Genomic Landscape of Cancer and Mutational Signatures

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Resell, M., Rabben, H.-L., Sharma, A., Hagen, L., Hoang, L., Skogaker, N. T., Aarvik, A., Bjåstad, E. K., Svensson, M. K., Amrutkar, M., Verbeke, C. S., Batra, S. K., Qvigstad, G., Wang, T. C., Rustgi, A., Chen, D., & Zhao, C.-M. (2025). Proteomics profiling of research models for studying pancreatic ductal adenocarcinoma. Scientific Data, 12(1). https://doi.org/10.1038/s41597-025-04522-x
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Kondo, Y., Ohashi, S., Katada, C., Nakai, Y., Yamamoto, Y., Tamaoki, M., Kikuchi, O., Yamada, A., Hirohashi, K., Mitani, Y., Kataoka, S., Saito, T., Vu, T. H. N., Kondo, T., Uneno, Y., Sunami, T., Yokoyama, A., Matsubara, J., Matsuda, T., … Muto, M. (2025). Aldh2 and the tumor suppressor Trp53 play important roles in alcohol-induced squamous field cancerization. Journal of Gastroenterology. https://doi.org/10.1007/s00535-024-02210-y
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Sommerhalder, D., Demel, K., Noel, M. S., Emamekhoo, H., Peguero, J., Balaraman, R., Moy, R. H., Scheuber, A., Haas, J., Chabas, D., Kumar, P., Daigle, S. R., Dasen, S., Zhang, X., Gutierrez, M., Sharma, S., & Hussain, A. (2024). 682 Ongoing phase 1/2 trial of the HPK1 inhibitor NDI-101150 as monotherapy and in combination with pembrolizumab: clinical safety update and renal cell carcinoma (RCC) efficacy analysis. Regular and Young Investigator Award Abstracts, A782–A783. https://doi.org/10.1136/jitc-2024-sitc2024.0682
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Daigle, S. R., Elliott, G., Boiko, S., Sommerhalder, D., Noel, M. S., Sharma, S., Balaraman, R., Gutierrez, M., Demel, K., Moy, R. H., Ciccone, D., Zhang, X., Scheuber, A., & Kumar, P. (2024). 83 Tumor immune microenvironment characterization from pre- and post-dose tumors collected from a phase 1/2 study of NDI-101150, a hematopoietic progenitor kinase 1 (HPK1) inhibitor. Regular and Young Investigator Award Abstracts, A91–A91. https://doi.org/10.1136/jitc-2024-sitc2024.0083
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Shafighi, S., Geras, A., Jurzysta, B., Sahaf Naeini, A., Filipiuk, I., Ra̧czkowska, A., Toosi, H., Koperski, Ł., Thrane, K., Engblom, C., Mold, J. E., Chen, X., Hartman, J., Nowis, D., Carbone, A., Lagergren, J., & Szczurek, E. (2024). Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-53374-3
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Luthria, K., Shah, P., Caldwell, B., Melms, J. C., Abuzaid, S., Jakubikova, V., Brodtman, D. Z., Bose, S., Amin, A. D., Ho, P., Biermann, J., Tagore, S., Ingham, M., Schwartz, G. K., & Izar, B. (2024). Single-cell profiling of sarcomas from archival tissue reveals programs associated with resistance to immune checkpoint blockade. Clinical Cancer Research. https://doi.org/10.1158/1078-0432.ccr-23-2976
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Kabeer, F., Tran, H., Andronescu, M., Singh, G., Lee, H., Salehi, S., Wang, B., Biele, J., Brimhall, J., Gee, D., Cerda, V., O’Flanagan, C., Algara, T., Kono, T., Beatty, S., Zaikova, E., Lai, D., Lee, E., … Moore, R. (2024). Single-cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers. Genome Biology, 25(1). https://doi.org/10.1186/s13059-024-03318-3
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Zaidi, S., Park, J., Chan, J. M., Roudier, M. P., Zhao, J. L., Gopalan, A., Wadosky, K. M., Patel, R. A., Sayar, E., Karthaus, W. R., Kates, D. H., Chaudhary, O., Xu, T., Masilionis, I., Mazutis, L., Chaligné, R., Obradovic, A., Linkov, I., Barlas, A., … Sawyers, C. L. (2024). Single-cell analysis of treatment-resistant prostate cancer: Implications of cell state changes for cell surface antigen–targeted therapies. Proceedings of the National Academy of Sciences, 121(28). https://doi.org/10.1073/pnas.2322203121
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Faber, E. B., Baca, Y., Xiu, J., Walker, P., Manji, G., Gholami, S., Saeed, A., Prakash, A., Botta, G. P., Sohal, D., Lenz, H. J., Shields, A. F., Nabhan, C., El-Deiry, W., Seeber, A., Chiu, V., Hwang, J., & Lou, E. (2024). Exploring the differences in the tumor microenvironment and immuno-oncologic targets in pancreatic ductal adenocarcinomas (PDAC) according to KRAS mutational status. ESMO Gastrointestinal Oncology, 4, 100042. https://doi.org/10.1016/j.esmogo.2024.100042
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Karloski, E., Dudley, B., Diergaarde, B., Blanco, A., Everett, J. N., Levinson, E., Rangarajan, T., Stanich, P. P., Childers, K., Brown, S., Drogan, C., Cavestro, G. M., Gordon, K., Singh, A., Simeone, D. M., Reich, H., Kastrinos, F., Zakalik, D., Hampel, H., … Brand, R. E. (2024). The role of family history in predicting germline pathogenic variant carriers who develop pancreatic cancer: Results of a multicenter collaboration. Cancer. Portico. https://doi.org/10.1002/cncr.35383
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Ali, A. M., & Raza, A. (2024). scRNAseq and High-Throughput Spatial Analysis of Tumor and Normal Microenvironment in Solid Tumors Reveal a Possible Origin of Circulating Tumor Hybrid Cells. Cancers, 16(7), 1444. https://doi.org/10.3390/cancers16071444
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Zogopoulos, G., Haimi, I., Sanoba, S. A., Everett, J. N., Wang, Y., Katona, B. W., Farrell, J. J., Grossberg, A. J., Paiella, S., Klute, K. A., Bi, Y., Wallace, M. B., Kwon, R. S., Stoffel, E. M., Wadlow, R. C., Sussman, D. A., Merchant, N. B., Permuth, J. B., Golan, T., … __. (2024). The Pancreatic Cancer Early Detection (PRECEDE) Study is a Global Effort to Drive Early Detection: Baseline Imaging Findings in High-Risk Individuals. Journal of the National Comprehensive Cancer Network, 22(3), 158–166. https://doi.org/10.6004/jnccn.2023.7097
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Atkins, M. B., Jegede, O. A., Haas, N. B., Mcdermott, D. F., Bilen, M. A., Stein, M., Sosman, J., Alter, R., Plimack, E. R., Ornstein, M. C., Hurwitz, M., Peace, D. J., Einstein, D., Catalano, P. J., Hammers, H., & Regan, M. M. (2024). Treatment-free survival outcomes from the phase II study of nivolumab and salvage nivolumab/ipilimumab in advanced clear cell renal cell carcinoma (HCRN GU16-260-Cohort A). Journal for ImmunoTherapy of Cancer, 12(4), e008293. https://doi.org/10.1136/jitc-2023-008293
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Fojo, T., LaRose, M., & Bates, S. E. (2024). The Impact of Exuberance on Equipoise in Oncology Clinical Trials: Sotorasib as Archetype. The Oncologist, 29(4), 275–277. https://doi.org/10.1093/oncolo/oyae042
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Ben-Ami, R., Wang, Q.-L., Zhang, J., Supplee, J. G., Fahrmann, J. F., Lehmann-Werman, R., Brais, L. K., Nowak, J., Yuan, C., Loftus, M., Babic, A., Irajizad, E., Davidi, T., Zick, A., Hubert, A., Neiman, D., Piyanzin, S., Gal-Rosenberg, O., Horn, A., … Wolpin, B. M. (2023). Protein biomarkers and alternatively methylated cell-free DNA detect early stage pancreatic cancer. Gut, gutjnl-2023-331074. https://doi.org/10.1136/gutjnl-2023-331074
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Wang, K., Du, R., Myall, N. J., Lewis, W. E., Uy, N., Hong, L., Skoulidis, F., Byers, L. A., Tsao, A., Cascone, T., Pozadzides, J., Tu, J., Negrao, M. V., Gibbons, D. L., Park, K., Rinsurongkawong, W., Lee, J. J., Gandara, D., Behl, D., … Le, X. (2024). Real-World Efficacy and Safety of Amivantamab for EGFR-Mutant NSCLC. Journal of Thoracic Oncology, 19(3), 500–506. https://doi.org/10.1016/j.jtho.2023.11.020
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Bellair, M., Amaral, E., Ouren, M., Roark, C., Kim, J., O’Connor, A., Soriano, A., Schindler, M. L., Wapner, R. J., Stone, J. L., Tavella, N., Merriam, A., Perley, L., Breman, A. M., & Beaudet, A. L. (2024). Noninvasive single‐cell‐based prenatal genetic testing: A proof of concept clinical study. Prenatal Diagnosis, 44(3), 304–316. Portico. https://doi.org/10.1002/pd.6529
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Galbraith, K., Vasudevaraja, V., Serrano, J., Shen, G., Tran, I., Abdallat, N., Wen, M., Patel, S., Movahed-Ezazi, M., Faustin, A., Spino-Keeton, M., Roberts, L. G., Maloku, E., Drexler, S. A., Liechty, B. L., Pisapia, D., Krasnozhen-Ratush, O., Rosenblum, M., Shroff, S., … Snuderl, M. (2023). Clinical utility of whole-genome DNA methylation profiling as a primary molecular diagnostic assay for central nervous system tumors—A prospective study and guidelines for clinical testing. Neuro-Oncology Advances, 5(1). https://doi.org/10.1093/noajnl/vdad076
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Diaz, M., Chudsky, S., Pentsova, E., & Miller, A. M. (2024). Clinical applications of cerebrospinal fluid liquid biopsies in central nervous system tumors. Translational Oncology, 41, 101881. https://doi.org/10.1016/j.tranon.2024.101881
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Levy, B., Kanagal‐Shamanna, R., Sahajpal, N. S., Neveling, K., Rack, K., Dewaele, B., Olde Weghuis, D., Stevens‐Kroef, M., Puiggros, A., Mallo, M., Clifford, B., Mantere, T., Hoischen, A., Espinet, B., Kolhe, R., Solé, F., Raca, G., & Smith, A. C. (2024). A framework for the clinical implementation of optical genome mapping in hematologic malignancies. American Journal of Hematology, 99(4), 642–661. Portico. https://doi.org/10.1002/ajh.27175
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Zhuo, X., Aggarwal, V., & Liao, J. (2024). P641: Application of AlphaMissense prediction to pathogenicity classification of missense variants from clinical exome sequencing. Genetics in Medicine Open, 2, 101547. https://doi.org/10.1016/j.gimo.2024.101547
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Chen, X., Li, Y., Zhu, F., Xu, X., Estrella, B., Pazos, M. A., McGuire, J. T., Karagiannis, D., Sahu, V., Mustafokulov, M., Scuoppo, C., Sánchez-Rivera, F. J., Soto-Feliciano, Y. M., Pasqualucci, L., Ciccia, A., Amengual, J. E., & Lu, C. (2023). Context-defined cancer co-dependency mapping identifies a functional interplay between PRC2 and MLL-MEN1 complex in lymphoma. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-39990-5
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Oxnard, G. R., Chen, R., Pharr, J. C., Koeller, D. R., Bertram, A. A., Dahlberg, S. E., Rainville, I., Shane-Carson, K., Taylor, K. A., Sable-Hunt, A., Sholl, L. M., Teerlink, C. C., Thomas, A., Cannon-Albright, L. A., Fay, A. P., Ashton-Prolla, P., Yang, H., Salvatore, M. M., Addario, B. J., … Garber, J. E. (2023). Germline EGFR Mutations and Familial Lung Cancer. Journal of Clinical Oncology, 41(34), 5274–5284. https://doi.org/10.1200/jco.23.01372
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Park, J., Lim, F., Prest, M., Ferris, J. S., Aziz, Z., Agyekum, A., Wagner, S., Gulati, R., & Hur, C. (2023). Quantifying the potential benefits of early detection for pancreatic cancer through a counterfactual simulation modeling analysis. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-46751-3
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Gui, G., Dillon, L. W., Ravindra, N., Hegde, P. S., Andrew, G., Mukherjee, D., Wong, Z., Auletta, J. J., El Chaer, F., Chen, E. C., Chen, Y.-B., Corner, A., Devine, S. M., Iyer, S. G., Jimenez Jimenez, A. M., de Lima, M., Litzow, M. R., Kebriaei, P., Saber, W., … Hourigan, C. S. (2023). Measurable Residual IDH2 before Allogeneic Transplant for Acute Myeloid Leukemia. Blood, 142(Supplement 1), 424–424. https://doi.org/10.1182/blood-2023-186822
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Chapman, O. S., Luebeck, J., Sridhar, S., Wong, I. T.-L., Dixit, D., Wang, S., Prasad, G., Rajkumar, U., Pagadala, M. S., Larson, J. D., He, B. J., Hung, K. L., Lange, J. T., Dehkordi, S. R., Chandran, S., Adam, M., Morgan, L., Wani, S., Tiwari, A., … Chavez, L. (2023). Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma. Nature Genetics, 55(12), 2189–2199. https://doi.org/10.1038/s41588-023-01551-3
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Rosenberg, S. M., McCue, S., He, J., Lafky, J. M., Carey, L. A., Galanis, E., Leonard, J. P., Meyerhardt, J., Ng, K., Schwartz, G. K., Stock, W., Paskett, E. D., Partridge, A. H., & George, S. (2023). Alliance A151945: Accrual and characteristics of adolescent and young adult patients in Alliance trials from 2000 to 2017. Cancer, 130(5), 750–769. Portico. https://doi.org/10.1002/cncr.35078
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Xu, J. J., Chen, Y., Pantazi, J., Fernando, S., Alija, B., Sudunagunta, V., Bhagat, G., & Viny, A. D. (2023). Synergy of Stag2-Cohesin Loss Results in Expansion of Npm1c-Mutant Hematopoietic Stem and Progenitor Cells. Blood, 142(Supplement 1), 954–954. https://doi.org/10.1182/blood-2023-190627
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Gui, G., Dillon, L. W., Ravindra, N., Hegde, P. S., Andrew, G., Mukherjee, D., Wong, Z., Auletta, J. J., El Chaer, F., Chen, E. C., Chen, Y.-B., Corner, A., Devine, S. M., Iyer, S. G., Jimenez Jimenez, A. M., de Lima, M., Litzow, M. R., Kebriaei, P., Saber, W., … Hourigan, C. S. (2023). Measurable Residual IDH1 before Allogeneic Transplant for Acute Myeloid Leukemia. Blood, 142(Supplement 1), 4316–4316. https://doi.org/10.1182/blood-2023-186376
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Leighl, N., Cho, B. C., Hiret, S., Han, J.-Y., Lee, K. H., Llacer Perez, C., Krebs, M. G., De Braud, F., Haura, E., Sanborn, R. E., Yang, J. C.-H., Shu, C. A., Goto, K., Nishio, M., Zhao, J., Wang, Z., Tomasini, P., Felip, E., Goldman, J. W., … Spira, A. I. (2023). OA21.04 Amivantamab in Patients with Advanced NSCLC and MET Exon 14 Skipping Mutation: Results from the CHRYSALIS Study. Journal of Thoracic Oncology, 18(11), S93–S94. https://doi.org/10.1016/j.jtho.2023.09.105
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Mckean, M., Chmielowski, B., Butler, M. O., Carvajal, R., Rodon, J., Carlino, M., Kim, K. B., Wise-draper, T., Khan, S., Salama, A. K. S., Moser, J., Reeves, J., Wilner, K. D., Maurer, M., Abed, M., Mitchell, B., Beaupre, D., & Orloff, M. (2023). 1081O ctDNA reduction and clinical efficacy of the darovasertib + crizotinib (daro + crizo) combination in metastatic uveal melanoma (MUM). Annals of Oncology, 34, S651. https://doi.org/10.1016/j.annonc.2023.09.2215
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Levy, B., Baughn, L. B., Akkari, Y., Chartrand, S., LaBarge, B., Claxton, D., Lennon, P. A., Cujar, C., Kolhe, R., Kroeger, K., Pitel, B., Sahajpal, N., Sathanoori, M., Vlad, G., Zhang, L., Fang, M., Kanagal-Shamanna, R., & Broach, J. R. (2023). Optical genome mapping in acute myeloid leukemia: a multicenter evaluation. Blood Advances, 7(7), 1297–1307. https://doi.org/10.1182/bloodadvances.2022007583
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Lee, T. D., Aisner, D. L., David, M. P., Eno, C. C., Gagan, J., Gocke, C. D., Guseva, N. V., Haley, L., Jajosky, A. N., Jones, D., Mansukhani, M. M., Mroz, P., Murray, S. S., Newsom, K. J., Paulson, V., Roy, S., Rushton, C., Segal, J. P., Senaratne, T. N., … Kim, A. S. (2023). Current clinical practices and challenges in molecular testing: a GOAL Consortium Hematopathology Working Group report. Blood Advances, 7(16), 4599–4607. https://doi.org/10.1182/bloodadvances.2023010149
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Bridge, J. A., Halling, K. C., Moncur, J. T., Souers, R. J., Hameed, M. R., Fernandes, H., Roy, A., Surrey, L., Tafe, L. J., Vasalos, P., & Lopez-Terrada, D. H. (2023). RNA Sequencing for Solid Tumor Fusion Gene Detection: Proficiency Testing Practice and Performance Comparison. Archives of Pathology & Laboratory Medicine, 148(5), 538–544. https://doi.org/10.5858/arpa.2023-0047-cp
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Manji, G. A., Labadie, B. W., Lee, S. M., Pellicciotta, I., Ge, L., Sta Ana, S., Sender, N., Ross, I., Wong, W., & Raufi, A. G. (2023). MEKiAUTO: A multicenter phase 1 study of combination therapy with the MEK inhibitor, cobimetinib, immune checkpoint blockade, atezolizumab, and the autophagy inhibitor hydroxychloroquine (HCQ) in KRAS-mutated advanced malignancies. JCO Global Oncology, 9(Supplement_1), 45–45. https://doi.org/10.1200/go.2023.9.supplement_1.45
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Tshering, L. F., Luo, F., Russ, S., Szenk, M., Rubel, D., Tutuska, K., Rail, J. G., Balázsi, G., Shen, M. M., & Talos, F. (2023). Immune mechanisms shape the clonal landscape during early progression of prostate cancer. Developmental Cell, 58(12), 1071-1086.e8. https://doi.org/10.1016/j.devcel.2023.04.010
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Okolo, O., Yu, V., Flashner, S., Martin, C., Nakagawa, H., Lin, D. T., Puram, S. V., & Parikh, A. S. (2023). Protocol for tumor dissociation and fluorescence-activated cell sorting of human head and neck cancers. STAR Protocols, 4(2), 102294. https://doi.org/10.1016/j.xpro.2023.102294
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Graff, S. L., Bansal, R., Adeyelu, T., Elliott, A., Bustos, M., Rodriguez, E., Accordino, M., Meisel, J., Gatti-Mays, M., Hsu, E., Lathrop, K. I., Kaklamani, V., Oberley, M., Sledge, G., & Sammons, S. (2023). 215P Impact of HER2 low on survival in patients treated with standard therapies in advanced breast cancer. ESMO Open, 8(1), 101404. https://doi.org/10.1016/j.esmoop.2023.101404
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Ravi, A., Hellmann, M. D., Arniella, M. B., Holton, M., Freeman, S. S., Naranbhai, V., Stewart, C., Leshchiner, I., Kim, J., Akiyama, Y., Griffin, A. T., Vokes, N. I., Sakhi, M., Kamesan, V., Rizvi, H., Ricciuti, B., Forde, P. M., Anagnostou, V., Riess, J. W., … Gainor, J. F. (2023). Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer. Nature Genetics, 55(5), 807–819. https://doi.org/10.1038/s41588-023-01355-5
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Spillmann, R. C., Tan, Q. K.-G., Reuter, C., Schoch, K., Kohler, J., Bonner, D., Zastrow, D., Alkelai, A., Baugh, E., Cope, H., Marwaha, S., Wheeler, M. T., Bernstein, J. A., Shashi, V., Acosta, M. T., Adam, M., Adams, D. R., Alvey, J., Amendola, L., … Zuchner, S. (2023). A concurrent dual analysis of genomic data augments diagnoses: Experiences of 2 clinical sites in the Undiagnosed Diseases Network. Genetics in Medicine, 25(4), 100353. https://doi.org/10.1016/j.gim.2022.12.001
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Columbia Affiliation
Oren, D., Moeller, C. M., Rubinstein, G., Lotan, D., DeFilippis, E. M., Mehlman, Y., Raja, A., Slomovich, S., Clerkin, K., Fried, J., Raikhelkar, J., Lin, E., Oh, K., Lee, S., Topkara, V., Latif, F., Majure, D., Sayer, G., & Uriel, N. (2023). (758) Evaluation of Donor Derived Cell-Free DNA in ABO Mismatched Heart Transplant Patients. The Journal of Heart and Lung Transplantation, 42(4), S334. https://doi.org/10.1016/j.healun.2023.02.772
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Fulop, D. J., Zylberberg, H. M., Wu, Y. L., Aronson, A., Labiner, A. J., Wisnivesky, J., Cohen, D. J., Sigel, K. M., & Lucas, A. L. (2023). Association of Antibiotic Receipt With Survival Among Patients With Metastatic Pancreatic Ductal Adenocarcinoma Receiving Chemotherapy. JAMA Network Open, 6(3), e234254. https://doi.org/10.1001/jamanetworkopen.2023.4254
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Santhanam, B., Oikonomou, P., & Tavazoie, S. (2023). Systematic assessment of prognostic molecular features across cancers. Cell Genomics, 3(3), 100262. https://doi.org/10.1016/j.xgen.2023.100262
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Vasciaveo, A., Arriaga, J. M., de Almeida, F. N., Zou, M., Douglass, E. F., Picech, F., Shibata, M., Rodriguez-Calero, A., de Brot, S., Mitrofanova, A., Chua, C. W., Karan, C., Realubit, R., Pampou, S., Kim, J. Y., Afari, S. N., Mukhammadov, T., Zanella, L., Corey, E., … Abate-Shen, C. (2022). OncoLoop: A Network-Based Precision Cancer Medicine Framework. Cancer Discovery, 13(2), 386–409. https://doi.org/10.1158/2159-8290.cd-22-0342
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de Castro, G., Rizvi, N. A., Schmid, P., Syrigos, K., Martin, C., Yamamoto, N., Cheng, Y., Moiseyenko, V., Summers, Y., Vynnychenko, I., Lee, S. Y., Bryl, M., Zer, A., Erman, M., Timcheva, C., Raja, R., Naicker, K., Scheuring, U., Walker, J., … Mok, T. (2023). NEPTUNE: Phase 3 Study of First-Line Durvalumab Plus Tremelimumab in Patients With Metastatic NSCLC. Journal of Thoracic Oncology, 18(1), 106–119. https://doi.org/10.1016/j.jtho.2022.09.223
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