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公开(公告)号：US20160085910A1
公开(公告)日：2016-03-24
申请号：US14854441
申请日：2015-09-15
Applicant: ILLUMINA, INC.
Inventor： Jocelyne Bruand , Johann Felix Schlesinger
IPC: G06F19/22
Abstract: Method includes receiving sequencing data including a plurality of sample reads that have corresponding sequences of nucleotides and assigning the sample reads to designated loci. The method also includes analyzing the assigned reads for each designated locus to identify corresponding regions-of-interest (ROIs) within the assigned reads. Each of the ROIs has one or more series of repeat motifs. The method also includes sorting the assigned reads based on the sequences of the ROIs such that the ROIs with different sequences are assigned as different potential alleles. The method also includes analyzing, for designated loci having multiple potential alleles, the sequences of the potential alleles to determine whether a first allele of the potential alleles is suspected stutter product of a second allele of the potential alleles.
Abstract translation: 方法包括接收测序数据，包括具有相应核苷酸序列的多个样本读取并将样本读取分配给指定的基因座。 该方法还包括分析每个指定轨迹的分配的读取以识别分配的读取内的相应的感兴趣区域（ROI）。 每个ROI都有一个或多个重复序列。 该方法还包括基于ROI的序列对所分配的读取进行排序，使得具有不同序列的ROI被分配为不同的潜在等位基因。 该方法还包括分析具有多个潜在等位基因的指定基因座的潜在等位基因的序列，以确定潜在等位基因的第一等位基因是否是潜在等位基因的第二等位基因的怀疑产物。
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公开(公告)号：US10971249B2
公开(公告)日：2021-04-06
申请号：US15705079
申请日：2017-09-14
Applicant: ILLUMINA, INC.
Inventor： Honglei Liu , Jocelyne Bruand
IPC: G16B30/00
Abstract: A computer-implemented method, computer system and computer-readable medium for identifying off-target matches from a set of candidate primer sequences on a genome reference sequence can include: receiving onto a data storage unit a plurality of candidate primer sequences; for each candidate primer sequence, calculating, using a processor, a plurality of candidate matches on the genome reference sequence for the candidate primer sequences; calculating, using the processor, verified matches on the genome reference sequence based on the candidate matching locations satisfying a plurality of matching verification rules; performing matching calculations of the verified matches to determine whether the verified matches form a match condition on the genome reference sequence; and generating a location profile on the genome reference sequence based on the match condition from the verified matches that meet a predetermined threshold.
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Patent Agency Ranking
公开(公告)号：US20210233612A1
公开(公告)日：2021-07-29
申请号：US17197976
申请日：2021-03-10
Applicant: ILLUMINA, INC.
Inventor： Honglei Liu , Jocelyne Bruand
IPC: G16B30/00
Abstract: A computer-implemented method, computer system and computer-readable medium for identifying off-target matches from a set of candidate primer sequences on a genome reference sequence can include: receiving onto a data storage unit a plurality of candidate primer sequences; for each candidate primer sequence, calculating, using a processor, a plurality of candidate matches on the genome reference sequence for the candidate primer sequences; calculating, using the processor, verified matches on the genome reference sequence based on the candidate matching locations satisfying a plurality of matching verification rules; performing matching calculations of the verified matches to determine whether the verified matches form a match condition on the genome reference sequence; and generating a location profile on the genome reference sequence based on the match condition from the verified matches that meet a predetermined threshold.
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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：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：US20210375396A1
公开(公告)日：2021-12-02
申请号：US17400165
申请日：2021-08-12
Applicant: Illumina, Inc.
Inventor： Jocelyne Bruand , Johann Felix Schlesinger
Abstract: Sample analyzer having a system controller that includes a plurality of modules. The plurality of modules include a first filter module that assigns sample reads to designated loci based on a sequence of nucleotides and an aligner module that analyzes the assigned reads to identify corresponding regions-of-interest (ROIs) within the assigned reads. A second filter module sorts the assigned reads based on the sequences of the ROIs such that the ROIs with different sequences are assigned as different potential alleles. Each potential allele has a sequence that is different from the sequences of other potential alleles within the designated locus. A stutter module analyzes the sequences of the potential alleles to determine whether a first allele of the potential alleles is suspected stutter product of a second allele of the potential alleles.
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