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2. Single-molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer

Author

Bruhm, Daniel C., Mathios, Dimitrios, Foda, Zachariah H., Annapragada, Akshaya V., Medina, Jamie E., Adleff, Vilmos, Chiao, Elaine Jiayuee, Ferreira, Leonardo, Cristiano, Stephen, White, James R., Mazzilli, Sarah A., Billatos, Ehab, Spira, Avrum, Zaidi, Ali H., Mueller, Jeffrey, Kim, Amy K., Anagnostou, Valsamo, Phallen, Jillian, Scharpf, Robert B., and Velculescu, Victor E.

Published
2023
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4. Early Noninvasive Detection of Response to Targeted Therapy in Non-Small Cell Lung Cancer

Author

Phallen, Jillian, Leal, Alessandro, Woodward, Brian D, Forde, Patrick M, Naidoo, Jarushka, Marrone, Kristen A, Brahmer, Julie R, Fiksel, Jacob, Medina, Jamie E, Cristiano, Stephen, Palsgrove, Doreen N, Gocke, Christopher D, Bruhm, Daniel C, Keshavarzian, Parissa, Adleff, Vilmos, Weihe, Elizabeth, Anagnostou, Valsamo, Scharpf, Robert B, Velculescu, Victor E, and Husain, Hatim

Subjects
Biotechnology, Cancer, Lung, Biomedical Imaging, Lung Cancer, Detection, screening and diagnosis, 4.1 Discovery and preclinical testing of markers and technologies, Good Health and Well Being, Adenocarcinoma, Aged, Aged, 80 and over, Biomarkers, Tumor, Carcinoma, Non-Small-Cell Lung, Carcinoma, Squamous Cell, Circulating Tumor DNA, DNA, Neoplasm, Female, Follow-Up Studies, Gene Expression Regulation, Neoplastic, Humans, Lung Neoplasms, Male, Middle Aged, Molecular Targeted Therapy, Mutation, Prognosis, Protein Kinase Inhibitors, Survival Rate, Tumor Burden, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

With the advent of precision oncology, there is an urgent need to develop improved methods for rapidly detecting responses to targeted therapies. Here, we have developed an ultrasensitive measure of cell-free tumor load using targeted and whole-genome sequencing approaches to assess responses to tyrosine kinase inhibitors in patients with advanced lung cancer. Analyses of 28 patients treated with anti-EGFR or HER2 therapies revealed a bimodal distribution of cell-free circulating tumor DNA (ctDNA) after therapy initiation, with molecular responders having nearly complete elimination of ctDNA (>98%). Molecular nonresponders displayed limited changes in ctDNA levels posttreatment and experienced significantly shorter progression-free survival (median 1.6 vs. 13.7 months, P < 0.0001; HR = 66.6; 95% confidence interval, 13.0-341.7), which was detected on average 4 weeks earlier than CT imaging. ctDNA analyses of patients with radiographic stable or nonmeasurable disease improved prediction of clinical outcome compared with CT imaging. These analyses provide a rapid approach for evaluating therapeutic response to targeted therapies and have important implications for the management of patients with cancer and the development of new therapeutics.Significance: Cell-free tumor load provides a novel approach for evaluating longitudinal changes in ctDNA during systemic treatment with tyrosine kinase inhibitors and serves an unmet clinical need for real-time, noninvasive detection of tumor response to targeted therapies before radiographic assessment.See related commentary by Zou and Meyerson, p. 1038.

Published
2019

6. Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

Author

Anagnostou, Valsamo, Smith, Kellie N, Forde, Patrick M, Niknafs, Noushin, Bhattacharya, Rohit, White, James, Zhang, Theresa, Adleff, Vilmos, Phallen, Jillian, Wali, Neha, Hruban, Carolyn, Guthrie, Violeta B, Rodgers, Kristen, Naidoo, Jarushka, Kang, Hyunseok, Sharfman, William, Georgiades, Christos, Verde, Franco, Illei, Peter, Li, Qing Kay, Gabrielson, Edward, Brock, Malcolm V, Zahnow, Cynthia A, Baylin, Stephen B, Scharpf, Robert B, Brahmer, Julie R, Karchin, Rachel, Pardoll, Drew M, and Velculescu, Victor E

Subjects
Prevention, Cancer, Immunization, Clinical Research, Lung, Lung Cancer, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Aetiology, 2.1 Biological and endogenous factors, Good Health and Well Being, Adult, Antibodies, Monoclonal, Antigens, Neoplasm, Antineoplastic Agents, Immunological, CTLA-4 Antigen, Carcinoma, Non-Small-Cell Lung, Cell Cycle Checkpoints, Cohort Studies, Drug Resistance, Neoplasm, Female, Humans, Immunotherapy, Ipilimumab, Janus Kinase 1, Janus Kinase 2, Lung Neoplasms, Male, Middle Aged, Mutation, Nivolumab, Programmed Cell Death 1 Receptor, Receptors, Antigen, T-Cell, Oncology and Carcinogenesis
Abstract

Immune checkpoint inhibitors have shown significant therapeutic responses against tumors containing increased mutation-associated neoantigen load. We have examined the evolving landscape of tumor neoantigens during the emergence of acquired resistance in patients with non-small cell lung cancer after initial response to immune checkpoint blockade with anti-PD-1 or anti-PD-1/anti-CTLA-4 antibodies. Analyses of matched pretreatment and resistant tumors identified genomic changes resulting in loss of 7 to 18 putative mutation-associated neoantigens in resistant clones. Peptides generated from the eliminated neoantigens elicited clonal T-cell expansion in autologous T-cell cultures, suggesting that they generated functional immune responses. Neoantigen loss occurred through elimination of tumor subclones or through deletion of chromosomal regions containing truncal alterations, and was associated with changes in T-cell receptor clonality. These analyses provide insight into the dynamics of mutational landscapes during immune checkpoint blockade and have implications for the development of immune therapies that target tumor neoantigens.Significance: Acquired resistance to immune checkpoint therapy is being recognized more commonly. This work demonstrates for the first time that acquired resistance to immune checkpoint blockade can arise in association with the evolving landscape of mutations, some of which encode tumor neoantigens recognizable by T cells. These observations imply that widening the breadth of neoantigen reactivity may mitigate the development of acquired resistance. Cancer Discov; 7(3); 264-76. ©2017 AACR.See related commentary by Yang, p. 250This article is highlighted in the In This Issue feature, p. 235.

Published
2017

7. Early evaluation of the effectiveness and cost-effectiveness of ctDNA-guided selection for adjuvant chemotherapy in stage II colon cancer

Author

Unit Opleiding Aios, Cancer, Onderzoek Medische Oncologie, MS Medische Oncologie, Kramer, Astrid, Greuter, Marjolein J E, Schraa, Suzanna J, Vink, Geraldine R, Phallen, Jillian, Velculescu, Victor E, Meijer, Gerrit A, van den Broek, Daan, Koopman, Miriam, Roodhart, Jeanine M L, Fijneman, Remond J A, Retèl, Valesca P, Coupé, Veerle M H, Unit Opleiding Aios, Cancer, Onderzoek Medische Oncologie, MS Medische Oncologie, Kramer, Astrid, Greuter, Marjolein J E, Schraa, Suzanna J, Vink, Geraldine R, Phallen, Jillian, Velculescu, Victor E, Meijer, Gerrit A, van den Broek, Daan, Koopman, Miriam, Roodhart, Jeanine M L, Fijneman, Remond J A, Retèl, Valesca P, and Coupé, Veerle M H

Published
2024

8. Early evaluation of the effectiveness and cost-effectiveness of ctDNA-guided selection for adjuvant chemotherapy in stage II colon cancer

Author

Kramer, Astrid, Greuter, Marjolein J.E., Schraa, Suzanna J., Vink, Geraldine R., Phallen, Jillian, Velculescu, Victor E., Meijer, Gerrit A., van den Broek, Daan, Koopman, Miriam, Roodhart, Jeanine M.L., Fijneman, Remond J.A., Retèl, Valesca P., Coupé, Veerle M.H., Kramer, Astrid, Greuter, Marjolein J.E., Schraa, Suzanna J., Vink, Geraldine R., Phallen, Jillian, Velculescu, Victor E., Meijer, Gerrit A., van den Broek, Daan, Koopman, Miriam, Roodhart, Jeanine M.L., Fijneman, Remond J.A., Retèl, Valesca P., and Coupé, Veerle M.H.

Abstract

Background: Current patient selection for adjuvant chemotherapy (ACT) after curative surgery for stage II colon cancer (CC) is suboptimal, causing overtreatment of high-risk patients and undertreatment of low-risk patients. Postoperative circulating tumor DNA (ctDNA) could improve patient selection for ACT. Objectives: We conducted an early model-based evaluation of the (cost-)effectiveness of ctDNA-guided selection for ACT in stage II CC in the Netherlands to assess the conditions for cost-effective implementation. Methods: A validated Markov model, simulating 1000 stage II CC patients from diagnosis to death, was supplemented with ctDNA data. Five ACT selection strategies were evaluated: the current guideline (pT4, pMMR), ctDNA-only, and three strategies that combined ctDNA status with pT4 and pMMR status in different ways. For each strategy, the costs, life years, quality-adjusted life years (QALYs), recurrences, and CC deaths were estimated. Sensitivity analyses were performed to assess the impact of the costs of ctDNA testing, strategy adherence, ctDNA as a predictive biomarker, and ctDNA test performance. Results: Model predictions showed that compared to current guidelines, the ctDNA-only strategy was less effective (+2.2% recurrences, −0.016 QALYs), while the combination strategies were more effective (−3.6% recurrences, +0.038 QALYs). The combination strategies were not cost-effective, since the incremental cost-effectiveness ratio was €67,413 per QALY, exceeding the willingness-to-pay threshold of €50,000 per QALY. Sensitivity analyses showed that the combination strategies would be cost-effective if the ctDNA test costs were lower than €1500, or if ctDNA status was predictive of treatment response, or if the ctDNA test performance improved substantially. Conclusion: Adding ctDNA to current high-risk clinicopathological features (pT4 and pMMR) can improve patient selection for ACT and can also potentially be cost-effective. Future studies should investi

Published
2024

9. Genome-wide repeat landscapes in cancer and cell-free DNA

Author

Annapragada, Akshaya V., primary, Niknafs, Noushin, additional, White, James R., additional, Bruhm, Daniel C., additional, Cherry, Christopher, additional, Medina, Jamie E., additional, Adleff, Vilmos, additional, Hruban, Carolyn, additional, Mathios, Dimitrios, additional, Foda, Zachariah H., additional, Phallen, Jillian, additional, Scharpf, Robert B., additional, and Velculescu, Victor E., additional

Published
2024
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10. Supplementary Table S12 from Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer

Author

Murray, Joseph C., primary, Sivapalan, Lavanya, primary, Hummelink, Karlijn, primary, Balan, Archana, primary, White, James R., primary, Niknafs, Noushin, primary, Rhymee, Lamia, primary, Pereira, Gavin, primary, Rao, Nisha, primary, Weksler, Benny, primary, Bahary, Nathan, primary, Phallen, Jillian, primary, Leal, Alessandro, primary, Bartlett, David L., primary, Marrone, Kristen A., primary, Naidoo, Jarushka, primary, Goel, Akul, primary, Levy, Benjamin, primary, Rosner, Samuel, primary, Hann, Christine L., primary, Scott, Susan C., primary, Feliciano, Josephine, primary, Lam, Vincent K., primary, Ettinger, David S., primary, Li, Qing Kay, primary, Illei, Peter B., primary, Monkhorst, Kim, primary, Scharpf, Robert B., primary, Brahmer, Julie R., primary, Velculescu, Victor E., primary, Zaidi, Ali H., primary, Forde, Patrick M., primary, and Anagnostou, Valsamo, primary

Published
2024
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11. Supplementary Figure S7 from Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer

Author

Murray, Joseph C., primary, Sivapalan, Lavanya, primary, Hummelink, Karlijn, primary, Balan, Archana, primary, White, James R., primary, Niknafs, Noushin, primary, Rhymee, Lamia, primary, Pereira, Gavin, primary, Rao, Nisha, primary, Weksler, Benny, primary, Bahary, Nathan, primary, Phallen, Jillian, primary, Leal, Alessandro, primary, Bartlett, David L., primary, Marrone, Kristen A., primary, Naidoo, Jarushka, primary, Goel, Akul, primary, Levy, Benjamin, primary, Rosner, Samuel, primary, Hann, Christine L., primary, Scott, Susan C., primary, Feliciano, Josephine, primary, Lam, Vincent K., primary, Ettinger, David S., primary, Li, Qing Kay, primary, Illei, Peter B., primary, Monkhorst, Kim, primary, Scharpf, Robert B., primary, Brahmer, Julie R., primary, Velculescu, Victor E., primary, Zaidi, Ali H., primary, Forde, Patrick M., primary, and Anagnostou, Valsamo, primary

Published
2024
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12. Data from Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer

Author

Murray, Joseph C., primary, Sivapalan, Lavanya, primary, Hummelink, Karlijn, primary, Balan, Archana, primary, White, James R., primary, Niknafs, Noushin, primary, Rhymee, Lamia, primary, Pereira, Gavin, primary, Rao, Nisha, primary, Weksler, Benny, primary, Bahary, Nathan, primary, Phallen, Jillian, primary, Leal, Alessandro, primary, Bartlett, David L., primary, Marrone, Kristen A., primary, Naidoo, Jarushka, primary, Goel, Akul, primary, Levy, Benjamin, primary, Rosner, Samuel, primary, Hann, Christine L., primary, Scott, Susan C., primary, Feliciano, Josephine, primary, Lam, Vincent K., primary, Ettinger, David S., primary, Li, Qing Kay, primary, Illei, Peter B., primary, Monkhorst, Kim, primary, Scharpf, Robert B., primary, Brahmer, Julie R., primary, Velculescu, Victor E., primary, Zaidi, Ali H., primary, Forde, Patrick M., primary, and Anagnostou, Valsamo, primary

Published
2024
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13. Detection and characterization of lung cancer using cell-free DNA fragmentomes

Author

Mathios, Dimitrios, Johansen, Jakob Sidenius, Cristiano, Stephen, Medina, Jamie E., Phallen, Jillian, Larsen, Klaus R., Bruhm, Daniel C., Niknafs, Noushin, Ferreira, Leonardo, Adleff, Vilmos, Chiao, Jia Yuee, Leal, Alessandro, Noe, Michael, White, James R., Arun, Adith S., Hruban, Carolyn, Annapragada, Akshaya V., Jensen, Sarah Østrup, Ørntoft, Mai-Britt Worm, Madsen, Anders Husted, Carvalho, Beatriz, de Wit, Meike, Carey, Jacob, Dracopoli, Nicholas C., Maddala, Tara, Fang, Kenneth C., Hartman, Anne-Renee, Forde, Patrick M., Anagnostou, Valsamo, Brahmer, Julie R., Fijneman, Remond J. A., Nielsen, Hans Jørgen, Meijer, Gerrit A., Andersen, Claus Lindbjerg, Mellemgaard, Anders, Bojesen, Stig E., Scharpf, Robert B., and Velculescu, Victor E.

Published
2021
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14. Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer

Author

Murray, Joseph C., primary, Sivapalan, Lavanya, additional, Hummelink, Karlijn, additional, Balan, Archana, additional, White, James R., additional, Niknafs, Noushin, additional, Rhymee, Lamia, additional, Pereira, Gavin, additional, Rao, Nisha, additional, Weksler, Benny, additional, Bahary, Nathan, additional, Phallen, Jillian, additional, Leal, Alessandro, additional, Bartlett, David L., additional, Marrone, Kristen A., additional, Naidoo, Jarushka, additional, Goel, Akul, additional, Levy, Benjamin, additional, Rosner, Samuel, additional, Hann, Christine L., additional, Scott, Susan C., additional, Feliciano, Josephine, additional, Lam, Vincent K., additional, Ettinger, David S., additional, Li, Qing Kay, additional, Illei, Peter B., additional, Monkhorst, Kim, additional, Scharpf, Robert B., additional, Brahmer, Julie R., additional, Velculescu, Victor E., additional, Zaidi, Ali H., additional, Forde, Patrick M., additional, and Anagnostou, Valsamo, additional

Published
2023
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15. Genome-wide cell-free DNA fragmentation in patients with cancer

Author

Cristiano, Stephen, Leal, Alessandro, Phallen, Jillian, Fiksel, Jacob, Adleff, Vilmos, Bruhm, Daniel C., and Jensen, Sarah Østrup

Subjects
Blood -- Medical examination, Cancer patients -- Medical examination, Cancer -- Diagnosis, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Cell-free DNA in the blood provides a non-invasive diagnostic avenue for patients with cancer.sup.1. However, characteristics of the origins and molecular features of cell-free DNA are poorly understood. Here we developed an approach to evaluate fragmentation patterns of cell-free DNA across the genome, and found that profiles of healthy individuals reflected nucleosomal patterns of white blood cells, whereas patients with cancer had altered fragmentation profiles. We used this method to analyse the fragmentation profiles of 236 patients with breast, colorectal, lung, ovarian, pancreatic, gastric or bile duct cancer and 245 healthy individuals. A machine learning model that incorporated genome-wide fragmentation features had sensitivities of detection ranging from 57% to more than 99% among the seven cancer types at 98% specificity, with an overall area under the curve value of 0.94. Fragmentation profiles could be used to identify the tissue of origin of the cancers to a limited number of sites in 75% of cases. Combining our approach with mutation-based cell-free DNA analyses detected 91% of patients with cancer. The results of these analyses highlight important properties of cell-free DNA and provide a proof-of-principle approach for the screening, early detection and monitoring of human cancer. Analyses of fragmentation patterns of cell-free DNA in the blood of patients with cancer and healthy individuals using a machine learning algorithm provide a proof-of principle approach for the early detection and screening of human cancer., Author(s): Stephen Cristiano [sup.1] [sup.2] , Alessandro Leal [sup.1] , Jillian Phallen [sup.1] , Jacob Fiksel [sup.1] [sup.2] , Vilmos Adleff [sup.1] , Daniel C. Bruhm [sup.1] , Sarah Østrup [...]

Published
2019
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16. White blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer

Author

Leal, Alessandro, van Grieken, Nicole C. T., Palsgrove, Doreen N., Phallen, Jillian, Medina, Jamie E., Hruban, Carolyn, Broeckaert, Mark A. M., Anagnostou, Valsamo, Adleff, Vilmos, Bruhm, Daniel C., Canzoniero, Jenna V., Fiksel, Jacob, Nordsmark, Marianne, Warmerdam, Fabienne A. R. M., Verheul, Henk M. W., van Spronsen, Dick Johan, Beerepoot, Laurens V., Geenen, Maud M., Portielje, Johanneke E. A., Jansen, Edwin P. M., van Sandick, Johanna, Meershoek-Klein Kranenbarg, Elma, van Laarhoven, Hanneke W. M., van der Peet, Donald L., van de Velde, Cornelis J. H., Verheij, Marcel, Fijneman, Remond, Scharpf, Robert B., Meijer, Gerrit A., Cats, Annemieke, and Velculescu, Victor E.

Published
2020
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17. Supplementary Tables from Detecting Liver Cancer Using Cell-Free DNA Fragmentomes

Author

Foda, Zachariah H., primary, Annapragada, Akshaya V., primary, Boyapati, Kavya, primary, Bruhm, Daniel C., primary, Vulpescu, Nicholas A., primary, Medina, Jamie E., primary, Mathios, Dimitrios, primary, Cristiano, Stephen, primary, Niknafs, Noushin, primary, Luu, Harry T., primary, Goggins, Michael G., primary, Anders, Robert A., primary, Sun, Jing, primary, Meta, Shruti H., primary, Thomas, David L., primary, Kirk, Gregory D., primary, Adleff, Vilmos, primary, Phallen, Jillian, primary, Scharpf, Robert B., primary, Kim, Amy K., primary, and Velculescu, Victor E., primary

Published
2023
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18. Data from Detecting Liver Cancer Using Cell-Free DNA Fragmentomes

Author

Foda, Zachariah H., primary, Annapragada, Akshaya V., primary, Boyapati, Kavya, primary, Bruhm, Daniel C., primary, Vulpescu, Nicholas A., primary, Medina, Jamie E., primary, Mathios, Dimitrios, primary, Cristiano, Stephen, primary, Niknafs, Noushin, primary, Luu, Harry T., primary, Goggins, Michael G., primary, Anders, Robert A., primary, Sun, Jing, primary, Meta, Shruti H., primary, Thomas, David L., primary, Kirk, Gregory D., primary, Adleff, Vilmos, primary, Phallen, Jillian, primary, Scharpf, Robert B., primary, Kim, Amy K., primary, and Velculescu, Victor E., primary

Published
2023
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19. Abstract 773: Early detection of ovarian cancer using cell-free DNA fragmentomes

Author

Annapragada, Akshaya V., primary, Medina, Jamie E., additional, Lof, Pien, additional, Mathios, Dimitrios, additional, Foda, Zachariah H., additional, Noë, Michaël, additional, Short, Sarah, additional, Bartolomucci, Adrianna, additional, Bruhm, Daniel C., additional, Jung, Euihye, additional, Canzoniero, Jenna, additional, Niknafs, Noushin, additional, Cristiano, Stephen, additional, Adleff, Vilmos, additional, Symecko, Heather, additional, van de Broek, Daan, additional, Baylin, Stephen B., additional, Press, Michael F., additional, Slamon, Dennis, additional, Konecny, Gottfried, additional, Domchek, Susan, additional, Drapkin, Ronny, additional, Phallen, Jillian, additional, Scharpf, Robert B., additional, Lok, Christianne, additional, and Velculescu, Victor E., additional

Published
2023
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20. Abstract 5587: Ultra-deep targeted sequencing of cell-free DNA and patient-matched white blood cells for treatment response evaluation in patients with metastatic colorectal cancer

Author

Erve, Iris van 't, primary, Medina, Jamie E., additional, Leal, Alessandro, additional, Papp, Eniko, additional, Phallen, Jillian, additional, Adleff, Vilmos, additional, Chiao, Elaine Jiayuee, additional, Arun, Adith S., additional, Bolhuis, Karen, additional, Simmons, John K., additional, Karandikar, Aanavi, additional, Valkenburg, Kenneth C., additional, Sausen, Mark, additional, Angiuoli, Samuel V., additional, Scharpf, Robert B., additional, Punt, Cornelis J., additional, Meijer, Gerrit J., additional, Velculescu, Victor E., additional, and Fijneman, Remond J., additional

Published
2023
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21. Abstract 3366: A machine learning approach to determine the cellular origin of variants in liquid biopsies

Author

Canzoniero, Jenna V., primary, Balan, Archana, additional, Phallen, Jillian, additional, Landon, Blair V., additional, Sivapalan, Lavanya, additional, Green, Benjamin, additional, Belcaid, Zineb, additional, Scott, Susan C., additional, Pereira, Gavin, additional, Lam, Vincent K., additional, Zaidi, Ali H., additional, Kelly, Ronan J., additional, Hann, Christine L., additional, Iams, Wade T., additional, Lovly, Christine M., additional, Forde, Patrick M., additional, Meijer, Gerrit A., additional, Vink, Geraldine R., additional, Fijneman, Remond J., additional, Group, The MEDOCC, additional, Velculescu, Victor E., additional, Scharpf, Robert B., additional, and Anagnostou, Valsamo, additional

Published
2023
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22. Supplementary Figures S1-S14 from Detecting Liver Cancer Using Cell-Free DNA Fragmentomes

Author

Foda, Zachariah H., primary, Annapragada, Akshaya V., primary, Boyapati, Kavya, primary, Bruhm, Daniel C., primary, Vulpescu, Nicholas A., primary, Medina, Jamie E., primary, Mathios, Dimitrios, primary, Cristiano, Stephen, primary, Niknafs, Noushin, primary, Luu, Harry T., primary, Goggins, Michael G., primary, Anders, Robert A., primary, Sun, Jing, primary, Meta, Shruti H., primary, Thomas, David L., primary, Kirk, Gregory D., primary, Adleff, Vilmos, primary, Phallen, Jillian, primary, Scharpf, Robert B., primary, Kim, Amy K., primary, and Velculescu, Victor E., primary

Published
2023
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23. Supplementary Tables S1 - S18 from Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

Author

Anagnostou, Valsamo, primary, Smith, Kellie N., primary, Forde, Patrick M., primary, Niknafs, Noushin, primary, Bhattacharya, Rohit, primary, White, James, primary, Zhang, Theresa, primary, Adleff, Vilmos, primary, Phallen, Jillian, primary, Wali, Neha, primary, Hruban, Carolyn, primary, Guthrie, Violeta B., primary, Rodgers, Kristen, primary, Naidoo, Jarushka, primary, Kang, Hyunseok, primary, Sharfman, William, primary, Georgiades, Christos, primary, Verde, Franco, primary, Illei, Peter, primary, Li, Qing Kay, primary, Gabrielson, Edward, primary, Brock, Malcolm V., primary, Zahnow, Cynthia A., primary, Baylin, Stephen B., primary, Scharpf, Robert B., primary, Brahmer, Julie R., primary, Karchin, Rachel, primary, Pardoll, Drew M., primary, and Velculescu, Victor E., primary

Published
2023
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24. Supplementary Figures S1 - S16 from Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

Author

Anagnostou, Valsamo, primary, Smith, Kellie N., primary, Forde, Patrick M., primary, Niknafs, Noushin, primary, Bhattacharya, Rohit, primary, White, James, primary, Zhang, Theresa, primary, Adleff, Vilmos, primary, Phallen, Jillian, primary, Wali, Neha, primary, Hruban, Carolyn, primary, Guthrie, Violeta B., primary, Rodgers, Kristen, primary, Naidoo, Jarushka, primary, Kang, Hyunseok, primary, Sharfman, William, primary, Georgiades, Christos, primary, Verde, Franco, primary, Illei, Peter, primary, Li, Qing Kay, primary, Gabrielson, Edward, primary, Brock, Malcolm V., primary, Zahnow, Cynthia A., primary, Baylin, Stephen B., primary, Scharpf, Robert B., primary, Brahmer, Julie R., primary, Karchin, Rachel, primary, Pardoll, Drew M., primary, and Velculescu, Victor E., primary

Published
2023
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25. Data from Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

Author

Anagnostou, Valsamo, primary, Smith, Kellie N., primary, Forde, Patrick M., primary, Niknafs, Noushin, primary, Bhattacharya, Rohit, primary, White, James, primary, Zhang, Theresa, primary, Adleff, Vilmos, primary, Phallen, Jillian, primary, Wali, Neha, primary, Hruban, Carolyn, primary, Guthrie, Violeta B., primary, Rodgers, Kristen, primary, Naidoo, Jarushka, primary, Kang, Hyunseok, primary, Sharfman, William, primary, Georgiades, Christos, primary, Verde, Franco, primary, Illei, Peter, primary, Li, Qing Kay, primary, Gabrielson, Edward, primary, Brock, Malcolm V., primary, Zahnow, Cynthia A., primary, Baylin, Stephen B., primary, Scharpf, Robert B., primary, Brahmer, Julie R., primary, Karchin, Rachel, primary, Pardoll, Drew M., primary, and Velculescu, Victor E., primary

Published
2023
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26. Supplementary Figure Legends from Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

Author

Anagnostou, Valsamo, primary, Smith, Kellie N., primary, Forde, Patrick M., primary, Niknafs, Noushin, primary, Bhattacharya, Rohit, primary, White, James, primary, Zhang, Theresa, primary, Adleff, Vilmos, primary, Phallen, Jillian, primary, Wali, Neha, primary, Hruban, Carolyn, primary, Guthrie, Violeta B., primary, Rodgers, Kristen, primary, Naidoo, Jarushka, primary, Kang, Hyunseok, primary, Sharfman, William, primary, Georgiades, Christos, primary, Verde, Franco, primary, Illei, Peter, primary, Li, Qing Kay, primary, Gabrielson, Edward, primary, Brock, Malcolm V., primary, Zahnow, Cynthia A., primary, Baylin, Stephen B., primary, Scharpf, Robert B., primary, Brahmer, Julie R., primary, Karchin, Rachel, primary, Pardoll, Drew M., primary, and Velculescu, Victor E., primary

Published
2023
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27. Supplementary Figures S1-S15 from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells

Author

van 't Erve, Iris, primary, Medina, Jamie E., primary, Leal, Alessandro, primary, Papp, Eniko, primary, Phallen, Jillian, primary, Adleff, Vilmos, primary, Chiao, Elaine Jiayuee, primary, Arun, Adith S., primary, Bolhuis, Karen, primary, Simmons, John K., primary, Karandikar, Aanavi, primary, Valkenburg, Kenneth C., primary, Sausen, Mark, primary, Angiuoli, Samuel V., primary, Scharpf, Robert B., primary, Punt, Cornelis J.A., primary, Meijer, Gerrit A., primary, Velculescu, Victor E., primary, and Fijneman, Remond J.A., primary

Published
2023
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28. Supplementary Data S1 from Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells

Author

van 't Erve, Iris, primary, Medina, Jamie E., primary, Leal, Alessandro, primary, Papp, Eniko, primary, Phallen, Jillian, primary, Adleff, Vilmos, primary, Chiao, Elaine Jiayuee, primary, Arun, Adith S., primary, Bolhuis, Karen, primary, Simmons, John K., primary, Karandikar, Aanavi, primary, Valkenburg, Kenneth C., primary, Sausen, Mark, primary, Angiuoli, Samuel V., primary, Scharpf, Robert B., primary, Punt, Cornelis J.A., primary, Meijer, Gerrit A., primary, Velculescu, Victor E., primary, and Fijneman, Remond J.A., primary

Published
2023
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29. Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells

Author

Epi Kanker Team B, Cancer, van 't Erve, Iris, Medina, Jamie E., Leal, Alessandro, Papp, Eniko, Phallen, Jillian, Adleff, Vilmos, Chiao, Elaine Jiayuee, Arun, Adith S., Bolhuis, Karen, Simmons, John K., Karandikar, Aanavi, Valkenburg, Kenneth C., Sausen, Mark, Angiuoli, Samuel V., Scharpf, Robert B., Punt, Cornelis J.A., Meijer, Gerrit A., Velculescu, Victor E., Fijneman, Remond J.A., Epi Kanker Team B, Cancer, van 't Erve, Iris, Medina, Jamie E., Leal, Alessandro, Papp, Eniko, Phallen, Jillian, Adleff, Vilmos, Chiao, Elaine Jiayuee, Arun, Adith S., Bolhuis, Karen, Simmons, John K., Karandikar, Aanavi, Valkenburg, Kenneth C., Sausen, Mark, Angiuoli, Samuel V., Scharpf, Robert B., Punt, Cornelis J.A., Meijer, Gerrit A., Velculescu, Victor E., and Fijneman, Remond J.A.

Published
2023

30. Supplementary Tables from Early Noninvasive Detection of Response to Targeted Therapy in Non–Small Cell Lung Cancer

Author

Phallen, Jillian, primary, Leal, Alessandro, primary, Woodward, Brian D., primary, Forde, Patrick M., primary, Naidoo, Jarushka, primary, Marrone, Kristen A., primary, Brahmer, Julie R., primary, Fiksel, Jacob, primary, Medina, Jamie E., primary, Cristiano, Stephen, primary, Palsgrove, Doreen N., primary, Gocke, Christopher D., primary, Bruhm, Daniel C., primary, Keshavarzian, Parissa, primary, Adleff, Vilmos, primary, Weihe, Elizabeth, primary, Anagnostou, Valsamo, primary, Scharpf, Robert B., primary, Velculescu, Victor E., primary, and Husain, Hatim, primary

Published
2023
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31. Supplementary Tables S1-S18 from Dynamics of Tumor and Immune Responses during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

Author

Anagnostou, Valsamo, primary, Forde, Patrick M., primary, White, James R., primary, Niknafs, Noushin, primary, Hruban, Carolyn, primary, Naidoo, Jarushka, primary, Marrone, Kristen, primary, Sivakumar, I.K. Ashok, primary, Bruhm, Daniel C., primary, Rosner, Samuel, primary, Phallen, Jillian, primary, Leal, Alessandro, primary, Adleff, Vilmos, primary, Smith, Kellie N., primary, Cottrell, Tricia R., primary, Rhymee, Lamia, primary, Palsgrove, Doreen N., primary, Hann, Christine L., primary, Levy, Benjamin, primary, Feliciano, Josephine, primary, Georgiades, Christos, primary, Verde, Franco, primary, Illei, Peter, primary, Li, Qing Kay, primary, Gabrielson, Edward, primary, Brock, Malcolm V., primary, Isbell, James M., primary, Sauter, Jennifer L., primary, Taube, Janis, primary, Scharpf, Robert B., primary, Karchin, Rachel, primary, Pardoll, Drew M., primary, Chaft, Jamie E., primary, Hellmann, Matthew D., primary, Brahmer, Julie R., primary, and Velculescu, Victor E., primary

Published
2023
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32. Supplementary Table S3 from Phase I Study of Rapid Alternation of Sunitinib and Regorafenib for the Treatment of Tyrosine Kinase Inhibitor Refractory Gastrointestinal Stromal Tumors

Author

Serrano, César, primary, Leal, Alessandro, primary, Kuang, Yanan, primary, Morgan, Jeffrey A., primary, Barysauskas, Constance M., primary, Phallen, Jillian, primary, Triplett, Olivia, primary, Mariño-Enríquez, Adrián, primary, Wagner, Andrew J., primary, Demetri, George D., primary, Velculescu, Victor E., primary, Paweletz, Cloud P., primary, Fletcher, Jonathan A., primary, and George, Suzanne, primary

Published
2023
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33. Data from Dynamics of Tumor and Immune Responses during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

Author

Anagnostou, Valsamo, primary, Forde, Patrick M., primary, White, James R., primary, Niknafs, Noushin, primary, Hruban, Carolyn, primary, Naidoo, Jarushka, primary, Marrone, Kristen, primary, Sivakumar, I.K. Ashok, primary, Bruhm, Daniel C., primary, Rosner, Samuel, primary, Phallen, Jillian, primary, Leal, Alessandro, primary, Adleff, Vilmos, primary, Smith, Kellie N., primary, Cottrell, Tricia R., primary, Rhymee, Lamia, primary, Palsgrove, Doreen N., primary, Hann, Christine L., primary, Levy, Benjamin, primary, Feliciano, Josephine, primary, Georgiades, Christos, primary, Verde, Franco, primary, Illei, Peter, primary, Li, Qing Kay, primary, Gabrielson, Edward, primary, Brock, Malcolm V., primary, Isbell, James M., primary, Sauter, Jennifer L., primary, Taube, Janis, primary, Scharpf, Robert B., primary, Karchin, Rachel, primary, Pardoll, Drew M., primary, Chaft, Jamie E., primary, Hellmann, Matthew D., primary, Brahmer, Julie R., primary, and Velculescu, Victor E., primary

Published
2023
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34. Supplementary Figure S1 from Phase I Study of Rapid Alternation of Sunitinib and Regorafenib for the Treatment of Tyrosine Kinase Inhibitor Refractory Gastrointestinal Stromal Tumors

Author

Serrano, César, primary, Leal, Alessandro, primary, Kuang, Yanan, primary, Morgan, Jeffrey A., primary, Barysauskas, Constance M., primary, Phallen, Jillian, primary, Triplett, Olivia, primary, Mariño-Enríquez, Adrián, primary, Wagner, Andrew J., primary, Demetri, George D., primary, Velculescu, Victor E., primary, Paweletz, Cloud P., primary, Fletcher, Jonathan A., primary, and George, Suzanne, primary

Published
2023
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35. Supplementary Figures S1-S14 from Dynamics of Tumor and Immune Responses during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

Author

Anagnostou, Valsamo, primary, Forde, Patrick M., primary, White, James R., primary, Niknafs, Noushin, primary, Hruban, Carolyn, primary, Naidoo, Jarushka, primary, Marrone, Kristen, primary, Sivakumar, I.K. Ashok, primary, Bruhm, Daniel C., primary, Rosner, Samuel, primary, Phallen, Jillian, primary, Leal, Alessandro, primary, Adleff, Vilmos, primary, Smith, Kellie N., primary, Cottrell, Tricia R., primary, Rhymee, Lamia, primary, Palsgrove, Doreen N., primary, Hann, Christine L., primary, Levy, Benjamin, primary, Feliciano, Josephine, primary, Georgiades, Christos, primary, Verde, Franco, primary, Illei, Peter, primary, Li, Qing Kay, primary, Gabrielson, Edward, primary, Brock, Malcolm V., primary, Isbell, James M., primary, Sauter, Jennifer L., primary, Taube, Janis, primary, Scharpf, Robert B., primary, Karchin, Rachel, primary, Pardoll, Drew M., primary, Chaft, Jamie E., primary, Hellmann, Matthew D., primary, Brahmer, Julie R., primary, and Velculescu, Victor E., primary

Published
2023
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36. Supplementary Figures from Early Noninvasive Detection of Response to Targeted Therapy in Non–Small Cell Lung Cancer

Author

Phallen, Jillian, primary, Leal, Alessandro, primary, Woodward, Brian D., primary, Forde, Patrick M., primary, Naidoo, Jarushka, primary, Marrone, Kristen A., primary, Brahmer, Julie R., primary, Fiksel, Jacob, primary, Medina, Jamie E., primary, Cristiano, Stephen, primary, Palsgrove, Doreen N., primary, Gocke, Christopher D., primary, Bruhm, Daniel C., primary, Keshavarzian, Parissa, primary, Adleff, Vilmos, primary, Weihe, Elizabeth, primary, Anagnostou, Valsamo, primary, Scharpf, Robert B., primary, Velculescu, Victor E., primary, and Husain, Hatim, primary

Published
2023
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37. Supplementary Methods from Phase I Study of Rapid Alternation of Sunitinib and Regorafenib for the Treatment of Tyrosine Kinase Inhibitor Refractory Gastrointestinal Stromal Tumors

Author

Serrano, César, primary, Leal, Alessandro, primary, Kuang, Yanan, primary, Morgan, Jeffrey A., primary, Barysauskas, Constance M., primary, Phallen, Jillian, primary, Triplett, Olivia, primary, Mariño-Enríquez, Adrián, primary, Wagner, Andrew J., primary, Demetri, George D., primary, Velculescu, Victor E., primary, Paweletz, Cloud P., primary, Fletcher, Jonathan A., primary, and George, Suzanne, primary

Published
2023
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38. Data from Early Noninvasive Detection of Response to Targeted Therapy in Non–Small Cell Lung Cancer

Author

Phallen, Jillian, primary, Leal, Alessandro, primary, Woodward, Brian D., primary, Forde, Patrick M., primary, Naidoo, Jarushka, primary, Marrone, Kristen A., primary, Brahmer, Julie R., primary, Fiksel, Jacob, primary, Medina, Jamie E., primary, Cristiano, Stephen, primary, Palsgrove, Doreen N., primary, Gocke, Christopher D., primary, Bruhm, Daniel C., primary, Keshavarzian, Parissa, primary, Adleff, Vilmos, primary, Weihe, Elizabeth, primary, Anagnostou, Valsamo, primary, Scharpf, Robert B., primary, Velculescu, Victor E., primary, and Husain, Hatim, primary

Published
2023
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39. Data Supplement from TLR9 Is Critical for Glioma Stem Cell Maintenance and Targeting

Author

Herrmann, Andreas, primary, Cherryholmes, Gregory, primary, Schroeder, Anne, primary, Phallen, Jillian, primary, Alizadeh, Darya, primary, Xin, Hong, primary, Wang, Tianyi, primary, Lee, Heehyoung, primary, Lahtz, Christoph, primary, Swiderski, Piotr, primary, Armstrong, Brian, primary, Kowolik, Claudia, primary, Gallia, Gary L., primary, Lim, Michael, primary, Brown, Christine, primary, Badie, Behnam, primary, Forman, Stephen, primary, Kortylewski, Marcin, primary, Jove, Richard, primary, and Yu, Hua, primary

Published
2023
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40. Data from TLR9 Is Critical for Glioma Stem Cell Maintenance and Targeting

Author

Herrmann, Andreas, primary, Cherryholmes, Gregory, primary, Schroeder, Anne, primary, Phallen, Jillian, primary, Alizadeh, Darya, primary, Xin, Hong, primary, Wang, Tianyi, primary, Lee, Heehyoung, primary, Lahtz, Christoph, primary, Swiderski, Piotr, primary, Armstrong, Brian, primary, Kowolik, Claudia, primary, Gallia, Gary L., primary, Lim, Michael, primary, Brown, Christine, primary, Badie, Behnam, primary, Forman, Stephen, primary, Kortylewski, Marcin, primary, Jove, Richard, primary, and Yu, Hua, primary

Published
2023
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41. Metastatic colorectal cancer treatment response evaluation by ultra-deep sequencing of cell-free DNA and matched white blood cells

Author

van 't Erve, Iris, primary, Medina, Jamie E., additional, Leal, Alessandro, additional, Papp, Eniko, additional, Phallen, Jillian, additional, Adleff, Vilmos, additional, Chiao, Elaine Jiayuee., additional, Arun, Adith S., additional, Bolhuis, Karen, additional, Simmons, John K., additional, Karandikar, Aanavi, additional, Valkenburg, Kenneth C., additional, Sausen, Mark, additional, Angiuoli, Samuel V., additional, Scharpf, Robert B., additional, Punt, Cornelis J.A., additional, Meijer, Gerrit A., additional, Velculescu, Victor E., additional, and Fijneman, Remond J.A., additional

Published
2022
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42. Detecting liver cancer using cell-free DNA fragmentomes

Author

Foda, Zachariah H., primary, Annapragada, Akshaya V., additional, Boyapati, Kavya, additional, Bruhm, Daniel C., additional, Vulpescu, Nicholas A., additional, Medina, Jamie E., additional, Mathios, Dimitrios, additional, Cristiano, Stephen, additional, Niknafs, Noushin, additional, Luu, Harry T., additional, Goggins, Michael G., additional, Anders, Robert A., additional, Sun, Jing, additional, Mehta, Shruti H., additional, Thomas, David L., additional, Kirk, Gregory D., additional, Adleff, Vilmos, additional, Phallen, Jillian, additional, Scharpf, Robert B., additional, Kim, Amy K., additional, and Velculescu, Victor E., additional

Published
2022
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44. Anti-PD-1 Blockade and Stereotactic Radiation Produce Long-Term Survival in Mice With Intracranial Gliomas

Author

Zeng, Jing, See, Alfred P., Phallen, Jillian, Jackson, Christopher M., Belcaid, Zineb, Ruzevick, Jacob, Durham, Nicholas, Meyer, Christian, Harris, Timothy J., Albesiano, Emilia, Pradilla, Gustavo, Ford, Eric, Wong, John, Hammers, Hans-Joerg, Mathios, Dimitris, Tyler, Betty, Brem, Henry, Tran, Phuoc T., Pardoll, Drew, Drake, Charles G., and Lim, Michael

Published
2013
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45. The genomic landscape of response to EGFR blockade in colorectal cancer

Author

Bertotti, Andrea, Papp, Eniko, Jones, Sian, Adleff, Vilmos, Anagnostou, Valsamo, Lupo, Barbara, Sausen, Mark, Phallen, Jillian, Hruban, Carolyn A., Tokheim, Collin, Niknafs, Noushin, Nesselbush, Monica, Lytle, Karli, Sassi, Francesco, Cottino, Francesca, Migliardi, Giorgia, Zanella, Eugenia R., Riberof, Dario, Russolillo, Nadia, Mellano, Alfredo, Muratore, Andrea, Paraluppi, Gianluca, Salizzoni, Mauro, Marsoni, Silvia, Kragh, Michael, Lantto, Johan, Cassingena, Andrea, Li, Qing Kay, Karchin, Rachel, Scharpf, Robert, Sartore-Bianchi, Andrea, Siena, Salvatore, Diaz, Jr., Luis A., Trusolino, Livio, and Velculescu, Victor E.

Subjects
Gene mutations -- Identification and classification -- Health aspects, Drug metabolism -- Genetic aspects, Colorectal cancer -- Genetic aspects -- Care and treatment, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Colorectal cancer is the third most common cancer worldwide, with 1.2 million patients diagnosed annually. In late-stage colorectal cancer, the most commonly used targeted therapies are the monoclonal antibodies cetuximab [...]

Published
2015

47. Abstract 5159: Towards population-scale screening of human cancer using genome-wide fragmentation profiles of cell-free DNA

Author

Annapragada, Akshaya V., primary, Mathios, Dimitrios, additional, Cristiano, Stephen, additional, Medina, Jamie E., additional, Adleff, Vilmos, additional, Niknafs, Noushin, additional, Carey, Jacob, additional, Dracopoli, Nic, additional, Bach, Peter, additional, Phallen, Jillian, additional, Velculescu, Victor E., additional, and Scharpf, Robert B., additional

Published
2022
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49. α5-GABAA receptors negatively regulate MYC-amplified medulloblastoma growth

Author

Sengupta, Soma, Weeraratne, Shyamal Dilhan, Sun, Hongyu, Phallen, Jillian, Rallapalli, Sundari K., Teider, Natalia, Kosaras, Bela, Amani, Vladimir, Pierre-Francois, Jessica, Tang, Yujie, Nguyen, Brian, Yu, Furong, Schubert, Simone, Balansay, Brianna, Mathios, Dimitris, Lechpammer, Mirna, Archer, Tenley C., Tran, Phuoc, Reimer, Richard J., Cook, James M., Lim, Michael, Jensen, Frances E., Pomeroy, Scott L., and Cho, Yoon-Jae

Published
2014
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