Patents Assigned to GRAIL, LLC
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Publication number: 20240132878Abstract: Diagnostic devices and methods are provided for screening for a disease condition, including a cancer condition or a mendelian disease. The diagnostic devices allow for in vivo contact of cell-free nucleic acids or circulating tumor cells. The diagnostic device has a needle with a body and a detection reaction module attached to the body.Type: ApplicationFiled: February 22, 2023Publication date: April 25, 2024Applicant: GRAIL, LLCInventor: M. Cyrus MAHER
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Patent number: 11961589Abstract: A processing system uses a Bayesian inference based model for targeted sequencing or variant calling. In an embodiment, the processing system generates candidate variants of a cell free nucleic acid sample. The processing system determines likelihoods of true alternate frequencies for each of the candidate variants in the cell free nucleic acid sample and in a corresponding genomic nucleic acid sample. The processing system filters or scores the candidate variants by the model using at least the likelihoods of true alternate frequencies. The processing system outputs the filtered candidate variants, which may be used to generate features for a predictive cancer or disease model.Type: GrantFiled: November 27, 2018Date of Patent: April 16, 2024Assignee: GRAIL, LLCInventors: Alexander W. Blocker, Earl Hubbell, Oliver Claude Venn, Qinwen Liu
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Publication number: 20240117435Abstract: Systems and methods for predicting survival outcomes in patients diagnosed with Myelodysplastic Syndrome (MDS) are disclosed. One method may include: receiving DNA sequencing data derived from a methylation assay performed on a biological sample associated with the at least one patient; computing methylation beta-values for one or more CpG-sites identified in the sequencing data; identifying one or more differentially methylated regions (DMRs) based on statistical analysis of the methylation beta-values for the one or more CpG-sites; selecting, via a feature selection process, a subset of the one or more DMRs to utilize as training data; and training, using the training data, the classifier to predict the survival outcome of the at least one patient. Other aspects are described and claimed.Type: ApplicationFiled: October 5, 2023Publication date: April 11, 2024Applicant: GRAIL, LLCInventors: Qinwen LIU, Alvin SHI, Oliver Claude VENN, Gordon CANN
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Patent number: 11929148Abstract: Systems and methods for determining a cancer class of a subject are provided in which a plurality of sequence reads, in electronic form, are obtained from a biological sample of the subject. The sample comprises a plurality of cell-free DNA molecules including respective DNA molecules longer than a threshold length of less than 160 nucleotides. The plurality of sequence reads excludes sequence reads of cell-free DNA molecules in the plurality of cell-free DNA molecules longer than the threshold length. The plurality of sequence reads is used to identify a relative copy number at each respective genomic location in a plurality of genomic locations in the genome of the subject. The genetic information about the subject obtained from the sample and the genetic information consisting of the identification of the relative copy number at each respective genomic location, is applied to a classifier that determines the cancer class of the subject.Type: GrantFiled: March 12, 2020Date of Patent: March 12, 2024Assignee: GRAIL, LLCInventors: Darya Filippova, Matthew H. Larson, M. Cyrus Maher, Monica Portela dos Santos Pimentel, Robert Abe Paine Calef
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Publication number: 20240070170Abstract: 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.Type: ApplicationFiled: August 31, 2023Publication date: February 29, 2024Applicant: GRAIL, LLCInventors: Kathan ROBERTS, Max Weiland ROSEN, Joerg BREDNO, Jafi LIPSON, Harit NANDANI
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Patent number: 11915797Abstract: In comparison to conventional sequencing pileup algorithms, the process described herein generates sequencing pileups that contains additional information not typically reported by conventional algorithms while also consuming fewer computational resources (e.g., time, processing power, and memory). First, each of a FASTA reference genome and BAM sequence read files are converted to an internal representation. This enables the rapid iteration across nucleotide bases of the sequence reads to determine support characteristics that summarize information of nucleic acid molecules corresponding to positions across the reference genome. Next, the support characteristics of positions across the reference genome are stored through a memory allocation process that utilizes a first and a second temporary storage. This enables the convenient freeing of one temporary storage while the other temporary storage is being used.Type: GrantFiled: June 11, 2019Date of Patent: February 27, 2024Assignee: Grail, LLCInventor: Christopher Chang
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Publication number: 20240062849Abstract: 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.Type: ApplicationFiled: August 31, 2023Publication date: February 22, 2024Applicant: GRAIL, LLCInventors: Virgil NICULA, Anton VALOUEV, Darya FILIPPOVA, Matthew H. LARSON, M. Cyrus MAHER, Monica Portela dos Santos Pimentel, Robert Abe Paine CALEF, Collin MELTON
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Publication number: 20240038335Abstract: 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.Type: ApplicationFiled: July 31, 2023Publication date: February 1, 2024Applicant: GRAIL, LLCInventors: Tracy NANCE, Joerg BREDNO, Oliver Claude VENN, Robert Abe Paine CALEF, Jennifer TOM
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Patent number: 11884966Abstract: Provided herein are compositions comprising tissue-specific markers for identifying a tissue of origin of a cell-free nucleic acid, e.g., a cell-free DNA molecule. Also provided herein are methods, compositions, and systems for identifying a tissue of origin of a cell-free nucleic acid by determining an absolute amount of cell-free nucleic acids comprising the tissue-specific marker. Also provided herein are methods, compositions, and systems for detecting a cancer in a tissue of an organism by analyzing tissue-specific markers.Type: GrantFiled: March 15, 2019Date of Patent: January 30, 2024Assignee: GRAIL, LLCInventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Wanxia Gai, Lu Ji
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Systems and methods for determining whether a subject has a cancer condition using transfer learning
Patent number: 11869661Abstract: Systems and methods for classifier training are provided. A first dataset is obtained that comprises, for each first subject, a corresponding plurality of bin values, each for a bin in a plurality of bins, and subject cancer condition. A feature extraction technique is applied to the first dataset thereby obtaining feature extraction functions, each of which is an independent linear or nonlinear function of bin values of the bins. A second dataset is obtained comprising, for each second subject, a corresponding plurality of bin values, each for a bin in the plurality of bins and subject cancer condition. The plurality of bin values of each corresponding subject in the second plurality are projected onto the respective feature extraction functions, thereby forming a transformed second dataset comprising feature values for each subject. The transformed second dataset and subject cancer condition serves to train a classifier on the cancer condition set.Type: GrantFiled: May 22, 2020Date of Patent: January 9, 2024Assignee: GRAIL, LLCInventor: M. Cyrus Maher -
Patent number: 11851650Abstract: Methods for preparing enriched sequencing libraries from test samples that contain double-stranded deoxyribonucleic acid (dsDNA) are provided.Type: GrantFiled: September 28, 2018Date of Patent: December 26, 2023Assignee: GRAIL, LLCInventors: Byoungsok Jung, Alex Aravanis
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Publication number: 20230412382Abstract: Systems and methods of providing access to a resource via an access management system may include: receiving, at an authorization server, a login request to a user profile from a client application, wherein the login request comprises a set of login credentials; transmitting, from the authorization server to an identity provider, the set of login credentials; authenticating, upon validation of the set of login credentials by the identity provider, the user; receiving, at the authorization server and subsequent to the authenticating, an authentication request from the client application; issuing, subsequent to validating the authentication request and by the authorization server, an access token to the client application; detecting, at a resource server, a request from the client application to access a resource, wherein the request comprises the access token; and enabling, by the resource server and responsive to validating the access token, the client application access to the resource.Type: ApplicationFiled: June 15, 2023Publication date: December 21, 2023Applicant: GRAIL, LLCInventors: Prabhu PALANISAMY, Satnam ALAG, Milan KARANGUTKAR
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Patent number: 11795513Abstract: 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: GrantFiled: June 3, 2022Date of Patent: October 24, 2023Assignee: GRAIL, LLCInventors: Samuel S. Gross, Oliver Claude Venn, Seyedmehdi Shojaee, John Beausang, Arash Jamshidi
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Publication number: 20230326556Abstract: 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.Type: ApplicationFiled: March 31, 2023Publication date: October 12, 2023Applicant: GRAIL, LLCInventors: Robert Abe Paine CALEF, Eric Michael SCOTT, Karina SAMUEL-GAMA
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Patent number: 11783915Abstract: 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.Type: GrantFiled: September 29, 2022Date of Patent: October 10, 2023Assignee: GRAIL, LLCInventors: Virgil Nicula, Anton Valouev, Darya Filippova, Matthew H. Larson, M. Cyrus Maher, Monica Portela dos Santos Pimentel, Robert Abe Paine Calef, Collin Melton
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Patent number: 11782957Abstract: 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.Type: GrantFiled: April 6, 2022Date of Patent: October 10, 2023Assignee: GRAIL, LLCInventors: Kathan Roberts, Max Weiland Rosen, Joerg Bredno, Jafi Lipson, Harit Nandani
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Patent number: 11773450Abstract: An analytics system marks duplicate fragments from an initial set of fragments from a subject. The analytics system generates a sample state vector for each fragment. Each sample state vector comprises a sample genomic location within a reference genome and a plurality of methylation states for a plurality of CpG sites in the fragment, the methylation states determined to be one of methylated, unmethylated, variant, and ambiguous. The analytics system identifies two fragments with methylation state vectors as being derived from a matching reference location, e.g., sharing a common plurality of CpG sites. The analytics system calculates a modified Hamming distance based on methylation states in the first sample state vector and methylation states in the second sample state vector. Based on the modified Hamming distance, the analytics system marks the first fragment and the second fragment as either duplicate fragments or non-duplicate fragments.Type: GrantFiled: April 3, 2020Date of Patent: October 3, 2023Assignee: GRAIL, LLCInventors: Alexander S. Yip, Samuel S. Gross, Seyedmehdi Shojaee
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Patent number: 11728007Abstract: Methods of identifying changes in genomic DNA copy number are disclosed. This disclosure provides methods for detecting chromosomal aberrations in a subject using Hidden Markov modeling. In some cases, methods provided herein use de novo sequence assembly to detect chromosomal aberrations in a subject. The methods can be used to detect copy number changes in cancerous tissue compared to normal tissue. The methods can be used to diagnose cancer and other diseases associated with chromosomal anomalies.Type: GrantFiled: November 30, 2018Date of Patent: August 15, 2023Assignee: GRAIL, LLCInventor: Srinka Ghosh
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Patent number: 11725251Abstract: 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: GrantFiled: December 21, 2022Date of Patent: August 15, 2023Assignee: GRAIL, LLCInventors: Samuel S. Gross, Oliver Claude Venn, Seyedmehdi Shojaee, John Beausang, Arash Jamshidi
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Patent number: 11685958Abstract: 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: GrantFiled: March 26, 2021Date of Patent: June 27, 2023Assignee: GRAIL, LLCInventors: Samuel S. Gross, Oliver Claude Venn, Seyedmehdi Shojaee, John Beausang, Arash Jamshidi