madison, primary, Suman, Shalabh, primary, Atwal, Gurnit, primary, Toomey, Michael, primary, Chen, Jie-Fu, primary, Chang, Jason C., primary, Vakiani, Efsevia, primary, Varghese, Anna M., primary, Balakrishnan Rema, Anoop, primary, Syed, Aijazuddin, primary, Schultz, Nikolaus, primary, Berger, Michael F., primary, and Morris, Quaid, primary

Published
2024
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47. Genomic Landscape of Adenocarcinomas Across the Gastroesophageal Junction

Author

Nakauchi, Masaya, primary, Walch, Henry S., additional, Nussenzweig, Samuel, additional, Carr, Rebecca, additional, Vos, Elvira, additional, Berger, Michael F., additional, Schultz, Nikolaus, additional, Janjigian, Yelena, additional, Wu, Abraham, additional, Tang, Laura, additional, Shah, Pari, additional, Jones, David R., additional, Coit, Dan, additional, Strong, Vivian E., additional, Molena, Daniela, additional, and Sihag, Smita, additional

Published
2024
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48. Genomic biomarkers of CNS-specific outcomes in patients with breast cancer brain metastases.

Author

Khatri, Ishaani S., primary, Eichholz, Jordan, additional, Boe, Lillian A, additional, Safonov, Anton, additional, Smith, Deborah Ruth, additional, Ferraro, Emanuela, additional, Shen, Junchao, additional, Imber, Brandon S., additional, Yu, Yao, additional, Yamada, Yoshiya, additional, Miao, Emily, additional, Moss, Nelson S., additional, Wilcox, Jessica, additional, Walch, Henry S., additional, Chatila, Walid Khaled, additional, Schultz, Nikolaus, additional, Razavi, Pedram, additional, and Pike, Luke R. G., additional

Published
2024
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49. Utility of circulating tumor DNA (ctDNA) from cerebrospinal fluid (CSF) for prognosis of patients with recurrent high grade glioma.

Author

Holle, Bridget M., primary, Nandakumar, Subhiksha, additional, Kreitzer, Christoph, additional, Song, Timothy, additional, Tartaro, Marlene, additional, Hertz, Charli Ann, additional, Rafailov, Johnathan, additional, Campos, Carl, additional, Reiner, Anne S., additional, Young, Robert J., additional, Meng, Alicia, additional, Pasquini, Luca, additional, Brannon, Angela Rose, additional, Socci, Nicholas D., additional, Arcila, Maria E., additional, Solit, David B., additional, Berger, Michael F., additional, Schultz, Nikolaus, additional, Mellinghoff, Ingo K., additional, and Miller, Alex, additional

Published
2024
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50. Tracking the FDA precision oncology drug approval landscape in OncoKB.

Author

Suehnholz, Sarah Phillips, primary, Kundra, Ritika, additional, Zhang, Hongxin, additional, Nissan, Moriah H, additional, Lu, Calvin, additional, Dhaneshwar, Amanda, additional, Fernandez, Nicole, additional, Nandakumar, Subhiksha, additional, Arcila, Maria E., additional, Ladanyi, Marc, additional, Berger, Michael F., additional, Syed, Aijazuddin, additional, Brannon, Angela Rose, additional, Levine, Ross L., additional, Dogan, Ahmet, additional, Drilon, Alexander E., additional, Solit, David B., additional, Schultz, Nikolaus, additional, and Chakravarty, Debyani, additional

Published
2024
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