公开(公告)号：US20220243279A1

公开(公告)日：2022-08-04

申请号：US17612966

申请日：2020-05-20

Applicant: Foundation Medicine, Inc.

Inventor： Bernard FENDLER ,  Jason D. HUGHES ,  Steven ROELS

IPC: C12Q1/6886 ,  G16B40/20 ,  G16B20/20

Abstract: Disclosed herein are, at least in part, methods of determining a tumor fraction of a sample from a subject. The methods can include, for example, acquiring a value for a target variable associated with a subgenomic interval in the sample; determining, from the target variable, a certainty metric; accessing a determined relationship between a stored certainty metric and a stored tumor fraction; and determining, with reference to the certainty metric and the determined relationship, the tumor fraction of the sample.

公开(公告)号：US20240404626A1

公开(公告)日：2024-12-05

申请号：US18698746

申请日：2022-10-07

Applicant: Foundation Medicine, Inc.

Inventor： Bernard FENDLER ,  Jason D. HUGHES

IPC: G16B20/10 ,  G16B20/20 ,  G16B30/10

Abstract: Methods and systems for automated calling of copy number alterations (CNAs) are described. The methods and systems utilize sequencing-based coverage ratio data, allele fraction data, segmentation data, and copy number model data for one or more gene loci within one or more subgenomic intervals in a sample from a subject to detect amplifications and deletions of gene loci, and apply a number of thresholds and filters to provide automated calling of CNAs with improved reliability while eliminating the need for process-matched controls and manual curation of the sequencing data.

公开(公告)号：US20240420797A1

公开(公告)日：2024-12-19

申请号：US18697958

申请日：2022-10-07

Applicant: Foundation Medicine, Inc.

Inventor： Jason D. HUGHES ,  Bernard FENDLER ,  Justin NEWBERG

IPC: G16B20/10 ,  C12Q1/6806 ,  C12Q1/6855 ,  C12Q1/6874 ,  G16B45/00 ,  G16H20/10 ,  G16H50/20 ,  G16H50/30

Abstract: Methods and systems for calling copy number alterations (CNAs), including methods and systems for fitting a grid-based copy number model to sequence read data are described herein. The method can include generating a minor allele coverage ratio and a major allele coverage ratio for a plurality of genetic loci, transforming the allele coverage data, and fitting a copy number grid model to the data. The fit copy number grid model may then be used to assign a copy number state or call a copy number alteration. The copy number grid model and the transformed allele coverage ratio data may be displayed for consideration of the presented model, which allows for more efficient data interpretation and calling of a copy number state or copy number alteration.