Patents by Inventor Darya Filippova
Darya Filippova has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 11929147Abstract: Described herein are methods for identifying quasispecies of genomes by clustering sequence reads for samples including the genomes based on the similarities of the sequence reads.Type: GrantFiled: September 12, 2018Date of Patent: March 12, 2024Assignee: Roche Sequencing Solutions, Inc.Inventors: Darya Filippova, Khai Luong, Garima Kushwaha
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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: 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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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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Publication number: 20230170048Abstract: 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.Type: ApplicationFiled: January 6, 2023Publication date: June 1, 2023Applicant: Grail, LLCInventors: M. Cyrus MAHER, Anton VALOUEV, Darya FILIPPOVA, Virgil NICULA, Karthik JAGADEESH, Oliver Claude VENN, Samuel S. GROSS, John F. BEAUSANG, Robert Abe Paine CALEF
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Publication number: 20230045925Abstract: 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: September 29, 2022Publication date: February 16, 2023Applicant: 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: 11581062Abstract: 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.Type: GrantFiled: December 10, 2019Date of Patent: February 14, 2023Assignee: GRAIL, LLCInventors: M. Cyrus Maher, Anton Valouev, Darya Filippova, Virgil Nicula, Karthik Jagadeesh, Oliver Claude Venn, Samuel S. Gross, John F. Beausang, Robert Abe Paine Calef
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Patent number: 11482303Abstract: 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: May 31, 2019Date of Patent: October 25, 2022Assignee: 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: 20210327534Abstract: Methods for determining a disease condition of a subject of a species are provided that comprises obtaining a dataset of fragment methylation patterns determined by methylation sequencing of nucleic acid from a biological sample of the subject. A fragment methylation pattern comprises the methylation state of each CpG site in the fragment. A patch including a channel comprising parameters for the methylation status of respective CpG sites in a set of CpG sites in a reference genome represented by the patch is constructed by populating, for each respective fragment in the plurality of fragments that aligns to the set of CpG sites, an instance of all or a portion of the plurality of parameters based on the methylation pattern of the respective fragment. Application of the patch to a patch convolutional neural network determines the disease condition of the subject.Type: ApplicationFiled: December 11, 2020Publication date: October 21, 2021Applicant: GRAIL, INC.Inventors: Virgil Nicula, Ognjen Nikolic, Yasushi Saito, Marius Eriksen, Josh Newman, Darya Filippova, Alexander Yip, Oliver Venn, Joerg Bredno, Qinwen Liu, Alexander P. Fields
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Publication number: 20200294624Abstract: 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: ApplicationFiled: March 12, 2020Publication date: September 17, 2020Inventors: Darya Filippova, Matthew H. Larson, M. Cyrus Maher, Monica Portela dos Santos Pimentel, Robert Abe Paine Calef
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Publication number: 20200211675Abstract: Described herein are methods for identifying quasispecies of genomes by clustering sequence reads for samples including the genomes based on the similarities of the sequence reads.Type: ApplicationFiled: September 12, 2018Publication date: July 2, 2020Inventors: Darya FILIPPOVA, Khai LUONG, Garima KUSHWAHA
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Publication number: 20200185059Abstract: 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.Type: ApplicationFiled: December 10, 2019Publication date: June 11, 2020Inventors: M. Cyrus Maher, Anton Valouev, Darya Filippova, Virgil Nicula, Karthik Jagadeesh, Oliver Claude Venn, Samuel S. Gross, John F. Beausang, Robert Abe Paine Calef
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Publication number: 20200005899Abstract: 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: May 31, 2019Publication date: January 2, 2020Inventors: 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: 20190316209Abstract: A predictive cancer model generates a cancer prediction for an individual of interest by analyzing values of one or more types of features that are derived from cfDNA obtained from the individual. Specifically, cfDNA from the individual is sequenced to generate sequence reads using one or more physical assays, examples of which include a small variant sequencing assay, whole genome sequencing assay, and methylation sequencing assay. The sequence reads of the physical assays are processed through corresponding computational analyses to generate each of small variant features, whole genome features, and methylation features. The values of features can be provided to a predictive cancer model that generates a cancer prediction. In some embodiments, the values of different types of features can be separately provided into different predictive models. Each separate predictive model can output a score that can serve as input into an overall model that outputs the cancer prediction.Type: ApplicationFiled: April 15, 2019Publication date: October 17, 2019Inventors: Earl Hubbell, Samuel S. Gross, Darya Filippova, Ling Shen, Oliver Claude Venn, Alexander Weaver Blocker, Nan Zhang, Tara Maddala, Alex Aravanis, Qinwen Liu, Anton Valouev, Virgil Nicula
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Publication number: 20190287649Abstract: A system, method and computer program product for analyzing data of high dimensionality (e.g., sequence reads of nucleic acid samples in connection with a disease condition) are provided.Type: ApplicationFiled: March 13, 2019Publication date: September 19, 2019Inventors: Darya Filippova, Anton Valouev, Virgil Nicula, Karthik Jagadeesh, M. Cyrus Maher, Matthew H. Larson, Monica Portela dos Santos Pimentel, Robert Abe Paine Calef