公开(公告)号：US20230170048A1

公开(公告)日：2023-06-01

申请号：US18151197

申请日：2023-01-06

Applicant: Grail, LLC

Inventor： M. Cyrus MAHER ,  Anton VALOUEV ,  Darya FILIPPOVA ,  Virgil NICULA ,  Karthik JAGADEESH ,  Oliver Claude VENN ,  Samuel S. GROSS ,  John F. BEAUSANG ,  Robert Abe Paine CALEF

IPC: G16B30/00 ,  G16B20/20 ,  G16B40/00 ,  G16H70/60 ,  G06N5/04 ,  G16H10/60 ,  G16H50/70 ,  G16H50/20 ,  G06N20/00 ,  G16H10/40

CPC classification number: G16B30/00 ,  G06N5/04 ,  G06N20/00 ,  G16B20/20 ,  G16B40/00 ,  G16H10/40 ,  G16H10/60 ,  G16H50/20 ,  G16H50/70 ,  G16H70/60

Abstract: Technical solutions for classifying patients with respect to multiple cancer classes are provided. The classification can be done using cell-free whole genome sequencing information from subjects. A reference set of subjects is used to train classifiers to recognize genomic markers that distinguish such cancer classes. The classifier training includes dividing the reference genome into a set of non-overlapping bins, applying a dimensionality reduction method to obtain a feature set, and using the feature set to train classifiers. For subjects with unknown cancer class, the trained classifiers provide probabilities or likelihoods that the subject has a respective cancer class for each cancer in a set of cancer classes. The present disclosure thus describes methods to improve the screening and detection of cancer class from among several cancer classes. This serves to facilitate early and appropriate treatment for subjects afflicted with cancer.

公开(公告)号：US20240062849A1

公开(公告)日：2024-02-22

申请号：US18240489

申请日：2023-08-31

Applicant: GRAIL, LLC

Inventor： Virgil NICULA ,  Anton VALOUEV ,  Darya FILIPPOVA ,  Matthew H. LARSON ,  M. Cyrus MAHER ,  Monica Portela dos Santos Pimentel ,  Robert Abe Paine CALEF ,  Collin MELTON

IPC: G16B30/10 ,  G16H50/20 ,  G16B40/30 ,  G16B40/20 ,  G06N3/04 ,  G06N3/084

CPC classification number: G16B30/10 ,  G16H50/20 ,  G16B40/30 ,  G16B40/20 ,  G06N3/04 ,  G06N3/084

Abstract: Classification of cancer condition, in a plurality of different cancer conditions, for a species, is provided in which, for each training subject in a plurality of training subjects, there is obtained a cancer condition and a genotypic data construct including genotypic information for the respective training subject. Genotypic constructs are formatted into corresponding vector sets comprising one or more vectors. Vector sets are provided to a network architecture including a convolutional neural network path comprising at least a first convolutional layer associated with a first filter that comprise a first set of filter weights and a scorer. Scores, corresponding to the input of vector sets into the network architecture, are obtained from the scorer. Comparison of respective scores to the corresponding cancer condition of the corresponding training subjects is used to adjust the filter weights thereby training the network architecture to classify cancer condition.

公开(公告)号：US20240038335A1

公开(公告)日：2024-02-01

申请号：US18362342

申请日：2023-07-31

Applicant: GRAIL, LLC

Inventor： Tracy NANCE ,  Joerg BREDNO ,  Oliver Claude VENN ,  Robert Abe Paine CALEF ,  Jennifer TOM

IPC: G16B30/00 ,  G16B40/20 ,  G16H10/40 ,  G16H50/50 ,  G16H50/20

CPC classification number: G16B30/00 ,  G16B40/20 ,  G16H10/40 ,  G16H50/50 ,  G16H50/20 ,  G16H50/30

Abstract: Systems and methods for detecting a subtype of a disease state and for determining the development of a resistance mechanism in a disease are disclosed. One method may include: receiving, at an input component of the system, a set of sequence reads associated with a nucleic acid sample; generating, using a processor of the system and via analysis of the set of sequence reads, methylation data; and analyzing, using the processor, the methylation data to identify the subtype of the disease state. Another method may include: obtaining methylation data from a targeted methylation sequencing assay, applying the methylation data to a trained machine learning model, and receiving an output indicating whether MRD is present in a test subject and/or whether a resistance mechanism has been developed by a disease. Other aspects are described and claimed.

公开(公告)号：US20230326556A1

公开(公告)日：2023-10-12

申请号：US18194250

申请日：2023-03-31

Applicant: GRAIL, LLC

Inventor： Robert Abe Paine CALEF ,  Eric Michael SCOTT ,  Karina SAMUEL-GAMA

IPC: G16B30/00 ,  G16B40/20 ,  G16H50/50

CPC classification number: G16B30/00 ,  G16H50/50 ,  G16B40/20

Abstract: Systems and methods for reducing noise for the analysis of low coverage sequencing data from a nucleic acid sample using a method, including: receiving, at an input component of the system, a set of sequence reads associated with the nucleic acid sample; allocating, using a processor component of the system, the set of sequence reads into a plurality of genomic bins; and introducing, subsequent to the allocating, a pseudocount number to bincount values to produce a smoothed dataset, wherein each of the bincount values is associated with one of the plurality of genomic bins. Other aspects are described and claimed.