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1. 发明公开

EP3405573A1 METHODS AND SYSTEMS FOR HIGH FIDELITY SEQUENCING 审中-公开
公开(公告)号：EP3405573A1
公开(公告)日：2018-11-28
申请号：EP17742055.1
申请日：2017-01-20
申请人： Grail, Inc.
发明人： VENN, Oliver Claude , DILTHEY, Alexander Tilo
IPC分类号： C12N15/10 , C12Q1/68 , G06F19/12 , G06F19/18 , G06F19/22
CPC分类号： G06F19/22 , C12Q1/6869 , G06F19/12 , G06F19/18 , C12Q2535/122
摘要： Systems and methods for high fidelity sequencing and identification of rare mutations at dilute concentrations in a sample are described herein. In various aspects, the use of specialized library preparation techniques including adapter ligation conditions and hybrid capture enrichment panels are used along with controls to increase yield of sequence-ready molecules and identify and minimize contamination and errors. Systems and methods also relate to analyzing sequencing data to differentiate true variants from false positives using ensembles and a quasi-maximum likelihood model.

2. 发明授权

EP2718862B1 METHOD FOR ASSEMBLY OF NUCLEIC ACID SEQUENCE DATA 有权
公开(公告)号：EP2718862B1
公开(公告)日：2018-10-31
申请号：EP12730271.9
申请日：2012-05-24
申请人： Koninklijke Philips N.V.
发明人： KUMAR, Sunil , SINGH, Randeep , DIMITROVA, Nevenka
IPC分类号： G06F19/22
CPC分类号： G06F19/22
摘要： The present invention relates to a method for assembly of nucleic acid sequence data comprising nucleic acid fragment reads into (a) contiguous nucleotide sequence segment(s), comprising the steps of: (a) obtaining a plurality of nucleic acid sequence data from a plurality of nucleic acid fragment reads; (b) aligning said plurality of nucleic acid sequence data to a reference sequence; (c) detecting one or more gaps or regions of non-assembly, or non-matching with the reference sequence in the alignment output of step (b); (d) performing de novo sequence assembly of nucleic acid sequence data mapping to said gaps or regions of non-assembly; and (e) combining the alignment output of step (b) and the assembly output of step (d) in order to obtain (a) contiguous nucleotide sequence segment(s). In addition, a corresponding program element or computer program for assembly of nucleic acid sequence data and a sequence assembly system for transforming nucleic acid sequence data comprising nucleic acid fragment reads into (a) contiguous nucleotide sequence segment(s) is provided.

3. 发明授权

EP3077539B8 METHOD FOR EVALUATING MINORITY VARIANTS IN A SAMPLE 有权转让
公开(公告)号：EP3077539B8
公开(公告)日：2018-10-10
申请号：EP14841366.9
申请日：2014-11-26
申请人： Personal Genome Diagnostics Inc.
发明人： OSBORNE, Robert , MUSGRAVE-BROWN, Esther
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , G06F19/22 , C12Q2535/122 , C12Q2545/101
摘要： A method of evaluating a sequence variation in a sample is provided. In some embodiments, the method may involve: amplifying a nucleic acid product from an initial sample; fragmenting an amount of the nucleic acid product to produce fragments; attaching an adaptor to each end of the fragments to produce adaptor-tagged fragments; sampling no more than 10% of the tagged fragments and amplifying them; sequencing at least some of the copies of the fragments to produce a plurality of sequence reads; grouping sequence reads for copies of fragments that have the same fragmentation breakpoints; deriving a consensus sequence for each of the read groups; and aligning the consensus sequences with a reference sequence.

4. 发明授权

EP2683833B1 METHODS FOR THE SELECTION AND OPTIMIZATION OF OLIGONUCLEOTIDE TAG SEQUENCES 有权
公开(公告)号：EP2683833B1
公开(公告)日：2018-09-26
申请号：EP12711081.5
申请日：2012-03-12
申请人： Gen-Probe Incorporated
发明人： NELSON, Norman C. , CHELLISERRY, Jijumon
IPC分类号： G06F19/20 , C12Q1/6811 , C12N15/10
CPC分类号： C12Q1/6811 , C12N15/1065 , G06F19/20 , G06F19/22
摘要： Methods for selecting tag-oligonucleotide sequences for use in an in vitro nucleic acid assay. The selected tag sequences are useful for nucleic acid assay wherein interference between the nucleic acid sequences is the assay is to be controlled. Selected tag sequences are incorporated into nucleic acid assay to improve the performance of and/or minimize any interference between nucleic acids in the assay compared to untagged assays.

5. 发明公开

EP3373175A1 SYSTEM AND METHOD FOR CLEANING NOISY GENETIC DATA AND USING DATA TO MAKE PREDICTIONS 审中-实审
公开(公告)号：EP3373175A1
公开(公告)日：2018-09-12
申请号：EP17207702.6
申请日：2006-11-22
申请人： Natera, Inc.
发明人： RABINOWITZ, Matthew , BANJEVIC, Milena , DEMKO, Zachary Paul , JOHNSON, David Scott
IPC分类号： G06F19/18 , G06F19/22 , G06F19/24
CPC分类号： G06F19/18 , G06F19/22 , G06F19/24
摘要： A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, and also for predicting likely phenotypic outcomes using mathematical models and given genetic, phenotypic and/or clinical data of an individual, and also relevant aggregated medical data consisting of genotypic, phenotypic, and/or clinical data from germane patient subpopulations. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In one embodiment of the invention, incomplete genetic data from an embryonic cell is reconstructed using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals. In another embodiment, incomplete genetic data from a fetus is acquired from fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals. In another embodiment, the genetic data can be reconstructed for the purposes of making phenotypic predictions. In another embodiment, the genetic data can be used to detect for aneuploides and uniparental disomy. In another embodiment, phenotypic predictions may be made using models based on contingency tables for genetic data that can be constructed from data available in genomic databases. In another embodiment, a plurality of models are created and tested using a set of test data, and the prediction is made using the model that is identified as the most accurate.

6. 发明公开

EP3365445A1 METHODS FOR GENOME ASSEMBLY, HAPLOTYPE PHASING, AND TARGET INDEPENDENT NUCLEIC ACID DETECTION 有权转让
公开(公告)号：EP3365445A1
公开(公告)日：2018-08-29
申请号：EP16858077.7
申请日：2016-10-18
申请人： Dovetail Genomics, LLC
发明人： GREEN, Richard E. , HARTLEY, Paul , TROLL, Christopher , MIN, Ei Ei
IPC分类号： C12N15/11 , C12Q1/68 , C40B40/06
CPC分类号： C12N15/1065 , C12Q1/6806 , C12Q1/6809 , C12Q1/6869 , C12Q1/6874 , G06F19/22 , G06F19/28 , C12Q2521/301 , C12Q2523/101 , C12Q2535/122
摘要： The disclosure provides methods to assemble genomes of eukaryotic or prokaryotic organisms. The disclosure provides methods for haplotype phasing and meta-genomics assemblies. The disclosure provides a streamlined method for accomplishing these tasks, such that intermediates need not be labeled by an affinity label to facilitate binding to a solid surface. The disclosure also provides methods and compositions for the de novo generation of scaffold information, linkage information, and genome information for unknown organisms in heterogeneous metagenomic samples or samples obtained from multiple individuals. Practice of the methods can allow de novo sequencing of entire genomes of uncultured or unidentified organisms in heterogeneous samples, or the determination of linkage information for nucleic acid molecules in samples comprising nucleic acids obtained from multiple individuals.

7. 发明公开

EP3356559A1 TYPING AND ASSEMBLING DISCONTINUOUS GENOMIC ELEMENTS 审中-公开
公开(公告)号：EP3356559A1
公开(公告)日：2018-08-08
申请号：EP16852406.4
申请日：2016-09-27
申请人： Ludwig Institute for Cancer Research Ltd
发明人： REN, Bing , DIXON, Jesse , SELVARAJ, Siddarth
IPC分类号： C12Q1/68 , G06F19/26
CPC分类号： C12Q1/6841 , C12Q1/68 , C12Q1/6869 , C12Q1/6876 , C12Q2600/172 , G06F19/18 , G06F19/22 , G06F19/26 , C12Q2521/301 , C12Q2523/101 , C12Q2563/131
摘要： This invention relates to methods and kits for typing and assembling discontinuous genomic elements.

8. 发明公开

EP3353696A2 PATHOGEN DETECTION USING NEXT GENERATION SEQUENCING 审中-公开
公开(公告)号：EP3353696A2
公开(公告)日：2018-08-01
申请号：EP16849519.0
申请日：2016-09-21
申请人： The Regents of the University of California
发明人： CHIU, Charles , NACCACHE, Samia , FEDERMAN, Scot , STRYKE, Doug , MILLER, Steve , SAMAYOA, Erik
IPC分类号： G06F19/22 , C40B30/02 , C40B20/00 , C12Q1/68
CPC分类号： G06F19/22 , G06F19/18
摘要： Embodiments are directed to systems and methods for pathogen detection using next-generation sequencing (NGS) analysis of a sample. Embodiments may apply alignment algorithms (e.g., SNAP and/or RAPSearch alignment algorithms) to align individual sequence reads from a sample in a next-generation sequencing (NGS) dataset against reference genome entries in a classified reference genome database. Embodiments of the present invention may include classifying, filtering, and displaying results to a clinician that can then quickly and easily obtain the results of the sequencing to identify a pathogen or other genetic material in a sample that is being tested. A negative sample and a corresponding database can be used to remove contaminants from a list of candidate pathogens. Thus, embodiments are directed to a system that is configured to filter the results of a sequencing alignment and classify a sample quickly.

9. 发明公开

EP3221695A4 PARALLEL-PROCESSING SYSTEMS AND METHODS FOR HIGHLY SCALABLE ANALYSIS OF BIOLOGICAL SEQUENCE DATA 有权
公开(公告)号：EP3221695A4
公开(公告)日：2018-07-25
申请号：EP15860295
申请日：2015-11-20
申请人： THE RES INSTITUTE AT NATIONWIDE CHILDRENS HOSPITAL
发明人： FITCH JAMES R , KELLY BENJAMIN J , WHITE PETER
IPC分类号： G01N33/48 , G06F3/06 , G06F19/22 , G06F19/28
CPC分类号： G06F19/28 , G06F3/0608 , G06F3/0641 , G06F3/067 , G06F19/22
摘要： An apparatus includes a memory configured to store a sequence that includes an estimation of a biological sequence. The sequence includes a set of elements. The apparatus also includes an assignment module implemented in a hardware processor. The assignment module is configured to receive the sequence from the memory, and assign each element to at least one segment from a set of segments, including, when an element maps to at least a first segment and a second segment, assigning the element set of segments specific to that hardware processor, and substantially simultaneous with the remaining hardware processors, remove at least a portion of duplicate elements in that segment to generate a deduplicated segment. Reorder the elements in the deduplicated segment to generate a realigned segment that has a reduced likelihood for alignment errors

10. 发明公开

EP3347496A1 METHOD AND SYSTEM FOR MICROBIOME-DERIVED DIAGNOSTICS AND THERAPEUTICS FOR ORAL HEALTH 审中-实审转让
公开(公告)号：EP3347496A1
公开(公告)日：2018-07-18
申请号：EP16845234.0
申请日：2016-09-09
申请人： Ubiome Inc.
发明人： APTE, Zachary , RICHMAN, Jessica , ALMONACID, Daniel , BEHBAHANI, Siavosh Rezvan
IPC分类号： C12Q1/68 , G06F19/10 , G06F19/18 , G06F19/20
CPC分类号： C12Q1/68 , C12Q1/6883 , C12Q1/689 , G06F19/00 , G06F19/18 , G06F19/22 , G06F19/24 , G16H50/20 , G16H50/50 , Y02A90/26
摘要： Methods, compositions, and systems are provided for detecting one or more a oral health issues by characterizing the microbiome of an individual, monitoring such effects, and/or determining, displaying, or promoting a therapy for the oral health issue. Methods, compositions, and systems are also provided for generating and comparing microbiome composition and/or functional diversity datasets. Methods, compositions, and systems are also provided for generating a characterization model and/or therapy model for dental decay issues and gingivitis issues.

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