公开(公告)号：US20230340571A1

公开(公告)日：2023-10-26

申请号：US18307482

申请日：2023-04-26

Applicant: Illumina, Inc. ,  Illumina Software, Inc.

Inventor： Sepideh Almasi ,  Yong Li ,  Anindita Dutta ,  Eric Vermaas ,  Rigoberto Pantoja

IPC: C12Q1/6811 ,  C12Q1/6874 ,  G16B25/20

CPC classification number: C12Q1/6811 ,  C12Q1/6874 ,  G16B25/20 ,  C12Q2600/156

Abstract: This disclosure describes methods, non-transitory computer readable media, and systems that can use a machine-learning model to classify or predict a probability of an oligonucleotide probe yielding an accurate genotype call or hybridizing with a target oligonucleotide—based on the oligonucleotide probe's nucleotide-sequence composition. To intelligently identify oligonucleotide probes that are more likely to yield accurate downstream genotyping—or more likely to successfully hybridize with target oligonucleotides—some embodiments of the disclosed machine-learning model include customized layers trained to detect motifs or other nucleotide-sequence patterns that correlate with favorable or unfavorable probe accuracy. By intelligently processing the nucleotide sequences of candidate oligonucleotide probes before implementing a microarray for a particular target oligonucleotide, the disclosed system can identify oligonucleotide probes with better genotyping accuracy (or better binding accuracy) than existing microarray systems for use in a microarray.

公开(公告)号：US20230175064A1

公开(公告)日：2023-06-08

申请号：US17922930

申请日：2022-02-07

Applicant: ILLUMINA, INC.

Inventor： Yong Li ,  Ryan Taft ,  Ali Genie Crawford ,  Nancy Kim

IPC: C12Q1/6883

CPC classification number: C12Q1/6883 ,  C12Q2600/158 ,  C12Q1/6869

Abstract: Methods, compositions, and systems are provided for monitoring tissue and organ health. The methods, compositions, and systems provided herein include, but are not limited to, whole genome sequence (WGS) based approaches for assessing copy number signals from cell free DNA (cfDNA) samples to identify tissue-specific cfDNA copy number profiles and enable quantification (830) of tissue fractions in the cfDNA samples.

公开(公告)号：US20200381079A1

公开(公告)日：2020-12-03

申请号：US16890982

申请日：2020-06-02

Applicant: Illumina, Inc.

Inventor： Yong Li

IPC: G16B20/10

Abstract: Presented herein are methods and compositions for copy number estimation of a target gene with close homologs, comprising determining sub-genic copy numbers. The methods are useful for estimating copy numbers of clinically important genes with high sequence similarity between gene of interest and their homologs, including non-functional pseudogenes.

公开(公告)号：US20210310067A1

公开(公告)日：2021-10-07

申请号：US17250814

申请日：2020-01-22

Applicant: Illumina, Inc.

Inventor： Yong Li

IPC: C12Q1/6881

Abstract: Methods, compositions, and systems are provided for monitoring tissue and organ health. The methods, compositions, and systems provided herein extract locus specific copy number signals from cell free DNA (cfDNA) samples to identify tissue-specific cfDNA copy number profiles and enable quantification of tissue fractions in the cfDNA samples.

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

IPC: G16B30/00 ,  G16B20/20 ,  G16B5/20

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.