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Analysis

1.WO/2023/003647METHODS FOR DETERMINING VARIANT FREQUENCY AND MONITORING DISEASE PROGRESSION
WO 26.01.2023
Int.Class G16B 20/20
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
20ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
20Allele or variant detection, e.g. single nucleotide polymorphism detection
Appl.No PCT/US2022/032725 Applicant FOUNDATION MEDICINE, INC. Inventor KENNEDY, Mark
Methods for determining a variant frequency in a test sample from a subject, and methods for labeling sequencing reads as having or not having a variant are described herein. Exemplary methods include generating a reference match score and a variant match score by aligning sequencing reads to a corresponding variant sequence and a corresponding reference sequence, and labeling the sequencing read as having or not having the variant based on the determined match scores. Also described herein are methods monitoring disease progression and methods of treating a subject having a disease. Further described are devices and systems for implementing such methods.
2.WO/2023/004323MACHINE-LEARNING MODEL FOR RECALIBRATING NUCLEOTIDE-BASE CALLS
WO 26.01.2023
Int.Class G16B 30/00
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
30ICT specially adapted for sequence analysis involving nucleotides or amino acids
Appl.No PCT/US2022/073899 Applicant ILLUMINA SOFTWARE, INC. Inventor PARNABY, Gavin Derek
This disclosure describes methods, non-transitory computer readable media, and systems that can utilize a machine learning model to recalibrate nucleotide-base calls (e.g., variant calls) of a call-generation model. For instance, the disclosed systems can train and utilize a call-recalibration-machine-learning model to generate a set of predicted variant-call classifications based on sequencing metrics associated with a sample nucleotide sequence. Leveraging the set of variant-call classifications, the disclosed systems can further update or modify nucleotide-base calls (e.g., variant calls) corresponding to genomic coordinates. Indeed, the disclosed systems can generate an initial nucleotide-base call based on sequencing metrics for nucleotide reads of a sample sequence utilizing a call-generation model and further utilize a call-recalibration-machine-learning model to generate classification predictions for updating or recalibrating the initial nucleotide-base call from a subset of the same sequencing metrics or other sequencing metrics.
3.WO/2023/004203USE OF GENETIC AND EPIGENETIC MARKERS TO DETECT CELL DEATH
WO 26.01.2023
Int.Class C12Q 1/6809
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
68involving nucleic acids
6809Methods for determination or identification of nucleic acids involving differential detection
Appl.No PCT/US2022/038242 Applicant GEORGETOWN UNIVERSITY Inventor KROEMER, Alexander, H.k.
A method of detecting donor cell death in a subject receiving foreign biological material from a donor. The method comprises sequencing cfDNA in a biospecimen from the subject; determining cellular origin of the cfDNA by identifying methylation patterns in the sequence of the cfDNA and comparing the methylation patterns in the sequence of the cfDNA to known methylation patterns associated with different cell types; and determining source origin of the cfDNA by genotyping the cfDNA and identifying whether the cfDNA originates from the foreign biological material or from the subject. Cell death is detected when the cfDNA has both a cellular origin of the type of foreign biological material that was received from the donor, and a source origin of the donor.
4.WO/2023/002325COMPOSITIONS AND METHODS FOR CHARACTERIZING A COMPLEX BIOLOGICAL SAMPLE
WO 26.01.2023
Int.Class C12Q 1/70
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
70involving virus or bacteriophage
Appl.No PCT/IB2022/056558 Applicant THE BROAD INSTITUTE, INC. Inventor EARL, Ashlee M.
The invention features compositions and methods that are useful for characterizing a complex biological sample.
5.WO/2023/004335SELECTION OF VIRAL-SPECIFIC CYTOTOXIC T-CELL LINES FOR THE MANAGEMENT OF VIRAL INFECTIONS
WO 26.01.2023
Int.Class G16H 20/10
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
HHEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
20ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
10relating to drugs or medications, e.g. for ensuring correct administration to patients
Appl.No PCT/US2022/073913 Applicant BOARD OF REGENTS, THE UNIVERSITY OF TEXAS SYSTEM Inventor REZVANI, Katy
Embodiments of the disclosure concern systems, methods, and compositions related to identification of a suitable cell therapy for an individual in need thereof. A cell line is selected from a plurality of cell lines for suitability for an individual based on an algorithm and cell identification number that includes values for HLA matching and the frequency of reactive CD4 and CD8 cytotoxic T lymphocytes as measured by interferon-γ and IL-2. Particular parameters for HLA matching and reactive frequencies are utilized to calculate points towards the cell identification number, and the cell line with the highest cell identification number may be utilized.
6.WO/2023/003076METHOD AND SYSTEM FOR REDUCTION OF GREENHOUSE GAS BY USING LIVESTOCK GENOME INFORMATION
WO 26.01.2023
Int.Class G16B 50/00
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
50ICT programming tools or database systems specially adapted for bioinformatics
Appl.No PCT/KR2021/012456 Applicant INDUSTRIAL COOPERATION FOUNDATION CHONBUK NATIONAL UNIVERSITY Inventor LEE, Hak Kyo
The present invention relates to a method and system for reduction of greenhouse gas by using livestock genome information. A method according to an embodiment of the present invention is a method for molecular breeding of carbon footprint reduction for populations and comprises the steps of: acquiring genome information about individuals in a reference population; setting a meat production amount inversely proportional to carbon emission amount per weight as a carbon emission-related trait of each individual, followed by estimating a breeding value of the carbon emission-related trait for each individual on the basis of the genome information; and selecting, as subjects to be crossed, individuals having a breeding value corresponding to or higher than a reference ratio among the breeding values.
7.WO/2023/003196METHOD FOR ENCRYPTING AND DECRYPTING GENOMIC INFORMATION
WO 26.01.2023
Int.Class G16B 50/40
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
50ICT programming tools or database systems specially adapted for bioinformatics
40Encryption of genetic data
Appl.No PCT/KR2022/009189 Applicant CLINOMICS INC. Inventor BHAK, Jong Hwa
The present invention relates to a method for encrypting and decrypting genomic information, and the objective to be solved is to, prior to encoding or encrypting genomic information in a binary format, by making it impossible to determine the authenticity of leaked genomic information by hiding actual genomic information, which looks like unencrypted genomic information, hide individual genomic information by encrypting individual variation information or original sequence information, and enable actual information to be decrypted only by a predetermined key value, such that the individual genomic information may be prevented from being leaked in a process of being stored in a computer or transmitted. For example, disclosed is a method for encrypting and decrypting genomic information, the method comprising the steps of: (a) identifying genotype and variation information about a subject from genome original sequence information for which genomic map mapping is completed; (b) aligning, in a chromosomal order, regions in which a single nucleotide variation exists in a key sample group in the genotype and variation information; (c) for each variation at a position corresponding to a first key parameter value included in pre-stored modulation/demodulation rule information in the aligned single nucleotide variation regions, modulating each genotype of the subject with respect to genotype frequency information in the key sample group, so as to encrypt the genomic information; and (d) demodulating the encrypted genomic information with respect to the modulation/demodulation rule information and the genotype frequency information, so as to decrypt the genomic information.
8.WO/2023/004204USE OF CIRCULATING CELL-FREE METHYLATED DNA TO DETECT TISSUE DAMAGE
WO 26.01.2023
Int.Class C12Q 1/6883
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
68involving nucleic acids
6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
6883for diseases caused by alterations of genetic material
Appl.No PCT/US2022/038244 Applicant GEORGETOWN UNIVERSITY Inventor KROEMER, Alexander, H.k.
Method of determining if a subject has suffered tissue damage from exposure to a toxic agent. The method comprises sequencing cell-free DNA (cfDNA) in a biospecimen from the subject; determining cellular origin of the cfDNA by identifying methylation patterns in one or more portions of the sequence of the cfDNA that contains methylation sites, in which the cellular origin of the cfDNA is determined when the methylation pattern in the one or more portions is the same as a known cell-type specific methylation patterns; measuring the quantity of the cfDNA of the determined cellular origin, and comparing the measured quantity of the cfDNA of the determined cellular origin with a normal quantity of cfDNA of the determined cellular origin. A greater quantity of the measured cfDNA of the determined cellular origin is indicative that the subject has suffered tissue damage.
9.WO/2023/002052METHOD OF EVALUATING A MUTATIONAL BURDEN
WO 26.01.2023
Int.Class G16B 20/10
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
20ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
10Ploidy or copy number detection
Appl.No PCT/EP2022/070705 Applicant QIAGEN GMBH Inventor SURYAPRAKASH, Vinay
The present disclosure relates to a method of evaluating a mutational burden in a sample. The method includes providing first data which represents allelic depths of the sample; calculating rate data based on the first data; segmenting the rate data into a plurality of segments of rate data using a wavelet transform; estimating parameters for each of the plurality of segments; classifying each of the plurality of segments based on the estimated parameters. The classifying includes, for each of a plurality of classification thresholds, generating a classification for the plurality of segments based on the classification threshold and determining an intermediate value based on the classification. The method further comprises determining a mutational burden of the sample based on the intermediate values.
10.WO/2023/002046DETERMINATION OF LYMPHOCYTE ABUNDANCE IN MIXED SAMPLES
WO 26.01.2023
Int.Class G16B 20/00
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
20ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
Appl.No PCT/EP2022/070694 Applicant THE FRANCIS CRICK INSTITUTE Inventor BENTHAM, Robert
Methods for determining the fraction of lymphocytes in a mixed sample comprising genomic material from multiple cell types are described. The methods comprise obtaining a read depth profile for the sample along a predetermined genomic region of interest including at least a portion of a genomic locus that undergoes VDJ recombination; obtaining a plurality of read depth ratios (ri) by normalising the read depths by reference to a baseline read depth derived from a subset of the region of interest; obtaining a summarised read depth ratio value (rVDJ) for a subset of the region of interest that is likely to be deleted through VDJ recombination; and determining the fraction of lymphocytes (f) in the sample as a function of the summarised read depth ratio value (rVDJ). Methods of providing a diagnosis or prognosis based on the lymphocyte fraction are also described, as well as related systems and products.