公开(公告)号：US20250131981A1

公开(公告)日：2025-04-24

申请号：US18579296

申请日：2021-07-14

Applicant: Foundation Medicine, Inc.

Inventor： Kyle GOWEN ,  Jason HUGHES ,  Meijuan LI ,  Lei YANG ,  Jeffrey LEIBOWITZ ,  Pei MA

IPC: G16B20/20 ,  C12Q1/6869 ,  G16H20/10 ,  G16H50/20 ,  G16H50/30

Abstract: Methods for detecting a deficient DNA repair mechanism and/or evaluating microsatellite instability in a sample from a subject are described. The disclosed methods comprise analyzing nucleic acid sequence data for a plurality of microsatellite loci to calculate a microsatellite instability (MSI) score for the sample from a ratio of the number of microsatellite loci that exhibit variant alleles to the total number of microsatellite loci that meet, e.g., a minimum sequencing coverage requirement. The MSI score is compared a first threshold and, m some cases, to a second threshold to assign a status of high microsatellite instability′(MSI-H), microsatellite stable (MSS), or equivocal microsatellite instability (MSI-E) for the sample.

公开(公告)号：US20230242975A1

公开(公告)日：2023-08-03

申请号：US18008410

申请日：2021-06-03

Applicant: Foundation Medicine, Inc.

Inventor： Yanmei HUANG ,  Jason D. HUGHES ,  Kyle GOWEN

IPC: C12Q1/6844 ,  C12Q1/6886 ,  G16B20/20 ,  C12Q1/6869 ,  G16B30/10

CPC classification number: C12Q1/6844 ,  C12Q1/6886 ,  G16B20/20 ,  C12Q1/6869 ,  G16B30/10 ,  C12Q2600/16

Abstract: Described herein are methods for distinguishing between somatic and germline variants, and devices for implementing such methods. In certain implementation of the methods, the method can include identifying a genomic sequence of interest in a patient sample at a genomic locus; identifying one or more proxy genomic sequences for the sequence of interest; comparing an observed frequency of the sequence of interest to a centrality measure of observed frequencies of the one or more proxy genomic sequences; and based on the comparison, characterizing the genomic sequence of interest as either germline or somatic.