公开(公告)号：US20240355476A1

公开(公告)日：2024-10-24

申请号：US18761410

申请日：2024-07-02

申请人： THE UNIVERSITY OF CHICAGO

发明人： Suzanne D. CONZEN ,  Lei HUANG ,  Maria KOCHERGINSKY ,  Diana SZYMANSKI

IPC分类号： G16H50/20 ,  C12Q1/6809 ,  C12Q1/6827 ,  C12Q1/6837 ,  C12Q1/6886 ,  G16H50/30

CPC分类号： G16H50/20 ,  C12Q1/6809 ,  C12Q1/6827 ,  C12Q1/6837 ,  C12Q1/6886 ,  G16H50/30 ,  C12Q2600/106 ,  C12Q2600/112 ,  C12Q2600/118 ,  C12Q2600/156 ,  C12Q2600/158

摘要： Embodiments are directed to kits and methods of treating a breast cancer patient with a glucocorticoid receptor antagonist with or without an anticancer agent or compound after the patient has been determined to be susceptible to treatment with the glucocorticoid receptor antagonist.

公开(公告)号：US20240336970A1

公开(公告)日：2024-10-10

申请号：US18751153

申请日：2024-06-21

申请人： Natera, Inc.

发明人： Matthew Rabinowitz ,  Matthew Micah Hill ,  Bernhard Zimmermann ,  Johan Baner ,  George Gemelos ,  Milena Banjevic ,  Allison Ryan ,  Styrmir Sigurjonsson ,  Zachary Demko

IPC分类号： C12Q1/6883 ,  C12Q1/6809 ,  C12Q1/6811 ,  C12Q1/6844 ,  C12Q1/6848 ,  C12Q1/6851 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q1/6874

CPC分类号： C12Q1/6883 ,  C12Q1/6809 ,  C12Q1/6811 ,  C12Q1/6844 ,  C12Q1/6848 ,  C12Q1/6851 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q2600/156

摘要： The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

公开(公告)号：US20240312561A1

公开(公告)日：2024-09-19

申请号：US18603727

申请日：2024-03-13

申请人： GRAIL, LLC

发明人： Robert Abe Paine Calef ,  Alexander P. Fields ,  Samuel S. Gross

IPC分类号： G16B20/20 ,  C12Q1/6809 ,  C12Q1/6886

CPC分类号： G16B20/20 ,  C12Q1/6809 ,  C12Q1/6886

摘要： The present disclosure relates to a method for improving sequencing panel assignments for samples from two or more individual. The system is configured to generate a sequencing panel assignment having an optimized set of samples for each panel that reduces sequencing costs but does not compromise Limit of Detection of the assay.

公开(公告)号：US20240309456A1

公开(公告)日：2024-09-19

申请号：US18678417

申请日：2024-05-30

申请人： Natera, Inc.

发明人： MATTHEW RABINOWITZ ,  Matthew Micah HILL ,  Bernhard A. ZIMMERMANN ,  Johan BANER ,  George GEMELOS ,  Milena BANJEVIC ,  Allison RYAN ,  Styrmir SIGURJONSSON ,  Zachary DEMKO

IPC分类号： C12Q1/6883 ,  C12Q1/6809 ,  C12Q1/6811 ,  C12Q1/6844 ,  C12Q1/6848 ,  C12Q1/6851 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q1/6874

CPC分类号： C12Q1/6883 ,  C12Q1/6809 ,  C12Q1/6811 ,  C12Q1/6844 ,  C12Q1/6848 ,  C12Q1/6851 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q2600/156

摘要： The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

公开(公告)号：US20240304279A1

公开(公告)日：2024-09-12

申请号：US18646630

申请日：2024-04-25

申请人： The Chinese University of Hong Kong

发明人： Rossa Wai Kwun Chiu ,  Kwan Chee Chan ,  Yuk-Ming Dennis Lo ,  Peiyong Jiang ,  Kun Sun

IPC分类号： G16B20/20 ,  C12Q1/6809 ,  C12Q1/689 ,  G16B20/00 ,  G16B20/10 ,  G16B30/00 ,  G16B30/10

CPC分类号： G16B20/20 ,  C12Q1/6809 ,  C12Q1/689 ,  G16B20/00 ,  G16B20/10 ,  G16B30/10 ,  C12Q2600/112 ,  C12Q2600/154 ,  G16B30/00

摘要： The contributions of different tissues to a DNA mixture are determined using methylation levels at particular genomic sites. Tissue-specific methylation levels of M tissue types can be used to deconvolve mixture methylation levels measured in the DNA mixture, to determine fraction contributions of each of the M tissue types. Various types of genomic sites can be chosen to have particular properties across tissue types and across individuals, so as to provide increased accuracy in determining contributions of the various tissue types. The fractional contributions can be used to detect abnormal contributions of a particular tissue, indicating a disease state for the tissue. A differential in fractional contributions for different sizes of DNA fragments can also be used to identify a diseased state of a particular tissue. A sequence imbalance for a particular chromosomal region can be detected in a particular tissue, e.g., identifying a location of a tumor.

公开(公告)号：US20240299932A1

公开(公告)日：2024-09-12

申请号：US18659536

申请日：2024-05-09

申请人： EMULATE, INC.

发明人： Catherine Karalis ,  Ville Kujala

IPC分类号： B01L3/00 ,  C12M1/12 ,  C12M3/06 ,  C12Q1/6809 ,  G01N33/50

CPC分类号： B01L3/5027 ,  C12M23/16 ,  C12Q1/6809 ,  G01N33/5023 ,  G01N33/5064 ,  G01N33/5091 ,  B01L2300/0819 ,  B01L2400/0487 ,  C12M25/02

摘要： The present invention relates to microfluidic fluidic devices, methods and systems for use in identifying epigenetic signatures in a range of sample types, e.g., cells established on a “chip” (including but not limited to single cell samples, cell populations, cell layers and whole tissues, such as a biopsy), immune cells, cfDNA, exosomes, and the like. More specifically, in some embodiments, a microfluidic chip containing a sample is contacted with a test compound (e.g. DNA altering test compound, an RNA expression altering test compound, etc.) for use in providing a diagnostic epigenetic signature for that type of sample (or cell type) exposed to that specific test compound. In some embodiments, after contact with a test compound, effluent fluids (e.g. fluids exiting the “chip” that contacted the cells) are derived for testing as a “virtual blood draw.” In some embodiments, epigenetic signatures include (but are not limited to) identifying specific combinations of modifications of chromosomes and specific modifications of DNA.

公开(公告)号：US20240294944A1

公开(公告)日：2024-09-05

申请号：US17909341

申请日：2021-03-09

申请人： The University of Tokyo

发明人： Takehiko Kobayashi ,  Tetsushi Iida

IPC分类号： C12N15/90 ,  C12N15/81 ,  C12N15/85 ,  C12N15/88 ,  C12Q1/6809

CPC分类号： C12N15/90 ,  C12N15/81 ,  C12N15/85 ,  C12N15/88 ,  C12Q1/6809 ,  C12Q2600/158

摘要： Provided is an artificial chromosome vector derived from a chromosome of a eukaryote, the vector comprising repetitive units of multiple ribosomal RNA genes (rDNA) and intergenic regions between the repetitive units, wherein an intergenic region 1 (IGS1) of the intergenic regions comprises a barcode sequence for incorporating and distinguishing a target gene.

公开(公告)号：US20240247306A1

公开(公告)日：2024-07-25

申请号：US18627211

申请日：2024-04-04

申请人： GRAIL, LLC

发明人： Onur Sakarya ,  Catalin Barbacioru

IPC分类号： C12Q1/6827 ,  C12Q1/6809 ,  G16B20/20 ,  G16B30/10 ,  G16B30/20 ,  G16B40/20 ,  G16B40/30

CPC分类号： C12Q1/6827 ,  C12Q1/6809 ,  G16B20/20 ,  G16B30/10 ,  G16B40/20 ,  G16B40/30 ,  G16B30/20

摘要： Cross-contamination of a test sample used to determine cancer is identified using gene sequencing data. Each test sample includes a number of test sequences that may include a single nucleotide polymorphism (SNP) that can be indicative of cancer. The test sequences are be filtered to remove or negate at least some of the SNPs from the test sequences. Negating the test sequences allows more test sequences to be simultaneously analyzed to determine cross-contamination. Cross-contamination is determined by modeling the variant allele frequency for the test sequences as a function of minor allele frequency, contamination level, and background noise. In some cases, the variant allele frequency is based on a probability function including the minor allele frequency. Cross-contamination of the test sample is determined if the determined contamination level is above a threshold and statistically significant.

公开(公告)号：US12046330B2

公开(公告)日：2024-07-23

申请号：US16934994

申请日：2020-07-21

申请人： 10X Genomics, Inc.

发明人： Sofia Kyriazopoulou-Panagiotopoulou ,  Patrick Marks

IPC分类号： G01N33/48 ,  C40B40/06 ,  G01N33/50 ,  G06F18/24 ,  G06N7/01 ,  G16B5/00 ,  G16B20/00 ,  G16B30/20 ,  G16B40/00 ,  C12Q1/6809 ,  C12Q1/6869 ,  G06N5/01 ,  G06N5/025 ,  G16B25/00

CPC分类号： G16B40/00 ,  C40B40/06 ,  G06F18/24 ,  G06N7/01 ,  G16B5/00 ,  G16B20/00 ,  G16B30/20 ,  B01J2219/00317 ,  C12Q1/6809 ,  C12Q1/6869 ,  G06N5/01 ,  G06N5/025 ,  G16B25/00

摘要： Systems and methods for analyzing first and second strings against a ground truth string are provided. A construct representing a plurality of components is obtained, each component for a different portion of the truth string. The construct comprises a plurality of measurement string sampling pools each having an identifier and a corresponding plurality of measurement samplings corresponding to one or two of the components. Each sampling has the identifier and a portion of the first or second string. Samplings are assigned to first, second or third classes when coding a portion of the first string, second string, or both the first and second string. First and second positions are tested for sequence events by calculating a plurality of sequence event models using assumptions on the components having samplings encompassing the first and second positions and class assignments. These assumptions are updated using the calculated models and the models are recalculated.

公开(公告)号：US20240203601A1

公开(公告)日：2024-06-20

申请号：US18523856

申请日：2023-11-29

申请人： Verinata Health, Inc.

发明人： Richard P. Rava ,  Brian K. Rhees

IPC分类号： G16H50/30 ,  C12Q1/6806 ,  C12Q1/6809 ,  C12Q1/6869 ,  C12Q1/6883 ,  C12Q1/6886 ,  G16B30/00 ,  G16B30/10 ,  G16H50/20

CPC分类号： G16H50/30 ,  C12Q1/6806 ,  C12Q1/6809 ,  C12Q1/6869 ,  G16B30/00 ,  G16B30/10 ,  G16H50/20 ,  C12Q1/6883 ,  C12Q1/6886 ,  C12Q2600/106

摘要： The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.