公开(公告)号：US11749381B2

公开(公告)日：2023-09-05

申请号：US16342017

申请日：2017-10-12

Applicant: BIOMÉRIEUX

Inventor： Pierre Mahe ,  Maud Tournoud ,  Stéphane Schicklin ,  Ghislaine Guigon ,  Etienne Ruppe

IPC: G16B40/20 ,  C12Q1/689 ,  G16B20/00 ,  G16B30/00 ,  C12Q1/6888

CPC classification number: G16B40/20 ,  C12Q1/689 ,  G16B20/00 ,  G16B30/00 ,  C12Q1/6888 ,  C12Q2600/106 ,  C12Q2600/158 ,  C12Q1/6888 ,  C12Q2600/156

Abstract: A method for identifying a pathogen contained in a metagenomic sample and for identifying pathogenic markers in the genome of the pathogen includes: processing the sample to extract DNA from pathogens, sequencing the extracted DNA, thereby producing a set of reads, comparing the reads to a database of genomes of known pathogens to assign reads to the pathogens; producing a pool of reads and assembling them to produce contigs, comparing the contigs to a second database of markers to check whether they contain a marker. The method further includes the step of comparing the reads to the second database to assign reads to the markers, a read being assigned to a marker if it falls entirely into or is astride the marker, and the pool also includes the reads assigned to the markers, the contigs thereby being assembled from reads assigned to a pathogen and reads assigned to markers.

公开(公告)号：US20230274790A1

公开(公告)日：2023-08-31

申请号：US18008004

申请日：2021-06-03

Applicant: Arc Bio, LLC

Inventor： Alejandro QUIROZ-ZARATE ,  Matt JOBIN

IPC: G16B20/00 ,  G16B40/20 ,  G16B30/10 ,  G06N3/02

CPC classification number: G16B20/00 ,  G16B40/20 ,  G16B30/10 ,  G06N3/02

Abstract: In accordance with some embodiments, systems, methods, and media for classifying genetic sequencing results based on pathogen-specific adaptive thresholds are provided. In some embodiments, a system comprises a processor programmed to: receive negative control results, each comprising values indicative of a number of reads detected in the respective negative control sample for an organism; generate a model based on the negative control results; receive a clinical sample result for a clinical sample, comprising values indicative of a number of reads detected in the clinical sample for an organism of a plurality of organisms; identify, utilizing the model, any values in the clinical sample that are likely to be diagnostically significant; generate a report based on the clinical sample result and organisms associated with a value likely to be diagnostically significant; and cause the report to be presented to a user.

公开(公告)号：US20230274428A1

公开(公告)日：2023-08-31

申请号：US18248706

申请日：2020-10-14

Applicant: GENOMEDIA INC. ,  NATIONAL CANCER CENTER JAPAN

Inventor： Satoshi FUJII ,  Takayuki YOSHINO ,  Tomoyuki YAMADA ,  Masahiro HATTORI

IPC: G06T7/00 ,  G06T7/11 ,  G06V20/69 ,  G06V10/26 ,  G06V10/77 ,  G16B20/20 ,  G16B40/20

CPC classification number: G06T7/0012 ,  G06T7/11 ,  G06V20/695 ,  G06V10/267 ,  G06V10/7715 ,  G16B20/20 ,  G16B40/20 ,  G06T2207/30096 ,  G06T2207/30028 ,  G06V2201/031

Abstract: An information processing system including units configured to: acquire a pathologic tissue image of a patient having a target disease; divide the pathologic tissue image into region images; input each of the region images to each of a plurality of feature prediction models constructed one-to-one for types of histopathological features; sort a plurality of region images of which respective combinations of presence or absence of the histopathological features based on the acquisition match a previously set combination of presence or absence of the histopathological features at time of sorting; input each of the region images selected by the sorting to each of gene mutation prediction models constructed one-to-one for types of gene mutations, the gene mutation prediction models each having a combination of presence or absence of the histopathological features; and output a prediction result of presence or absence of at least one gene mutation in the patient.

公开(公告)号：US20230274423A1

公开(公告)日：2023-08-31

申请号：US18045342

申请日：2022-10-10

Applicant: Altius Institute for Biomedical Sciences

Inventor： John A. Stamatoyannopoulos ,  Shreeram Akilesh ,  Alexander Muratov ,  Wouter Meuleman ,  William Kerwin

IPC: G06T7/00 ,  G06N20/00 ,  G16B40/30 ,  G16B40/20

CPC classification number: G06T7/0012 ,  G06N20/00 ,  G16B40/30 ,  G16B40/20 ,  G06T2207/20081 ,  G06T2207/20084 ,  G06T2207/30024

Abstract: Disclosed herein are methods of utilizing machine learning methods to analyze microscope images of populations of cells.

公开(公告)号：US20230272477A1

公开(公告)日：2023-08-31

申请号：US17993597

申请日：2022-11-23

Applicant: GRAIL, LLC

Inventor： Samuel S. Gross ,  Siddhartha Bagaria

IPC: C12Q1/6886 ,  G16H50/20 ,  G16B40/20

CPC classification number: C12Q1/6886 ,  G16H50/20 ,  G16B40/20 ,  C12Q2600/156 ,  G01N2800/7028

Abstract: Methods and systems for detecting contaminated fragments in a biological sample for cancer classification are disclosed. The system identifies multiple SNP site contamination markers and indel site contamination markers. The multiple SNP site contamination markers include at least two SNP sites within a threshold distance, having population haplotype frequency within a range of threshold frequencies, excluding guanine-adenine polymorphisms and/or cytosine-thymine polymorphisms, ensuring Hardy-Weinberg equilibrium, or any combination of the parameters above. The indel site contamination markers include indel sequences that are within a threshold length, having high complexity, having population haplotype frequency within a range of threshold frequencies, ensuring Hardy-Weinberg equilibrium, or any combination of the parameters above. The system identifies contamination markers for which the sample is homozygous. The system estimates the contamination level of the sample by identifying fragments having a haplotype that is different than the homozygous haplotype of the respective contamination marker site.

公开(公告)号：US20230263872A1

公开(公告)日：2023-08-24

申请号：US18023674

申请日：2021-08-27

Applicant: Envisagenics, Inc.

Inventor： Maria Luisa Pineda ,  Martin Akerman ,  Gayatri Arun ,  Naomi Yudanin ,  Priyanka Dhingra

IPC: A61K39/00 ,  C07K14/47 ,  A61P35/00 ,  G16B15/00 ,  G16B40/20 ,  G01N33/50 ,  G16H50/50

CPC classification number: A61K39/0011 ,  A61K39/4611 ,  A61K39/4632 ,  A61K39/4631 ,  C07K14/4748 ,  A61P35/00 ,  G16B15/00 ,  G16B40/20 ,  G01N33/5011 ,  G16H50/50

Abstract: Provided herein are systems and methods for identifying alternative splicing derived cell surface antigens. Also provided are methods and compositions for using the identified cell surface antigens. Further provided are methods, compositions, and systems for diagnosing diseases in a subject using the identified cell surface antigens or treating diseases using the same.

公开(公告)号：US11725251B2

公开(公告)日：2023-08-15

申请号：US18069502

申请日：2022-12-21

Applicant: GRAIL, LLC

Inventor： Samuel S. Gross ,  Oliver Claude Venn ,  Seyedmehdi Shojaee ,  John Beausang ,  Arash Jamshidi

IPC: C12Q1/6886 ,  C12Q1/6869 ,  G16B30/10 ,  G16B5/00 ,  G16B40/00 ,  G16B25/20 ,  G16B20/00 ,  G16B40/20

CPC classification number: C12Q1/6886 ,  C12Q1/6869 ,  C12Q2600/154 ,  G16B5/00 ,  G16B20/00 ,  G16B25/20 ,  G16B30/10 ,  G16B40/00 ,  G16B40/20

Abstract: The present description provides a cancer assay panel for targeted detection of cancer-specific methylation patterns. Further provided herein are methods of designing, making, and using the cancer assay panel for the diagnosis of cancer.

公开(公告)号：US20230253070A1

公开(公告)日：2023-08-10

申请号：US18176476

申请日：2023-02-28

Applicant: Tempus Labs, Inc.

Inventor： Joshua Drews ,  Bonnie Dougherty ,  Lee Langer ,  Catherine Igartua ,  Andrew J. Sedgwick ,  Justin Guinney

IPC: G16B25/10 ,  G16B5/20 ,  G16B30/10 ,  G16B40/30 ,  G16B40/20

CPC classification number: G16B25/10 ,  G16B5/20 ,  G16B30/10 ,  G16B40/30 ,  G16B40/20

Abstract: Disclosed herein are systems, methods, and compositions useful for determining cellular pathway disruption comprising the use of RNA expression level information. This determined level of disruption can assist in the identification of genetic variants that alter pathway activity, to correlate these variants with disease state and disease progression, and to identify those therapeutics most likely to be effective and which should be avoided.

公开(公告)号：US20230245724A9

公开(公告)日：2023-08-03

申请号：US16208149

申请日：2018-12-03

Applicant: ILLUMINA, INC.

Inventor： Shile Zhang ,  Mengchi Wang ,  Aaron Wise ,  Han Kang ,  Vitor Ferreira Onuchic ,  Kristina Kruglyak

IPC: G16B40/20 ,  C12Q1/6886 ,  G16H50/20 ,  G16H50/50 ,  G16B45/00 ,  G16B50/30 ,  G16B50/20 ,  G06F17/15 ,  G06F17/16 ,  G06F17/18

CPC classification number: G16B40/20 ,  C12Q1/6886 ,  G16H50/20 ,  G16H50/50 ,  G06F17/18 ,  G16B50/30 ,  G16B50/20 ,  G06F17/153 ,  G06F17/16 ,  G16B45/00

Abstract: Provided is a computer-implemented method, including inputting to a trained machine learning classifier genomic information of a non-training subject that includes features from a tumor sample, wherein the trained machine learning classifier trained on features of tumor samples obtained from training subjects and their a responsiveness to checkpoint inhibition treatment and the machine-learning classifier is trained to predict responsiveness to the treatment, and generating a checkpoint inhibition responsiveness classification predictive of the subject's responding to the checkpoint inhibition with the trained machine-learning classifier, and reporting the checkpoint inhibition responsiveness classification using a graphical user interface. Also provided are a computer system for performing the method and a machine learning classifier trained by the method.

公开(公告)号：US11710536B2

公开(公告)日：2023-07-25

申请号：US17735494

申请日：2022-05-03

Applicant: Algen Biotechnologies, Inc.

Inventor： Spencer Charles Knight ,  Chun-Hao Huang

IPC: G16B20/00 ,  G16B40/20 ,  C12N5/09 ,  C12N9/22 ,  C12N15/10 ,  C12N15/11 ,  C12N15/86 ,  G06N20/00

CPC classification number: G16B20/00 ,  C12N5/0693 ,  C12N5/0694 ,  C12N9/22 ,  C12N15/1058 ,  C12N15/1089 ,  C12N15/1096 ,  C12N15/11 ,  C12N15/86 ,  G06N20/00 ,  G16B40/20 ,  C12N2310/20 ,  C12N2740/15043 ,  C12N2800/80

Abstract: The present disclosure provides methods and systems for identification of genomic regions for therapeutic targeting. A method for identifying one or more genomic regions for therapeutic targeting, which may facilitate re-programming of a cell from one phenotypic state to another, may comprise: providing single-cell RNA-seq data for a plurality of diseased cells and a plurality of normal cells of a cell type; mapping the single-cell RNA-seq data for the plurality of diseased cells and the plurality of normal cells into a latent space corresponding to a plurality of phenotypic states of the cell type; identifying, based at least in part on a topology of the latent space, the one or more genomic regions for therapeutic targeting; and electronically outputting the one or more genomic regions for therapeutic targeting.