公开(公告)号：US20240412812A1

公开(公告)日：2024-12-12

申请号：US18698747

申请日：2022-10-07

Applicant: Foundation Medicine, Inc.

Inventor： Jason D. HUGHES ,  Justin NEWBERG

IPC: G16B20/10 ,  G16B20/20

Abstract: Methods and systems for performing iterative contamination detection and segmentation of sequence read data are described. The methods are based on comparing a distribution of minor allele frequencies (MAPs) for a plurality of single nucleotide polymorphisms (SNPs) detected in the sample to an expected distribution of minor allele frequencies for a plurality of selected SNP loci, and adjusting a MAP threshold used to discriminate between aberrant SNPs (SNPs exhibiting a different distribution of MAP values than that expected for the plurality of selected SNPs) and those conforming to the expected distribution of minor allele frequencies for the plurality of selected SNP loci. The methods may be used to estimate the degree of contamination in a sample and to provide segmentation of sequence read data for the sample, and may further comprise building a copy number model that predicts a copy number for one or more gene loci.

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.

公开(公告)号：US20230140123A1

公开(公告)日：2023-05-04

申请号：US17899470

申请日：2022-08-30

Applicant: Foundation Medicine, Inc.

Inventor： Ethan SOKOL ,  Jay MOORE ,  Justin NEWBERG ,  Dexter JIN ,  Kuei-Ting CHEN ,  Russell MADISON

IPC: G16B20/20 ,  C12Q1/6886 ,  G16B20/10 ,  G16B40/20

Abstract: Described herein are methods, devices, and systems for identifying a subset of a plurality of features, using one or more feature importance metrics, for training and using a homologous repair deficiency (HRD) classification model. Further described are methods, devices, and systems for classifying a tumor of a cancer, such as pancreatic cancer, as likely HRD positive or likely HRD negative, and for calling the tumor as HRD positive or HRD negative. Also described herein are methods of treating a tumor of a cancer, such as pancreatic cancer, based on the classifications