Genomic Landscape of Cancer and Mutational Signatures

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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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Ilozumba, M. N., Yao, S., Llanos, A. A. M., Omilian, A. R., Zhang, W., Datta, S., Hong, C.-C., Davis, W., Khoury, T., Bandera, E. V., Higgins, M., Ambrosone, C. B., & Cheng, T.-Y. D. (2022). mTOR pathway gene expression in association with race and clinicopathological characteristics in Black and White breast cancer patients. Discover Oncology, 13(1). https://doi.org/10.1007/s12672-022-00497-y
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Cordo’, V., Meijer, M. T., Hagelaar, R., de Goeij-de Haas, R. R., Poort, V. M., Henneman, A. A., Piersma, S. R., Pham, T. V., Oshima, K., Ferrando, A. A., Zaman, G. J. R., Jimenez, C. R., & Meijerink, J. P. P. (2022). Phosphoproteomic profiling of T cell acute lymphoblastic leukemia reveals targetable kinases and combination treatment strategies. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-28682-1
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Columbia Affiliation
de Leval, L., Alizadeh, A. A., Bergsagel, P. L., Campo, E., Davies, A., Dogan, A., Fitzgibbon, J., Horwitz, S. M., Melnick, A. M., Morice, W. G., Morin, R. D., Nadel, B., Pileri, S. A., Rosenquist, R., Rossi, D., Salaverria, I., Steidl, C., Treon, S. P., Zelenetz, A. D., … Scott, D. W. (2022). Genomic profiling for clinical decision making in lymphoid neoplasms. Blood, 140(21), 2193–2227. https://doi.org/10.1182/blood.2022015854
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Molina, J. C., Chinnabhandar, V., Fabrizio, V. A., Kunicki, M., Pacenta, H., Rossoff, J., Stefanski, H. E., Talano, J., Moskop, A., Verneris, M. R., Myers, G. D., Karras, N., Baggott, C., Qayed, M., Hermiston, M. L., Satwani, P., Krupski, C., Keating, A. K., Baumeister, S. H. C., … Smith, S. M. (2022). Standard Cytogenetic Risk Stratification Is Not Predictive of CD19 CAR Outcomes and Impact of Disease Burden Varies between Cytogenetic Risk Groups. Blood, 140(Supplement 1), 10386–10388. https://doi.org/10.1182/blood-2022-165951
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Koff, J. L., Kositsky, R., Jaye, D. L., Churnetski, M. C., Baird, K., O’Leary, C. B., Flowers, C. R., Leppa, S., Karjalainen-Lindsberg, M.-L., Li, S., Xu, J., Pedersen, M. Ø., Gang, A. O., Naresh, K. N., Leeman-Neill, R. J., Au Yeung, K. H. R., Qureishi, H. N., Iqbal, J., Chapman-Fredricks, J. R., … Cohen, J. B. (2022). Mutations of ATM Confer a Risk of Inferior Survival in Patients with TP53-wild Type Mantle Cell Lymphoma. Blood, 140(Supplement 1), 3500–3503. https://doi.org/10.1182/blood-2022-168002
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Van Egeren, D., Kohli, K., Warner, J. L., Bedard, P. L., Riely, G., Lepisto, E., Schrag, D., LeNoue-Newton, M., Catalano, P., Kehl, K. L., Michor, F., Fiandalo, M., Foti, M., Khotskaya, Y., Lee, J., Peters, N., Sweeney, S., Abraham, J., … Walther, Z. (2022). Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-21448-1
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Castro, M., Iwamoto, F., Ahluwalia, M., Usmani, S., Kumar, A., Kapoor, S., Suseela, R. P., Kulkarni, S., Mohanty, J., Shyamasundar, V., Ghosh, A., Prasad, N., Patil, M., Choudhury, S. R., Chauhan, J., Sauban, M., Joseph, V., Kumari, P., Mitra, U., … Basu, S. (2022). EPCO-06. THE IMPACT OF MISMATCH REPAIR DEFICIENCY (MMRD) ON SURVIVAL OF TEMOZOLOMIDE (TMZ)-TREATED PATIENTS WITH MGMT METHYLATED (M-MGMT) GLIOBLASTOMA (GBM): A CELLWORKS COMPUTATIONAL BIOSIMULATION PILOT STUDY. Neuro-Oncology, 24(Supplement_7), vii116–vii117. https://doi.org/10.1093/neuonc/noac209.441
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Hou, J. Y., Chapman, J. S., Kalashnikova, E., Pierson, W., Smith-McCune, K., Pineda, G., Vattakalam, R. M., Ross, A., Mills, M., Suarez, C. J., Davis, T., Edwards, R., Boisen, M., Sawyer, S., Wu, H.-T., Dashner, S., Aushev, V. N., George, G. V., Malhotra, M., … Ford, J. M. (2022). Circulating tumor DNA monitoring for early recurrence detection in epithelial ovarian cancer. Gynecologic Oncology, 167(2), 334–341. https://doi.org/10.1016/j.ygyno.2022.09.004
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Liao, C.-Y., Johnson, B., Spira, A., Carbone, D., Henick, B., Overman, M., Polite, B., Roychowdhury, S., Mahipal, A., Ahn, D., Johnson, M., Schenk, D., Bae, K., Davis, M., Jooss, K., Ferguson, A., & Solomon, B. (2022). 660 Clinicopathologic characteristics of patients with metastatic colorectal cancer with molecular responses following treatment with an individualized neoantigen vaccine regimen. Regular and Young Investigator Award Abstracts, A691–A691. https://doi.org/10.1136/jitc-2022-sitc2022.0660
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Ellingson, B., Wen, P. Y., Chang, S., van den Bent, M., Vogelbaum, M., Li, G., Li, S., Kim, J., Youssef, G., Wick, W., Lassman, A., Gilbert, M., de Groot, J., Weller, M., Galanis, E., & Cloughesy, T. (2022). NIMG-42. DURABLE OVERALL RESPONSE RATE (ORR) TARGETS FOR RECURRENT GLIOBLASTOMA (RGBM) CLINICAL TRIALS BASED ON THE HISTORIC ASSOCIATION BETWEEN ORR AND MEDIAN OVERALL SURVIVAL (MOS). Neuro-Oncology, 24(Supplement_7), vii172–vii173. https://doi.org/10.1093/neuonc/noac209.660
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Flerlage, J. E., Birz, S., Castellino, S. M., Appel, B., Furner, B., Graglia, L., Henderson, T. O., Hodgson, D., Hoppe, B. S., Kahn, J., Keller, F. G., Kessel, S., Li, C., Li, M., Lucas, J., Mccarten, K., Metzger, M., Milgrom, S., Parsons, S. K., … Kelly, K. M. (2022). P086: Advancing Pediatric Hodgkin Lymphoma Research Through NODAL. HemaSphere, 6, 39–40. https://doi.org/10.1097/01.hs9.0000890912.56229.80
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Miller, A. M., Szalontay, L., Bouvier, N., Hill, K., Ahmad, H., Rafailov, J., Lee, A. J., Rodriguez-Sanchez, M. I., Yildirim, O., Patel, A., Bale, T. A., Benhamida, J. K., Benayed, R., Arcila, M. E., Donzelli, M., Dunkel, I. J., Gilheeney, S. W., Khakoo, Y., Kramer, K., … Karajannis, M. A. (2022). Next-generation sequencing of cerebrospinal fluid for clinical molecular diagnostics in pediatric, adolescent and young adult brain tumor patients. Neuro-Oncology, 24(10), 1763–1772. https://doi.org/10.1093/neuonc/noac035
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Pass, H., Kim, A. W., Felip, E., Shu, C. A., Ferris, A., Frueh, M., Gitlitz, B. J., Troutman, S., Petrek, H., Liu, X., Hsu, J., Patil, N., & Meng, R. D. (2022). 970TiP SKYSCRAPER-05: Phase II study of neoadjuvant atezolizumab (Atezo) + tiragolumab (Tira) with or without platinum-based chemotherapy (CT) in patients (Pts) with locally advanced resectable stage II‒IIIB NSCLC. Annals of Oncology, 33, S990–S991. https://doi.org/10.1016/j.annonc.2022.07.1096
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Lai, D., Gade, M., Yang, E., Koh, H. Y., Lu, J., Walley, N. M., Buckley, A. F., Sands, T. T., Akman, C. I., Mikati, M. A., McKhann, G. M., Goldman, J. E., Canoll, P., Alexander, A. L., Park, K. L., Von Allmen, G. K., Rodziyevska, O., Bhattacharjee, M. B., Lidov, H. G. W., … Heinzen, E. L. (2022). Somatic variants in diverse genes leads to a spectrum of focal cortical malformations. Brain, 145(8), 2704–2720. https://doi.org/10.1093/brain/awac117
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Dar, P., Jacobsson, B., MacPherson, C., Egbert, M., Malone, F., Wapner, R. J., Roman, A. S., Khalil, A., Faro, R., Madankumar, R., Edwards, L., Haeri, S., Silver, R., Vohra, N., Hyett, J., Clunie, G., Demko, Z., Martin, K., Rabinowitz, M., … Norton, M. E. (2022). Cell-free DNA screening for trisomies 21, 18, and 13 in pregnancies at low and high risk for aneuploidy with genetic confirmation. American Journal of Obstetrics and Gynecology, 227(2), 259.e1-259.e14. https://doi.org/10.1016/j.ajog.2022.01.019
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de Prisco, N., Botta, S., Lee, W., Rezazadeh, S., Chemiakine, A., & Gennarino, V. A. (2022). Determining the effects of loss of function mutations in human cell lines. STAR Protocols, 3(2), 101232. https://doi.org/10.1016/j.xpro.2022.101232
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Gounder, M. M., Agaram, N. P., Trabucco, S. E., Robinson, V., Ferraro, R. A., Millis, S. Z., Krishnan, A., Lee, J., Attia, S., Abida, W., Drilon, A., Chi, P., Angelo, S. P. D., Dickson, M. A., Keohan, M. L., Kelly, C. M., Agulnik, M., Chawla, S. P., Choy, E., … Jin, D. X. (2022). Clinical genomic profiling in the management of patients with soft tissue and bone sarcoma. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-30496-0
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Hill, K., Miller, A. M., Li, B. K., Bouvier, N., Li, S., Alano, T., Doe-Tetteh, S., Huereca, C., DiNapoli, S., Lee, A., Szalontay, L., Riviere-Cazaux, C., Burns, T. C., Haque, S., Bale, T., Benhamida, J., Dogan, S., Vanderbilt, C., Ross, D., … Karajannis, M. (2022). PATH-16. Noninvasive diagnosis of gliomas through CSF cfDNA sequencing in pediatric and adolescent and young adult (AYA) patients. Neuro-Oncology, 24(Supplement_1), i162–i162. https://doi.org/10.1093/neuonc/noac079.600
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Akkari, Y. M. N., Baughn, L. B., Dubuc, A. M., Smith, A. C., Mallo, M., Dal Cin, P., Diez Campelo, M., Gallego, M. S., Granada Font, I., Haase, D. T., Schlegelberger, B., Slavutsky, I., Mecucci, C., Levine, R. L., Hasserjian, R. P., Solé, F., Levy, B., & Xu, X. (2022). Guiding the global evolution of cytogenetic testing for hematologic malignancies. Blood, 139(15), 2273–2284. https://doi.org/10.1182/blood.2021014309
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Rahimi, A., Simmons, A., Kim, D. N., Leitch, M., Haas, J., Gu, X., Ahn, C., Gao, A., Spangler, A., Morgan, H. E., Goudreau, S., Seiler, S., Farr, D., Wooldridge, R., Haley, B., Bahrami, S., Neufeld, S., Mendez, C., Alluri, P., … Timmerman, R. D. (2022). Preliminary Results of Multi-Institutional Phase 1 Dose Escalation Trial Using Single-Fraction Stereotactic Partial Breast Irradiation for Early Stage Breast Cancer. International Journal of Radiation Oncology*Biology*Physics, 112(3), 663–670. https://doi.org/10.1016/j.ijrobp.2021.10.010
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Palmer, A. C., Izar, B., Hwangbo, H., & Sorger, P. K. (2022). Predictable Clinical Benefits without Evidence of Synergy in Trials of Combination Therapies with Immune-Checkpoint Inhibitors. Clinical Cancer Research, 28(2), 368–377. https://doi.org/10.1158/1078-0432.ccr-21-2275
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Das, A., Sudhaman, S., Morgenstern, D., Coblentz, A., Chung, J., Stone, S. C., Alsafwani, N., Liu, Z. A., Karsaneh, O. A. A., Soleimani, S., Ladany, H., Chen, D., Zatzman, M., Cabric, V., Nobre, L., Bianchi, V., Edwards, M., Sambira Nahum, L. C., Ercan, A. B., … Tabori, U. (2022). Genomic predictors of response to PD-1 inhibition in children with germline DNA replication repair deficiency. Nature Medicine, 28(1), 125–135. https://doi.org/10.1038/s41591-021-01581-6
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Thomas, A., Kwon, W., Tehranifar, P., Sugahara, K., Schrope, B., Chabot, J., Genkinger, J., & Kluger, M. (2022). Barriers to Standard of Care in the United States: Trends in the Treatment of Locally Advanced Pancreatic Cancer in the Modern Era of Chemotherapy. HPB, 24, S36. https://doi.org/10.1016/j.hpb.2022.05.071
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Wang, Z., Fan, X., Shen, Y., Pagadala, M. S., Signer, R., Cygan, K. J., Fairbrother, W. G., Carter, H., Chung, W. K., & Huang, K. (2021). Non-cancer-related pathogenic germline variants and expression consequences in ten-thousand cancer genomes. Genome Medicine, 13(1). https://doi.org/10.1186/s13073-021-00964-1
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Rodriguez, D. A., Yang, J., Durante, M. A., Shoushtari, A. N., Moschos, S. J., Wrzeszczynski, K. O., Harbour, J. W., & Carvajal, R. D. (2021). Multiregional genetic evolution of metastatic uveal melanoma. Npj Genomic Medicine, 6(1). https://doi.org/10.1038/s41525-021-00233-5
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Ahuno, S. T., Doebley, A.-L., Ahearn, T. U., Yarney, J., Titiloye, N., Hamel, N., Adjei, E., Clegg-Lamptey, J.-N., Edusei, L., Awuah, B., Song, X., Vanderpuye, V., Abubakar, M., Duggan, M., Stover, D. G., Nyarko, K., Bartlett, J. M. S., Aitpillah, F., Ansong, D., … Biritwum, R. (2021). Circulating tumor DNA is readily detectable among Ghanaian breast cancer patients supporting non-invasive cancer genomic studies in Africa. Npj Precision Oncology, 5(1). https://doi.org/10.1038/s41698-021-00219-7
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Canterbury, C. R., Fernandes, H., Crapanzano, J. P., Murty, V. V., Mansukhani, M. M., Shu, C. A., Szabolcs, M., & Saqi, A. (2021). ALK Gene Rearrangements in Lung Adenocarcinomas: Concordance of Immunohistochemistry, Fluorescence In Situ Hybridization, RNA In Situ Hybridization, and RNA Next-Generation Sequencing Testing. JTO Clinical and Research Reports, 2(10), 100223. https://doi.org/10.1016/j.jtocrr.2021.100223
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Love, C., Pillai, R., Ondrejka, S. L., Bhagat, G., Chadburn, A., McKinney, M., Koff, J. L., Soliman, D. S., Czader, M., Louissaint, A., Li, S., Ong, C. K., Behdad, A., Evens, A. M., Natkunam, Y., Norgaard, P. H., Leppa, S., Tse, E., Chapman, J. R., … Dave, S. (2021). The Atlas of Blood Cancer Genomes (ABCG) Project: A Comprehensive Molecular Characterization of Leukemias and Lymphomas. Blood, 138(Supplement 1), 2213–2213. https://doi.org/10.1182/blood-2021-151346
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Paolino, J. D., Harris, M. H., Stevenson, K. E., Koch, V., Cole, P. D., Gennarini, L. M., Kahn, J. M., Kelly, K. M., Kirsch, Ii., Michon, B., Place, A. E., Tran, T. H., Welch, J. J. G., & Silverman, L. B. (2021). Performance of Next Generation Sequencing for Minimal Residual Disease Detection for Pediatric Patients with Acute Lymphoblastic Leukemia: Results from the Prospective Clinical Trial DFCI 16-001. Blood, 138(Supplement 1), 3485–3485. https://doi.org/10.1182/blood-2021-152369
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Blomquist, M., Noviello, T., D’Angelo, F., Sereduk, C., Rabichow, B., Miller, A., Marin, B.-M., White, F., Sarkaria, J., Lasorella, A., Iavarone, A., Ceccarelli, M., & Tran, N. (2021). CSIG-08. ABT-414 RESISTANT GBM TUMORS HARBOR THE TEK S466I MUTATION AND EXHIBIT INCREASED STEMNESS. Neuro-Oncology, 23(Supplement_6), vi34–vi35. https://doi.org/10.1093/neuonc/noab196.134
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Katona, B. W., Long, J. M., Ahmad, N. A., Attalla, S., Bradbury, A. R., Carpenter, E. L., Clark, D. F., Constantino, G., Das, K. K., Domchek, S. M., Dudzik, C., Ebrahimzadeh, J., Ginsberg, G. G., Heiman, J., Kochman, M. L., Maxwell, K. N., McKenna, D. B., Powers, J., Shah, P. D., … Rustgi, A. K. (2021). EUS-based Pancreatic Cancer Surveillance in BRCA1/BRCA2/PALB2/ATM Carriers Without a Family History of Pancreatic Cancer. Cancer Prevention Research, 14(11), 1033–1040. https://doi.org/10.1158/1940-6207.capr-21-0161
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Reinfeld, B., Madden, M., Wolf, M., Cubas, A. de, Haake, S., Hongo, R., Axelrod, M., Bader, J., Obradovic, A., Greenwood, D., Ye, X., Balko, J., Beckermann, K., Vincent, B., Rini, B., Drake, C., Rathmell, J., & Rathmell, W. (2021). 906 Immunogenomic evaluation of clear cell renal carcinoma uncovers HK3 as a myeloid specific metabolic enzyme. Regular and Young Investigator Award Abstracts, A951–A951. https://doi.org/10.1136/jitc-2021-sitc2021.906
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Rahimi, A. S., Kim, D. N., Leitch, M., Gu, X., Haas, J. A., Ahn, C., Spangler, A., Neufeld, S., Bahrami, S., Goudreau, S., Seiler, S., Farr, D., Wooldridge, R., Haley, B., Alluri, P. G., Nwachukwu, C. R., Rao, R., & Timmerman, R. D. (2021). Early Follow-Up of Multi-Institutional Trial of Phase I Dose Escalation Using Single Fraction Stereotactic Partial Breast Irradiation (S-PBI) for Early-Stage Breast Cancer. International Journal of Radiation Oncology*Biology*Physics, 111(3), e228. https://doi.org/10.1016/j.ijrobp.2021.07.782
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Saleh, T., El-Sadoni, M., Alhesa, A., Awad, H., Jaradat, M., Al-Hazaimeh, M., Dawoud, R., Mryyian, A., & Azab, B. (2021). Expression of Senescence and Apoptosis Biomarkers in Synchronous Bilateral Breast Cancer: A Case Report. Current Oncology, 28(5), 3836–3845. https://doi.org/10.3390/curroncol28050327
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Park, K., Haura, E. B., Leighl, N. B., Mitchell, P., Shu, C. A., Girard, N., Viteri, S., Han, J.-Y., Kim, S.-W., Lee, C. K., Sabari, J. K., Spira, A. I., Yang, T.-Y., Kim, D.-W., Lee, K. H., Sanborn, R. E., Trigo, J., Goto, K., Lee, J.-S., … Cho, B. C. (2021). Amivantamab in EGFR Exon 20 Insertion–Mutated Non–Small-Cell Lung Cancer Progressing on Platinum Chemotherapy: Initial Results From the CHRYSALIS Phase I Study. Journal of Clinical Oncology, 39(30), 3391–3402. https://doi.org/10.1200/jco.21.00662
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He, Y., Rivera, J., Diossy, M., Duan, H., Bowman-Colin, C., Reed, R., Jennings, R., Novak, J., Tran, S. V., Cohen, E. F., Szuts, D., Giobbie-Hurder, A., Bronson, R. T., Bass, A. J., Signoretti, S., Szallasi, Z., Livingston, D. M., & Pathania, S. (2021). BRCA1/Trp53 heterozygosity and replication stress drive esophageal cancer development in a mouse model. Proceedings of the National Academy of Sciences, 118(41). https://doi.org/10.1073/pnas.2108421118
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Bondarenko, I., Sezer, A., Kilickap, S., Gümüş, M., Özgüroğlu, M., Gogishvili, M., Turk, H. M., Cicin, I., Bentsion, D., Gladkov, O., Clingan, P., Sriuranpong, V., Rizvi, N., Mcginniss, J., Pouliot, J., Lee, S., Seebach, F., Lowy, I., Gullo, G., & Rietschel, P. (2021). FP04.03 Clinical Benefit of First-Line Cemiplimab in Patients with Locally Advanced NSCLC: Subgroup Analysis from EMPOWER-Lung 1. Journal of Thoracic Oncology, 16(10), S951. https://doi.org/10.1016/j.jtho.2021.08.217
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Dinh, K. N., Jaksik, R., Corey, S. J., & Kimmel, M. (2021). Predicting time to relapse in acute myeloid leukemia through stochastic modeling of minimal residual disease based on clonality data. Computational and Systems Oncology, 1(3). Portico. https://doi.org/10.1002/cso2.1026
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Peters, S., Rizvi, N. A., Kuziora, M., Lai, Z., Shrestha, Y., Dey, A., Barrett, J. C., Scheuring, U., Poole, L., Abbosh, C., Raja, R., & Hellmann, M. D. (2021). 1264P Early circulating tumour DNA (ctDNA) dynamics for predicting and monitoring response to immunotherapy (IO) vs chemotherapy (CT) in patients with 1L metastatic (m) NSCLC: Analyses from the phase III MYSTIC trial. Annals of Oncology, 32, S989–S990. https://doi.org/10.1016/j.annonc.2021.08.1866
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