Patents Assigned to Counsyl, Inc.
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Publication number: 20180300450Abstract: A computer-implemented method for optimizing performance of a DNA-based noninvasive prenatal screen includes generating a plurality of synthetic sequencing datasets by, for each of the plurality of synthetic sequencing datasets, (i) generating at least one of a plurality of synthetic copy number variants comprising a synthetic number of copies of at least a portion of a region of interest represented by a synthetic number of sequencing reads from one or more segments within the region of interest, and (ii) modifying a real sequencing dataset, which includes genetic sequencing data from a real test sample comprising maternal and fetal cfDNA, by replacing a number of real sequencing reads from the one or more segments within the region of interest in the real test sample with the synthetic number of sequencing reads. Various other methods and systems are also disclosed.Type: ApplicationFiled: March 8, 2018Publication date: October 18, 2018Applicant: Counsyl, Inc.Inventors: Gregory John Hogan, Kristjan Eerik Kaseniit, Dale E. Muzzey
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Publication number: 20180292425Abstract: A robotic system is provided for accurately and quickly sorting sample tubes within or between sample tube racks.Type: ApplicationFiled: April 17, 2018Publication date: October 11, 2018Applicant: Counsyl, Inc.Inventors: Kyle Lapham, Ethan Nash, Peter Turner, Kevin Haas, Christopher Wong
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Publication number: 20180237845Abstract: A method of identifying and quantifying copy number variations in a gene of interest for a genomic DNA sample includes (i) fragmenting a genomic DNA sample to produce a plurality of polynucleotide fragments, (ii) isolating a plurality of target polynucleotide fragments, (iii) sequencing the plurality of target polynucleotide fragments, (iv) aligning fragment sequences to a reference sequence, (v) calculating read depths for base positions of the plurality of target polynucleotide fragments, (vi) calculating copy number likelihoods for each base position of the reference sequence, (vii) performing a breakpoint analysis on a set of fragment sequences to identify at least one sequence variation located between selected breakpoint regions of the target gene and calculate modified copy number likelihoods for base positions of the reference sequence based on the at least one sequence variation, and (viii) determining whether the target gene includes at least one copy number variation.Type: ApplicationFiled: January 30, 2018Publication date: August 23, 2018Applicant: Counsyl, Inc.Inventors: Jared R. Maguire, Alexander D. Robertson, Eric A. Evans
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Publication number: 20180214880Abstract: Automated diagnostic laboratory and laboratory management system for high throughout and methods of using the same, including subsystems and components for use with the same and devices for removing lids from microplates and methods of using the same.Type: ApplicationFiled: December 22, 2017Publication date: August 2, 2018Applicant: Counsyl, Inc.Inventor: Clayton Salinger Ketner
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Publication number: 20180216183Abstract: Disclosed are high concentration reagents for use in preparing DNA samples in low volume reactions. Such reagents include, for example, DNA end repair buffers for use in low volume DNA blunting and phosphorylating reactions, DNA adenylating buffers for use in a low volume DNA adenylating reaction, and DNA ligation buffers for use in low volume DNA adaptor ligation reactions with adaptors. Also disclosed are customized reagent plates and kits containing one or more of these low volume buffers for use in low volume DNA blunting, phosphorylating, adenylating, and ligation reactions. Methods of using the high concentration reagents (low volume buffers) and the customized reagent plates for preparing DNA sequencing libraries in low volume reactions are also disclosed.Type: ApplicationFiled: January 29, 2018Publication date: August 2, 2018Applicant: Counsyl, Inc.Inventors: Henry H. Lai, Clement S. Chu
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Publication number: 20180214840Abstract: Disclosed are high concentration reagents for use in preparing DNA samples in low volume reactions. Such reagents include, for example, DNA end repair buffers for use in low volume DNA blunting and phosphorylating reactions, DNA adenylating buffers for use in a low volume DNA adenylating reaction, and DNA ligation buffers for use in low volume DNA adaptor ligation reactions with adaptors. Also disclosed are customized reagent plates and kits containing one or more of these low volume buffers for use in low volume DNA blunting, phosphorylating, adenylating, and ligation reactions. Methods of using the high concentration reagents (low volume buffers) and the customized reagent plates for preparing DNA sequencing libraries in low volume reactions are also disclosed.Type: ApplicationFiled: January 29, 2018Publication date: August 2, 2018Applicant: Counsyl, Inc.Inventors: Henry H. Lai, Clement S. Chu
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Publication number: 20180216253Abstract: Disclosed are high concentration reagents for use in preparing DNA samples in low volume reactions. Such reagents include, for example, DNA end repair buffers for use in low volume DNA blunting and phosphorylating reactions, DNA adenylating buffers for use in a low volume DNA adenylating reaction, and DNA ligation buffers for use in low volume DNA adaptor ligation reactions with adaptors. Also disclosed are customized reagent plates and kits containing one or more of these low volume buffers for use in low volume DNA blunting, phosphorylating, adenylating, and ligation reactions. Methods of using the high concentration reagents (low volume buffers) and the customized reagent plates for preparing DNA sequencing libraries in low volume reactions are also disclosed.Type: ApplicationFiled: January 29, 2018Publication date: August 2, 2018Applicant: Counsyl, Inc.Inventors: Henry H. Lai, Clement S. Chu
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Patent number: 10031149Abstract: A robotic system is provided for accurately and quickly sorting sample tubes within or between sample tube racks.Type: GrantFiled: December 22, 2016Date of Patent: July 24, 2018Assignee: Counsyl, Inc.Inventors: Kyle Lapham, Ethan Nash, Peter Turner, Kevin Haas, Christopher Wong
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Publication number: 20170190056Abstract: A robotic system is provided for accurately and quickly sorting sample tubes within or between sample tube racks.Type: ApplicationFiled: December 22, 2016Publication date: July 6, 2017Applicant: Counsyl, Inc.Inventors: Kyle Lapham, Ethan Nash, Peter Turner, Kevin Haas, Christopher Wong
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Publication number: 20170192030Abstract: Disclosed herein are high-throughput sample processing systems and waste management systems, and methods of using the same.Type: ApplicationFiled: March 22, 2017Publication date: July 6, 2017Applicant: Counsyl, Inc.Inventors: Kyle Allen Lapham, James Frederick Cregg, Daniel Delubac, Stuart Ira Glaser
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Patent number: 9643185Abstract: Disclosed herein are high-throughput sample processing systems and waste management systems, and methods of using the same.Type: GrantFiled: April 9, 2016Date of Patent: May 9, 2017Assignee: Counsyl, Inc.Inventors: Kyle Allen Lapham, James Frederick Cregg, Daniel Delubac, Stuart Ira Glaser
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Publication number: 20170045542Abstract: Integrated modular liquid handling systems are described. The modular liquid handling systems may be customized for use in a variety of applications, including sample processing, assays, diagnostic analyses, and separation of biomolecules. The liquid handling systems may include a variety of integrated modules that provide functions including dispensing of liquids, aspiration of liquids, sensing of liquid parameters, and detection of signals.Type: ApplicationFiled: August 6, 2016Publication date: February 16, 2017Applicant: Counsyl, Inc.Inventors: Kyle Lapham, Tony Hyun Kim, Christopher Bremner
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Publication number: 20160354783Abstract: Disclosed herein are high-throughput sample processing systems and waste management systems, and methods of using the same.Type: ApplicationFiled: April 9, 2016Publication date: December 8, 2016Applicant: Counsyl, Inc.Inventors: Kyle Allen Lapham, James Frederick Cregg, Daniel Delubac, Stuart Ira Glaser
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Publication number: 20160103959Abstract: Provided herein are methods, systems, and devices for genetic screening. The genetic screening of two or more individuals can be utilized to predict the phenotype of a child from the group of individuals. Also disclosed is prediction of a phenotype of a child from a subset of biological relatives, such as a potential mother and father, before conception. In many instances, the methods, systems and devices herein are utilized to predict the probability of a child developing a rare genetic disease.Type: ApplicationFiled: December 16, 2015Publication date: April 14, 2016Applicant: Counsyl, Inc.Inventors: Balaji S. Srinivasan, Balaji K. Srinivasan, Eric Evans, Ranji Srinivasan, Kumaranayagam Balakrishnan
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Publication number: 20160045918Abstract: Disclosed herein are high-throughput sample processing systems and waste management systems, and methods of using the same.Type: ApplicationFiled: June 2, 2015Publication date: February 18, 2016Applicant: COUNSYL, INC.Inventors: Kyle Allen Lapham, James Frederick Cregg, Daniel Delubac, Stuart Ira Glaser
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Patent number: 9092401Abstract: 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: GrantFiled: October 31, 2012Date of Patent: July 28, 2015Assignee: Counsyl, Inc.Inventors: Hunter Richards, Eric Evans, Balaji Srinivasan, Subramaniam Srinivasan, Abhik Shah, A. Scott Patterson, Clement Chu
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Publication number: 20140162278Abstract: 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.Type: ApplicationFiled: December 10, 2013Publication date: June 12, 2014Applicant: Counsyl, Inc.Inventors: Hunter Richards, Eric Evans, Balaji Srinivasan, Subramaniam Srinivasan, Clement Chu
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Publication number: 20140121116Abstract: 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: October 31, 2012Publication date: May 1, 2014Applicant: Counsyl, Inc.Inventors: Hunter Richards, Eric EVANS, Balaji SRINIVASAN, Subramaniam SRINIVASAN, Abhik SHAH, A. Scott Patterson, Clement CHU
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Publication number: 20140024542Abstract: 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.Type: ApplicationFiled: July 17, 2012Publication date: January 23, 2014Applicant: Counsyl, Inc.Inventors: Hunter Richards, Eric Evans, Balaji Srinivasan, Subramaniam Srinivasan, Clement Chu
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Publication number: 20140024536Abstract: 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.Type: ApplicationFiled: July 17, 2012Publication date: January 23, 2014Applicant: Counsyl, Inc.Inventors: Hunter Richards, Eric Evans, Balaji Srinivasan, Subramaniam Srinivasan, Clement Chu