Neoantigens and uses thereof for treating cancer

US12331359B2 · kind B2 · utility

Assignees

• Michael Laessig · US
• ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · US
• The Simons Center for Systems Biology at the Institute for Advanced Study · US
• Memorial Sloan Kettering Cancer Center · US

Inventors

• Marta Luksza · New York, US
• Vinod P. Balachandran · New York, US
• Arnold J. Levine · Princeton, US
• Jedd D. Wolchok · New York, US
• Taha Merghoub · New York, US
• Steven D. Leach · Baltimore, US
• Timothy A. Chan · Somers, US
• Benjamin D. Greenbaum · New York, US
• Michael Laessig · Cologne, DE

Key dates

• Filing date: Jan 18, 2018
• Grant date: Jun 17, 2025
• Expiry date: Oct 11, 2041

Classification

• Technology area (CPC G): Physics
• CPC primary: G16B30/00
• WIPO field: Pharmaceuticals
• WIPO sector: Chemistry

Abstract

Systems and methods for determining the likely responsiveness of a human cancer subject to a checkpoint blockade immunotherapy regimen are provided. Sequencing reads are obtained from samples from the subject representative of the cancer. A human leukocyte antigen type and a plurality of clones is determined from the sequencing reads. For each clone, an initial frequency Xα in the one or more samples is determined and a corresponding clone fitness score of the clone is computed, thereby computing clone fitness scores. Each such fitness score is computed by identifying neoantigens in the respective clone, computing a recognition potential for each neoantigen, and determining the corresponding clone fitness score of the respective clone as an aggregate of these recognition potentials. A total fitness, quantifying the likely responsiveness of the subject to the regimen, is computed by summing the clone fitness scores across the plurality of clones.