Patents Assigned to MYRIAD WOMEN'S HEALTH, INC.
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Publication number: 20240117343Abstract: Methods and compositions are provided for preparing DNA libraries. Enzymes, adaptors, and sample nucleic acids are provided in a single reaction mixture to facilitate library preparation.Type: ApplicationFiled: October 19, 2023Publication date: April 11, 2024Applicant: Myriad Women's Health, Inc.Inventors: Henry H. Lai, Clement S. Chu
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Patent number: 11932910Abstract: The present disclosure relates to methods for detecting unique genetic signatures derived from markers such as, for example, mutations, somatic or germ-line, in nucleic acids obtained from biological samples. The sensitivity of the methods provides for detection of mutations associated with a disease, e.g., cancer mutations, or with inherited disease, e.g., an autosomal recessive disease, in a noninvasive manner at ultra-low proportions of sequences carrying mutations to sequences carrying normal, e.g., non-cancer sequences, or a reference sequence, e.g., a human reference genome.Type: GrantFiled: July 22, 2021Date of Patent: March 19, 2024Assignee: Myriad Women's Health, Inc.Inventors: Jared Robert Maguire, Clement S. Chu, Imran Saeedul Haque, Eric Andrew Evans, Noah Welker
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Publication number: 20240076750Abstract: The present disclosure relates to a laboratory execution system that provides for automation of laboratory processes. A centralized data management system may be dynamically updated and used to facilitate management of components of the laboratory execution system, such as an automation system and an analytics results management system that may facilitate complex analytical functions, such as synthesizing raw test data. Potential workflows include the detection of specific molecules of interest.Type: ApplicationFiled: November 8, 2023Publication date: March 7, 2024Applicant: Myriad Women's Health, Inc.Inventors: Jared Robert Maguire, Clement S. Chu, Imran Saeedul Haque, Eric Andrew Evans, Noah Welker
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Publication number: 20240038339Abstract: A method and system for analyzing sex-chromosome aneuploidies of an individual are provided. In one embodiment, a method comprises training a neural network model based on predetermined information related to at least one sex chromosome. The method also comprises determining a respective sex-chromosome status based on a normalized read depth for a gene in a genome of the individual using a machine learning algorithm. The machine learning algorithm is configured to receive, as inputs, the normalized read depth, and output the respective sex-chromosome status of the individual. In another embodiment, a system I is provided including a neural network model trained based on predetermined information related to at least one sex chromosome and is adapted to determine a respective sex-chromosome status based on a normalized read depth for a gene in a genome of the individual using a machine learning algorithm.Type: ApplicationFiled: August 5, 2021Publication date: February 1, 2024Applicant: Myriad Women's Health, Inc.Inventors: Albert Lee, Kevin Haas, Kevin D'Auria
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Publication number: 20230416729Abstract: High-fidelity, high-throughput nucleic acid sequencing enables healthcare practitioners and patients to gain insight into genetic variants and potential health risks. However, previous methods of nucleic acid sequencing often introduces sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are sequencing adapters comprising a nondegenerate or variable length molecular barcode and compositions comprising a plurality of sequencing adapters, which can be useful for sequencing nucleic acids. Further provided are methods of using the sequencing adapters, including methods of sequencing nucleic acids, methods of identifying an error in a nucleic acid sequence, and methods of determining the number of nucleic acid molecules in a library.Type: ApplicationFiled: June 12, 2023Publication date: December 28, 2023Applicant: MYRIAD WOMEN'S HEALTH, INC.Inventors: Eric Andrew Evans, Imran Saeedul Haque, Kyle Beauchamp, Clement Chu, Carlo G. Artieri, Noah Welker
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Patent number: 11854666Abstract: Fetal maternal samples taken from pregnant women include both maternal cell-free DNA and fetal cell-free DNA. Described herein are methods for determining a chromosomal abnormality of a test chromosome or a portion thereof in a fetus by analyzing a test maternal sample of a woman carrying said fetus, wherein the test maternal sample comprises fetal cell-free DNA and maternal cell-free DNA. The chromosomal abnormality can be, for example, aneuploidy or the presence of a microdeletion. In some embodiments, the chromosomal abnormality is determined by measuring a dosage of the test chromosome or portion thereof in the test maternal sample, measuring a fetal fraction of cell-free DNA in the test maternal sample, and determining an initial value of likelihood that the test chromosome or the portion thereof in the fetal cell-free DNA is abnormal based on the measured dosage, an expected dosage of the test chromosome or portion thereof, and the measured fetal fraction.Type: GrantFiled: September 29, 2017Date of Patent: December 26, 2023Assignee: Myriad Women's Health, Inc.Inventors: Dale Muzzey, Carlo G. Artieri, Eric Andrew Evans, Imran Saeedul Haque
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Patent number: 11820980Abstract: Methods and compositions are provided for preparing DNA libraries. Enzymes, adaptors, and sample nucleic acids are provided in a single reaction mixture to facilitate library preparation.Type: GrantFiled: April 27, 2020Date of Patent: November 21, 2023Assignee: Myriad Women's Health, Inc.Inventors: Henry H. Lai, Clement S. Chu
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Publication number: 20230295716Abstract: The present disclosure relates to a laboratory execution system that provides for automation of laboratory processes. A centralized data management system may be dynamically updated and used to facilitate management of components of the laboratory execution system, such as an automation system and an analytics results management system that may facilitate complex analytical functions, such as synthesizing raw test data. Potential workflows include the detection of specific molecules of interest.Type: ApplicationFiled: August 8, 2022Publication date: September 21, 2023Applicant: MYRIAD WOMEN'S HEALTH, INC.Inventors: Jared Robert Maguire, Clement S. Chu, Imran Saeedul Haque, Eric Andrew Evans, Noah Welker
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Patent number: 11708574Abstract: High-fidelity, high-throughput nucleic acid sequencing enables healthcare practitioners and patients to gain insight into genetic variants and potential health risks. However, previous methods of nucleic acid sequencing often introduces sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are sequencing adapters comprising a nondegenerate or variable length molecular barcode and compositions comprising a plurality of sequencing adapters, which can be useful for sequencing nucleic acids. Further provided are methods of using the sequencing adapters, including methods of sequencing nucleic acids, methods of identifying an error in a nucleic acid sequence, and methods of determining the number of nucleic acid molecules in a library.Type: GrantFiled: June 9, 2017Date of Patent: July 25, 2023Assignee: Myriad Women's Health, Inc.Inventors: Eric Andrew Evans, Imran Saeedul Haque, Kyle Beauchamp, Clement Chu, Carlo G. Artieri, Noah Welker
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Publication number: 20230220448Abstract: The present disclosure relates to methods of preparing cell-free DNA samples from expecting mothers or pregnant women, and related methods of analysis of such samples.Type: ApplicationFiled: January 10, 2023Publication date: July 13, 2023Applicant: Myriad Women's Health, Inc.Inventors: Dale Muzzey, Genevieve Gould
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Publication number: 20230193247Abstract: Described herein are methods for enriching test samples for target nucleic acid molecules for further genetic screening. Methods may comprise isolating nucleic acid from test subjects, preparing nucleic acid libraries wherein the nucleic acid molecules are tagged or barcoded to identify sample of origin, determining fragment size distribution, determining abundance of a target nucleic acid population, calculating numerical offset values to determine amount of libraries to add for fragment size selection, performing fragment size selection, and performing a diagnostic assay on a sample enriched for a target nucleic acid.Type: ApplicationFiled: May 18, 2021Publication date: June 22, 2023Applicant: Myriad Women's Health, Inc.Inventors: Clement Chu, Mark Theilmann, Noah Welker, Peter Grauman
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Publication number: 20230170046Abstract: A computer-implemented method for Error! Reference source not found. may include (i) generating a reference matrix representing a genetic reference panel in terms of dosages for given reference samples at given loci, (ii) decomposing the reference matrix via non-negative matrix factorization into an ancestral genotype matrix and an ancestral attribution matrix, (iii) resampling the reference matrix, (iv) deriving an ancestral alternate reads matrix that, when multiplied with the ancestral attribution matrix, approximates the resampled reference matrix, (v) deriving an ancestral attribution vector that, when multiplied with the ancestral alternate reads matrix, approximates a vector representing the test sample, and (vi) determining the genetic ancestry of the subject based on the ancestral attribution vector. Various other methods, systems, and computer-readable media are also disclosed.Type: ApplicationFiled: December 5, 2022Publication date: June 1, 2023Applicant: Myriad Women's Health, Inc.Inventors: Kristjan Eerik Kaseniit, Imran Saeedul Haque
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Publication number: 20220396785Abstract: Provided are methods and compositions for enriching cfDNA fragments from a biological fluid sample. A biological fluid sample, such as a urine sample, is collected and, in certain examples, pretreated before enrichment of the cfDNA. For the pretreatment, the sample is centrifuged to remove large cells and large cellular debris. As part of the pretreatment, the sample is also cleared of additional large cellular debris and excess volume by subjecting the sample to anion exchange chromatography and eluting bound DNA. Following any pretreatment of the sample, different concentrations an alcoholic solution are used—along with a mixture of DNA-binding particles and a chaotropic agent—to enrich the sample with cfDNA fragments having different sizes. For example, a biological sample can be enriched with small cfDNA fragments less than about 100 base pairs in length or large cfDNA fragments greater than about 100 base pairs in length.Type: ApplicationFiled: April 8, 2022Publication date: December 15, 2022Applicant: MYRIAD WOMEN'S HEALTH, INC.Inventors: Noah C. Welker, Clement S. Chu
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Patent number: 11527304Abstract: A computer-implemented method for inferring genetic ancestry from low-coverage genomic data may include (i) generating a reference matrix representing a genetic reference panel in terms of dosages for given reference samples at given loci, (ii) decomposing the reference matrix via non-negative matrix factorization into an ancestral genotype matrix and an ancestral attribution matrix, (iii) resampling the reference matrix, (iv) deriving an ancestral alternate reads matrix that, when multiplied with the ancestral attribution matrix, approximates the resampled reference matrix, (v) deriving an ancestral attribution vector that, when multiplied with the ancestral alternate reads matrix, approximates a vector representing the test sample, and (vi) determining the genetic ancestry of the subject based on the ancestral attribution vector. Various other methods, systems, and computer-readable media are also disclosed.Type: GrantFiled: July 26, 2019Date of Patent: December 13, 2022Assignee: MYRIAD WOMEN'S HEALTH, INC.Inventors: Kristjan Eerik Kaseniit, Imran Saeedul Haque
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Publication number: 20220333188Abstract: High-fidelity, high-throughput nucleic acid sequencing enables healthcare practitioners and patients to gain insight into genetic variants and potential health risks. However, previous methods of nucleic acid sequencing often introduce sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are methods and compositions for sequencing nucleic acids. Further provided are methods of identifying an error in a nucleic acid sequence.Type: ApplicationFiled: April 22, 2022Publication date: October 20, 2022Applicant: Myriad Women's Health, Inc.Inventors: Clement S. Chu, Noah C. Welker, Henry H. Lai
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Publication number: 20220290229Abstract: The present disclosure relates to methods for detecting unique genetic signatures derived from markers such as, for example, mutations, somatic or germ-line, in nucleic acids obtained from biological samples. The sensitivity of the methods provides for detection of mutations associated with a disease, e.g., cancer mutations, or with inherited disease, e.g., an autosomal recessive disease, in a noninvasive manner at ultra-low proportions of sequences carrying mutations to sequences carrying normal, e.g., non-cancer sequences, or a reference sequence, e.g., a human reference genome.Type: ApplicationFiled: February 23, 2022Publication date: September 15, 2022Applicant: MYRIAD WOMEN'S HEALTH, INC.Inventors: Jared Robert Maguire, Clement S. Chu, Imran Saeedul Haque, Eric Andrew Evans, Noah Welker
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Publication number: 20220284985Abstract: The method described herein combines experimental and analytical approaches to resolve the structure of a genomic region in the genome of a subject whose sequence is highly homologous to one or more other regions of the genome. For example, the genomic region may be a gene and the highly homologous other region may be a pseudogene or functional homolog. The method involves independent alignment, pairing, and analysis of sequence reads from the genomic region and the highly homologous other region to identify genetic variation. Also described herein is a computer-assisted method for such methods.Type: ApplicationFiled: January 23, 2020Publication date: September 8, 2022Applicant: MYRIAD WOMEN'S HEALTH, INC.Inventors: Peter Grauman, Genevieve Gould, Dale Muzzey
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Publication number: 20220267837Abstract: Disclosed is a method of determining whether a human subject is not a carrier of spinal muscular atrophy (SMA). This method includes the steps of (i) collecting a genomic deoxyribonucleic acid (DNA) sample from a human subject; (ii) screening the genomic DNA sample to determine the human subject's copy number of survival of motor neuron 1 (SMN1) gene and whether one of the copies of the SMN1 gene is positive for a polymorphism associated with non-carriers of SMA having two copies of the SMN1 gene; and (iii) determining the human subject as not a carrier of SMA if the human subject includes two copies of the SMN1 gene with one of those copies being positive for the polymorphism. Also disclosed is a method of determining whether an individual has a decreased risk of being a carrier of spinal muscular atrophy (SMA), where the individual is identified to have a decreased risk of being a carrier of SMA when the individual has two copies of the SMN1 gene with one of those copies being positive for the polymorphism.Type: ApplicationFiled: March 14, 2022Publication date: August 25, 2022Applicant: MYRIAD WOMEN'S HEALTH, INC.Inventor: Daniel Edmund DAVISON
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Publication number: 20220254443Abstract: The invention provides methods, apparatuses, and compositions for high-throughput amplification sequencing of specific target sequences in one or more samples. In some aspects, barcode-tagged polynucleotides are sequenced simultaneously and sample sources are identified on the basis of barcode sequences. In some aspects, sequencing data are used to determine one or more genotypes at one or more loci comprising a causal genetic variant. In some aspects, systems and methods of detecting genetic variation are provided.Type: ApplicationFiled: January 24, 2022Publication date: August 11, 2022Applicant: MYRIAD WOMEN'S HEALTH, INC.Inventors: Hunter Richards, Eric Evans, Balaji Srinivasan, Subramaniam Srinivasan, Abhik Shah, A. Scott Patterson, Clement Chu
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Patent number: 11339431Abstract: High-fidelity, high-throughput nucleic acid sequencing enables healthcare practitioners and patients to gain insight into genetic variants and potential health risks. However, previous methods of nucleic acid sequencing often introduce sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are methods and compositions for sequencing nucleic acids. Further provided are methods of identifying an error in a nucleic acid sequence.Type: GrantFiled: July 14, 2020Date of Patent: May 24, 2022Assignee: Myriad Women's Health, Inc.Inventors: Clement S. Chu, Noah C. Welker, Henry H. Lai