Dr. Valsamo Anagnostou

Publications

• Palmer T, Kessler MD, Shao XM, Balan A, Yarchoan M, Zaidi N, Lopez-Vidal TY, Saeed A, Gore J, Azad NS, Favorov AV, Anagnostou V, Karchin R, Gaykalova DA, Danilova L, Fertig EJ (2024) SpliceMutr enables pan-cancer analysis of splicing-derived neoantigen burden in tumors bioRxiv, May 26. doi: 10.1101/2023.05.26.542165
• Albert BA, Yang Y, Shao XM, Singh D, Smith KN, Anagnostou V, Karchin R Deep neural networks predict class I major histocompatibility complex epitope presentation and transfer learn neoepitope immunogenicity (2023) Nat Mach Intell. https://doi.org/10.1038/s42256-023-00694-6
• Niknafs N, Balan A, Cherry C, Hummelink K, Monkhorst K, Shao XM, Belcaid Z, Marrone KA, Murray J, Smith KN, Levy B, Feliciano J, Hann CL, Lam V, Pardoll DM, Karchin R, Seiwert TY, Brahmer JR, Forde PM, Velculescu VE, Anagnostou V. (2023) Persistent mutation burden drives sustained anti-tumor immune responses. Nat Med. Feb;29(2):440-449
• Scott SC, Shao XM, Niknafs N, Balan A, Pereira G, Marrone KA, Lam VK, Murray JC, Feliciano JL, Levy BP, Ettinger DS, Hann CL, Brahmer JR, Forde PM, Karchin R, Naidoo J, Anagnostou V. (2022) Sex-specific differences in immunogenic features of response to immune checkpoint blockade Front Oncol. 2022 Aug;12:945798.
• Shao XM, Huang J, Niknafs N, Balan A, Cherry C, White J, Velculescu VE, Anagnostou V, Karchin R. HLA class II immunogenic mutation burden predicts response to immune checkpoint blockade. Ann Oncol. 2022 Jul;33(7):728-738. doi: 10.1016/j.annonc.2022.03.013. Epub 2022 Mar 23. Erratum in: Ann Oncol. 2023 Jul;34(7):634. PMID: 35339648; PMCID: PMC10621650.
• Forde PM, Anagnostou V, Sun Z, Dahlberg SE, Kindler HL, Niknafs N, Purcell T, Santana-Davila R, Dudek AZ, Borghaei H, Lanis M, Belcaid Z, Smith KN, Balan A, White JR, Cherry C, Ashok Sivakumar IK, Shao XM, Chan HY, Singh D, Thapa S, Illei PB, Pardoll DM, Karchin R, Velculescu VE, Brahmer JR, Ramalingam SS.(2021) Durvalumab with platimum-pemetrexed for unresectable pleural mesothelioma: survival, genomic and immunologic analyses from the phase 2 PrE0505 trial Nat Med. Nov;27(11):1910-1920
• Anagnostou V, Bruhm DC, Niknafs N, White JR, Shao XM, Sidhom JW, Stein J, Tsai HL, Wang H, Belcaid Z, Murray J, Balan A, Ferreira L, Ross-Macdonald P, Wind-Rotolo M, Baras AS, Taube J, Karchin R, Scharpf RB, Grasso C, Ribas A, Pardoll DM, Topalian SL, Velculescu VE.. (2020) Integrative tumor and immune cell multi-omic analyses predict response to immune checkpoint blockade in melanoma Cell Rep Med. Nov 17;1(8):100139
• Anagnostou V, Niknafs N, Marrone K, Bruhm DC, White JR, Naidoo J, Hummelink K, Monkhorst K, Lalezari F, Lanis M, Rosner S, Reuss JE, Smith KN, Adleff V, Rodgers K,Belcaid Z, Rhymee L, Levy B, Feliciano J, Hann CL, Ettinger DS, Georgiades C, Verde F, Illei P, Li QK, Baras AS, Gabrielson E, Brock MB, Karchin R, Pardoll DM, Baylin SB, Brahmer JR, Scharpf RB, Forde PM, Velculescu VE. (2020) Multimodal genomic features predict outcome of immune checkpoint blockade in non-small-cell lung cancer Nature Cancer 1 (1), 99-111
• Shao XM, Bhattacharya R, Huang J, Sivakumar IKA, Tokheim C, Zheng L, Hirsch D, Kaminow B, Omdahl A, Bonsack M, Riemer AB, Velculescu VE, Anagnostou V, Pagel KA, Karchin R. High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets. Cancer Immunol Res. 2020 Mar;8(3):396-408. doi: 10.1158/2326-6066.CIR-19-0464. Epub 2019 Dec 23. PMID: 31871119; PMCID: PMC7056596.
• Anagnostou V, Forde PM, White JR, Niknafs N, Hruban C, Naidoo J, Marrone KA, Sivakumar IKA, Bruhm DC, Rosner S, Phallen J, Leal A, Adleff V, Smith KN, Cottrell TR, Rhymee L, Palsgrove DN, Hann CL, Levy B, Feliciano J, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Isbell JM, Sauter JL, Taube J, Scharpf RB, Karchin R, Pardoll DM, Chaft JE, Hellmann MD, Brahmer JR, Velculescu VE. (2019). Dynamics of tumor and immune responses during immune checkpoint blockade in non-small cell lung cancer. Cancer Research. Dec 12. pii: canres.1127.2018. doi: 10.1158/0008-5472.CAN-18-1127. [Epub ahead of print]
• Anagnostou V, Smith KN, Forde PM, Niknafs N, Bhattacharya R, White J, Zhang T, Adleff V, Phallen J, Wali N, Hruban C, Guthrie VB, Rodgers K, Naidoo J, Kang H, Sharfman W, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Zahnow CA, Baylin SB, Scharpf RB, Brahmer JR, Karchin R, Pardoll DM, Velculescu VE. Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer. Cancer Discov. 2017 Mar;7(3):264-276. doi: 10.1158/2159-8290.CD-16-0828. Epub 2016 Dec 28. PMID: 28031159; PMCID: PMC5733805.
• Bertotti A, Papp E, Jones S, Adleff V, Anagnostou V, Sausen M, Phallen J, Tokheim C, Niknafs N, Nesselbush M, Lytle K, Cottino F, Migliardi G, Zanella ER, Ribero D, Russolillo N, Mellano A, Muratore A, Paraluppi G, Salizzoni M, Marsoni S, Kragh M, Lantto J, Cassingena A, Li QK, Karchin R, Scharpf R, Sartore-Bianchi A, Siena S, Diaz LA, Trusolino L, Velculescu VE (2015) The Genomic Landscape of Response to EGFR Blockade in Colorectal Cancer. Nature. 526(7572):263-7