公开(公告)号：US20250104876A1

公开(公告)日：2025-03-27

申请号：US18905014

申请日：2024-10-02

Applicant: Foundation Medicine, Inc.

Inventor： Kuei-Ting CHEN ,  Ericka EBOT ,  Radwa SHARAF ,  Lee Alan ALBACKER

IPC: G16H50/30 ,  G06N20/00 ,  G16B20/10 ,  G16B20/20 ,  G16H10/60 ,  G16H20/10

Abstract: Methods for selecting an anti-cancer therapy for or treating a subject having cancer with an anti-cancer therapy comprising determining risk scores that predict the likelihood of response to the treatment are described. The methods may comprise, for example, obtaining genomic data comprising aneuploidy status or loss of heterozygosity data for one or more subgenomic intervals in a sample from the subject; analyzing the genomic data for the subject using a model configured to receive genomic data comprising aneuploidy status or loss of heterozygosity data for the one or more identified subgenomic intervals in the subject and output a risk score for the subject, wherein the risk score predicts the subject's response to a selected treatment. Also described are biomarkers for specific diseases (e.g., metastatic pancreatic cancer) and methods for treating subjects having cancer based on the determined risk scores.

公开(公告)号：US20250101537A1

公开(公告)日：2025-03-27

申请号：US18892130

申请日：2024-09-20

Applicant: Foundation Medicine, Inc.

Inventor： Brennan DECKER ,  Alexander FINE ,  Zheng KUANG ,  Douglas A. MATA ,  Jason D. HUGHES ,  Meagan Kathleen MONTESION ,  Radwa SHARAF

IPC: C12Q1/70 ,  C12Q1/6886 ,  G16B30/00 ,  G16B40/20

Abstract: Disclosed herein are methods and systems for determining an origin of viral sequence reads detected in a sample (e.g., a liquid biopsy sample) from an individual. The sample may contain cfDNA fragments of varying fragment lengths. Embodiments of the present disclosure can receive sequence read data associated with the sample, which may be a liquid biopsy sample. The sequence read data can be used to determine if one or more viral sequence reads are detected in the sample. If the viral sequence reads are detected, the system can determine one or more fragmentomic features based on the sequence read data. The system can then generate an output indicative of the origin of the viral sequence reads by inputting the fragmentomic features into a statistical model including, for example, a trained machine-learning model. Based on the output, the system can then determine whether the viral sequence reads originate from a tumor.