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公开(公告)号：US20240404638A1
公开(公告)日：2024-12-05
申请号：US18668853
申请日：2024-05-20
Applicant: ILLUMINA, INC.
IPC: G16B40/00
Abstract: Computer methods and systems for quantifying a nucleic acid sample comprising nucleic acid of one or more contributors to: receive nucleic acid sequence reads obtained from the nucleic acid sample and mapped to alleles at polymorphism loci; determine, using the nucleic acid sequence reads, allele counts for each of the alleles at the polymorphism loci; use a probabilistic mixture model that applies a probabilistic mixture model to the allele counts, and that uses probability distributions to model the allele counts at the polymorphism loci; quantify, using the probabilistic mixture model, one or more fractions of nucleic acid of the one or more contributors in the nucleic acid sample; determine a probability that a specific contributor among the one or more contributors has a specific genotype; and call, based on the posterior probability, that the nucleic acid sample includes nucleic acid from the specific contributor.
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公开(公告)号：US20220262460A1
公开(公告)日：2022-08-18
申请号：US16622814
申请日：2018-06-19
Applicant: ILLUMINA, INC.
Abstract: Computer methods and systems for quantifying a nucleic acid sample comprising nucleic acid of one or more contributors to: receive nucleic acid sequence reads obtained from the nucleic acid sample and mapped to alleles at polymorphism loci; determine, using the nucleic acid sequence reads, allele counts for each of the alleles at the polymorphism loci; use a probabilistic mixture model that applies a probabilistic mixture model to the allele counts, and that uses probability distributions to model the allele counts at the polymorphism loci; quantify, using the probabilistic mixture model, one or more fractions of nucleic acid of the one or more contributors in the nucleic acid sample; determine a probability that a specific contributor among the one or more contributors has a specific genotype; and call, based on the posterior probability, that the nucleic acid sample includes nucleic acid from the specific contributor.
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公开(公告)号：US20210151125A1
公开(公告)日：2021-05-20
申请号：US16622822
申请日：2018-06-19
Applicant: ILLUMINA, INC.
Inventor： Yong Li , Jocelyne Bruand , Ryan Matthew Kelley , Chih Lee , Konrad Scheffler
Abstract: Methods and systems are provided for quantifying and deconvolving nucleic acid mixture samples including nucleic acid of one or more contributors having known or unknown genomes. The methods and systems provided herein implement processes that use Bayesian probabilistic modeling techniques to determine the abundances and confidence intervals of genetically distinct contributors in a chimerism sample, thereby improving specificity, accuracy and sensitivity, and greatly expanded the application scope over conventional methods.
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公开(公告)号：US11990208B2
公开(公告)日：2024-05-21
申请号：US16622814
申请日：2018-06-19
Applicant: ILLUMINA, INC.
IPC: G16B40/00
CPC classification number: G16B40/00
Abstract: Computer methods and systems for quantifying a nucleic acid sample comprising nucleic acid of one or more contributors to: receive nucleic acid sequence reads obtained from the nucleic acid sample and mapped to alleles at polymorphism loci; determine, using the nucleic acid sequence reads, allele counts for each of the alleles at the polymorphism loci; use a probabilistic mixture model that applies a probabilistic mixture model to the allele counts, and that uses probability distributions to model the allele counts at the polymorphism loci; quantify, using the probabilistic mixture model, one or more fractions of nucleic acid of the one or more contributors in the nucleic acid sample; determine a probability that a specific contributor among the one or more contributors has a specific genotype; and call, based on the posterior probability, that the nucleic acid sample includes nucleic acid from the specific contributor.
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Patent Agency Ranking
公开(公告)号：US20240117341A1
公开(公告)日：2024-04-11
申请号：US18542058
申请日：2023-12-15
Applicant: ILLUMINA, INC.
Inventor： John S. Vieceli , Ryan Matthew Kelley
IPC: C12N15/10 , C12Q1/6876 , G16B25/10
CPC classification number: C12N15/1072 , C12Q1/6876 , G16B25/10
Abstract: Presented herein are techniques for indexing of nucleic acid, e.g., for use in conjunction with sequencing. The techniques include generating indexed nucleic acid fragments from an individual sample, whereby the index sequence incorporated into each index site of the nucleic acid fragment is selected from a plurality of distinguishable of index sequences and such that the population of generated nucleic acid fragments represents each index sequence from the plurality. In this manner, the generated indexed nucleic acid fragments from a single sample are indexed with a diverse mix of index sequences that reduce misassignment due to index read errors associated with low sequence diversity.
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公开(公告)号：US11891600B2
公开(公告)日：2024-02-06
申请号：US16181114
申请日：2018-11-05
Applicant: ILLUMINA, INC.
Inventor： John S. Vieceli , Ryan Matthew Kelley
IPC: C12N15/10 , G16B25/10 , C12Q1/6876
CPC classification number: C12N15/1072 , C12Q1/6876 , G16B25/10 , C12Q1/6869 , C12Q2525/191 , C12Q2563/179 , C12Q1/6806 , C12Q2525/191 , C12Q2535/122 , C12Q2563/179
Abstract: Presented herein are techniques for indexing of nucleic acid, e.g., for use in conjunction with sequencing. The techniques include generating indexed nucleic acid fragments from an individual sample, whereby the index sequence incorporated into each index site of the nucleic acid fragment is selected from a plurality of distinguishable of index sequences and such that the population of generated nucleic acid fragments represents each index sequence from the plurality. In this manner, the generated indexed nucleic acid fragments from a single sample are indexed with a diverse mix of index sequences that reduce misassignment due to index read errors associated with low sequence diversity.
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公开(公告)号：US11495325B2
公开(公告)日：2022-11-08
申请号：US16035470
申请日：2018-07-13
Applicant: Illumina, Inc.
Abstract: Disclosed herein are systems and methods for multiplex primer design and selection. In one example, a system includes non-transitory memory configured to store executable instructions; and a hardware processor programmed by the executable instructions to receive a plurality of target gene sequences and determine a set of primers for each target gene sequence based on a penalty score associated with the set of primers, wherein the penalty score is based on a non-linear combination of a primer-level penalty score and a set-level penalty score.
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公开(公告)号：US20200017994A1
公开(公告)日：2020-01-16
申请号：US16035470
申请日：2018-07-13
Applicant: Illumina, Inc.
IPC: C40B30/02
Abstract: Disclosed herein are systems and methods for multiplex primer design and selection. In one example, a system includes non-transitory memory configured to store executable instructions; and a hardware processor programmed by the executable instructions to receive a plurality of target gene sequences and determine a set of primers for each target gene sequence based on a penalty score associated with the set of primers, wherein the penalty score is based on a non-linear combination of a primer-level penalty score and a set-level penalty score.
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公开(公告)号：US20190218545A1
公开(公告)日：2019-07-18
申请号：US16181114
申请日：2018-11-05
Applicant: ILLUMINA, INC.
Inventor： John S. Vieceli , Ryan Matthew Kelley
IPC: C12N15/10 , C12Q1/6876 , G16B25/10
CPC classification number: C12N15/1072 , C12Q1/6876 , G16B25/10 , G16B35/10 , C12Q1/6869 , C12Q2525/191 , C12Q2563/179 , C12Q1/6806 , C12Q2535/122
Abstract: Presented herein are techniques for indexing of nucleic acid, e.g., for use in conjunction with sequencing. The techniques include generating indexed nucleic acid fragments from an individual sample, whereby the index sequence incorporated into each index site of the nucleic acid fragment is selected from a plurality of distinguishable of index sequences and such that the population of generated nucleic acid fragments represents each index sequence from the plurality. In this manner, the generated indexed nucleic acid fragments from a single sample are indexed with a diverse mix of index sequences that reduce misassignment due to index read errors associated with low sequence diversity.
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