Patents by Inventor Imran Saeedul HAQUE
Imran Saeedul HAQUE 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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Publication number: 20240150846Abstract: 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: January 11, 2024Publication date: May 9, 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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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: 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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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: 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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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: 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: 20210348229Abstract: 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: July 22, 2021Publication date: November 11, 2021Applicant: Myriad Women's Health, Inc.Inventors: Jared Robert MAGUIRE, Clement CHU, Imran Saeedul HAQUE, Eric Andrew EVANS, Noah WELKER
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Publication number: 20200157622Abstract: 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 7, 2020Publication date: May 21, 2020Applicant: MYRIAD WOMEN'S HEALTH, INC.Inventors: Jared Robert MAGUIRE, Clement CHU, Imran Saeedul HAQUE, Eric Andrew EVANS, Noah WELKER
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Patent number: 10597717Abstract: 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: March 21, 2017Date of Patent: March 24, 2020Assignee: MYRIAD WOMEN'S HEALTH, INC.Inventors: Jared Robert Maguire, Clement Chu, Imran Saeedul Haque, Eric Andrew Evans, Noah Welker
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Publication number: 20190348147Abstract: 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: ApplicationFiled: July 26, 2019Publication date: November 14, 2019Applicant: MYRIAD WOMEN'S HEALTH, INC.Inventors: Kristjan Eerik KASENIIT, Imran Saeedul HAQUE
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Publication number: 20180089364Abstract: 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: ApplicationFiled: September 29, 2017Publication date: March 29, 2018Inventors: Dale MUZZEY, Carlo G. ARTIERI, Eric Andrew EVANS, Imran Saeedul HAQUE
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Publication number: 20170355984Abstract: 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 9, 2017Publication date: December 14, 2017Inventors: Eric Andrew EVANS, Imran Saeedul HAQUE, Kyle BEAUCHAMP, Clement CHU, Carlo G. ARTIERI, Noah WELKER
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Publication number: 20170321270Abstract: Prenatal genetic testing allows early detection of genetic disease in a fetus. Described herein are methods of detecting the presence or absence of a genetic variant in a region of interest in the genome of a fetus in a pregnant woman. The methods are noninvasive, and can use cell-free DNA (cfDNA) present in the plasma of the pregnant woman. A DNA library is constructed from the cfDNA, and DNA molecules comprising the region of interest or portions thereof are enriched and analyzed, for example by sequencing. The methods described herein can also rely on constructing a maternal haplotype to provide even higher resolution fetal genetic variant determination.Type: ApplicationFiled: May 5, 2017Publication date: November 9, 2017Inventors: Imran Saeedul HAQUE, Jared Robert MAGUIRE, Clement CHU, Eric Andrew EVANS
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Publication number: 20170298436Abstract: According to one aspect, systems and processes for assaying a plurality of nucleic acid samples are provided. In an exemplary process, a matrix is generated including pools and samples using a pooling scheme with decoding capability equal to a number D. Matrix organization includes assigning one pool in a set of pools per row by one sample in a set of samples per column. Sample assignment creates a known pattern of pools, wherein each sample in the set of pools is assigned a total number of D+1 times and any two pools have at most one sample in common. Samples are pooled based on a pooling scheme, where pooled samples are assayed. Positive pools are determined and one or more positive samples are identified. The matrix is displayed as a visual pattern representing the known pattern of pools, the identified positive samples, and the determined positive pools.Type: ApplicationFiled: April 14, 2017Publication date: October 19, 2017Inventors: Kristjan Eerik KASENIIT, Mark R. THEILMANN, Alexander De Jong ROBERTSON, Eric Andrew EVANS, Imran Saeedul HAQUE
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Publication number: 20170275689Abstract: 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: March 21, 2017Publication date: September 28, 2017Inventors: Jared Robert MAGUIRE, Clement CHU, Imran Saeedul HAQUE, Eric Andrew EVANS, Noah WELKER
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Publication number: 20160371431Abstract: Recent developments in cost-effective DNA sequencing allows for individualized genomic screening of a subject for genetic sequence variants. Training a pathogenicity prediction model using semi-supervised training methods produces a better model for predicting the pathogenicity of a test genetic sequence variant. Provided herein are methods for predicting the pathogenicity of a test genetic sequence variant by utilizing a training data set comprising labeled benign genetic sequence variants unlabeled genetic sequence variants, the unlabeled genetic sequence variants comprising a mixture of benign genetic sequence variants and pathogenic genetic sequence variants. The genetic sequences are annotated with one or more features and a machine learning model is trained in a semi-supervised process based on the training data.Type: ApplicationFiled: June 22, 2016Publication date: December 22, 2016Inventors: Imran Saeedul HAQUE, Eric Andrew EVANS, Sharad Mandyam VIKRAM, Matthew David RASMUSSEN