Abstract: Cell free nucleic acids from a test sample obtained from an individual are analyzed to identify possible fusion events. Cell free nucleic acids are sequenced and processed to generate fragments. Fragments are decomposed into kmers and the kmers are either analyzed de novo or compared to targeted nucleic acid sequences that are known to be associated with fusion gene pairs of interest. Thus, kmers that may have originated from a fusion event can be identified. These kmers are consolidated to generate gene ranges from various genes that match sequences in the fragment. A candidate fusion event can be called given the spanning of one or more gene ranges across the fragment.
Type:
Grant
Filed:
June 12, 2018
Date of Patent:
October 18, 2022
Assignee:
GRAIL, LLC
Inventors:
Xiao Yang, Hyunsung John Kim, Wenying Pan, Matthew H. Larson, Eric Michael Scott, Pranav Parmjit Singh, Mohini Jangi Desai
Abstract: A method for extracting information from a dataset, e.g., a document, includes: receiving the dataset at an information handling device, optionally, extracting, via optical character recognition implemented by a processor of the information handling device, textual information associated with the dataset, and classifying the dataset into one of a plurality of classes. Classifying the dataset may include computing a similarity score for each of the plurality of classes for each of a plurality of window regions of the dataset, calculating a subset of highest similarity scores for each of the plurality of classes for each of the plurality of window regions, determining overall similarity scores for each of the plurality of classes, and classifying the dataset as corresponding to a class with a highest overall similarity score.
Abstract: Provided herein are methods and systems for identifying chimeric nucleic acid fragments, e.g., organism-pathogen chimeric nucleic acid fragments and chromosomal rearrangement chimeric nucleic acid fragments. Also provided herein are methods and systems relating to determining a pathogen integration profile or a chromosomal rearrangement in a biological sample and determining a classification of pathology based at least in part on a pathogen integration profile or a chromosomal rearrangement in a biological sample. In certain aspects of the present disclosure, cell-free nucleic acid molecules from a biological sample are analyzed.
Abstract: The present description provides a cancer assay panel for targeted detection of cancer-specific methylation patterns. Further provided herein are methods of designing, making, and using the cancer assay panel for the diagnosis of cancer.
Type:
Grant
Filed:
March 26, 2021
Date of Patent:
August 9, 2022
Assignee:
GRAIL, LLC
Inventors:
Samuel S. Gross, Oliver Claude Venn, Seyedmehdi Shojaee, John Beausang, Arash Jamshidi
Abstract: A method for training a convolutional neural net for contamination analysis is provided. A training dataset is obtained comprising, for each respective training subject in a plurality of subjects, a variant allele frequency of each respective single nucleotide variant in a respective plurality of single nucleotide variants, and a respective contamination indication. First and second subsets of the plurality of training subjects have first and second contamination indication values, respectively. A corresponding first channel comprising a first plurality of parameters that include a respective parameter for a single nucleotide variant allele frequency of each respective single nucleotide variant in a set of single nucleotide variants in a reference genome is constructed for each respective training subject.
Type:
Application
Filed:
September 29, 2021
Publication date:
March 31, 2022
Applicant:
GRAIL, LLC
Inventors:
Christopher-James A.V. Yakym, Onur Sakarya
Abstract: In various aspects, the present disclosure provides methods, compositions, reactions mixtures, kits, and systems for sequencing both RNA and DNA from a single source sample. In some embodiments, RNA is treated so as to differentiate RNA sequences from DNA sequences derived from the same sample. In some embodiments, the RNA and DNA are cell-free polynucleotides.
Type:
Grant
Filed:
October 31, 2018
Date of Patent:
November 23, 2021
Assignee:
GRAIL, LLC
Inventors:
Matthew Larson, H. John Kim, Nick Eattock, Arash Jamshidi