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Analysis

1.WO/2023/002402METHOD FOR THE IDENTIFICATION OF THE WHOLE SEQUENCE OF THE VARIABLE REGION OF THE HEAVY AND LIGHT CHAINS OF IMMUNOGLOBULINS
WO 26.01.2023
Int.Class C12Q 1/6806
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
6806Preparing nucleic acids for analysis, e.g. for polymerase chain reaction assay
Appl.No PCT/IB2022/056700 Applicant UNIVERSITA' DEGLI STUDI DI PAVIA Inventor NUVOLONE, Mario Ulisse
The present invention relates to a method for the identification of the whole nucleotide sequence of the variable region of the heavy and or light chains of immunoglobulins in a biological sample and the quantification of their relative frequency. The invention is particularly used for the identification of monoclonal heavy and light chains, i.e. tumours, in biological samples from patients suffering from a monoclonal gammapathy.
2.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.
3.WO/2023/001262NICK-LIGATE STLFR
WO 26.01.2023
Int.Class C12Q 1/6806
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
6806Preparing nucleic acids for analysis, e.g. for polymerase chain reaction assay
Appl.No PCT/CN2022/107241 Applicant MGI TECH CO., LTD. Inventor DRMANAC, Radoje T.
This application relates to methods and compositions for preparing a library of polynucleotides for sequencing comprises in a single reaction mixture. The method comprises contacting a double-stranded target nucleic acid with one or more nicking agents to produce overlapping nucleic acid fragments separated by staggered single-stranded breaks; and contacting a partially double-stranded first adapter with at least one of the nucleic acid fragments in the presence of a ligase, thereby ligating the 5' terminus of the double-stranded region of the first adapter to the 3' terminus of the at least one of the nucleic acid fragments using a DNA ligase via 3' branch ligation. The first adapter comprises (i) a double-stranded blunt end having a 5' terminus and a 3' terminus and (ii) a single-stranded region comprising a barcode.
4.WO/2023/003917METHODS OF DISEASE DIAGNOSTICS UTILIZING MICROBIAL EXTRACELLULAR VESICLE (MEV) ANALYTES
WO 26.01.2023
Int.Class C12Q 1/689
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
6888for detection or identification of organisms
689for bacteria
Appl.No PCT/US2022/037647 Applicant MICRONOMA, INC. Inventor FRARACCIO, Serena
Methods and systems are presented herein for predicting a disease of a subject through a combination of fungal and non-fungal molecular analyte features of a biological sample.
5.WO/2023/003872METHODS FOR MULTI-DIMENSIONAL LABELING OF NUCLEIC ACIDS OF A CELLULAR SAMPLE IN SITU
WO 26.01.2023
Int.Class C12Q 1/6841
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
6813Hybridisation assays
6841In situ hybridisation
Appl.No PCT/US2022/037583 Applicant SCALE BIOSCIENCES INC. Inventor STEEMERS, Frank
Provided herein, among other things, is a method to spatially-label nucleic acid barcodes in or on a cellular sample in situ. In some embodiments, the method may comprise: obtaining a cellular sample comprising analytes or derivatives, fixing the analytes to their native location, providing a population of barcoded nucleic acids, and applying a stimulus to distribute the barcoded nucleic acids over the sample thereby differentially labeling areas and analytes of the sample. This process may include repeating the steps one or more times in various dimensions.
6.WO/2023/004082COMPOSITIONS AND METHODS FOR DETECTION OF PROSTATE CANCER
WO 26.01.2023
Int.Class C07K 16/30
CCHEMISTRY; METALLURGY
07ORGANIC CHEMISTRY
KPEPTIDES
16Immunoglobulins, e.g. monoclonal or polyclonal antibodies
18against material from animals or humans
28against receptors, cell surface antigens or cell surface determinants
30from tumour cells
Appl.No PCT/US2022/037938 Applicant MERCY BIOANALYTICS, INC. Inventor SEDLAK, Joseph Charles
The present disclosure in one aspect provides technologies for detection of prostate cancer, e.g., early detection of prostate cancer. In another aspect, technologies provided herein are useful for selecting and/or monitoring and/or evaluating efficacy of, a treatment administered to a subject determined to have or susceptible to prostate cancer. In some embodiments, technologies provided herein are useful for development of companion diagnostics, e.g., by measuring tumor burdens and changes in tumor burdens in conjunction with therapeutics. In some embodiments, technologies provided herein are useful for development of companion diagnostics, e.g., by identifying biomarkers in subjects' bodily fluid samples (e.g., blood samples) that are associated with therapeutic response.
7.WO/2023/002943BIOMARKER FOR PREDICTING PROGNOSIS OF CANCER PATIENT, METHOD FOR PREDICTING PROGNOSIS OF CANCER PATIENT, METHOD FOR PREDICTING EFFECT OF CANCER THERAPEUTIC DRUG ON CANCER PATIENT, AND KIT FOR PREDICTING PROGNOSIS OF CANCER PATIENT
WO 26.01.2023
Int.Class C12N 15/11
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
15Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
09Recombinant DNA-technology
11DNA or RNA fragments; Modified forms thereof
Appl.No PCT/JP2022/027853 Applicant TOHOKU UNIVERSITY Inventor TAKAI Toshiyuki
A biomarker for predicting the prognosis of a cancer patient, said biomarker comprising immunosuppressive receptor LILRB4 or immunosuppressive receptor LILRB4 gene; a method for predicting the prognosis of a cancer patient, said method comprising a step for measuring the expression level of immunosuppressive receptor LILRB4 or immunosuppressive receptor LILRB4 gene in a biological sample from the cancer patient; a method for predicting the effect of a substance, which inhibits the binding of fibronectin to immunosuppressive receptor LILRB4, as a cancer therapeutic drug on a cancer patient, said method comprising a step for measuring the expression level of immunosuppressive receptor LILRB4 or immunosuppressive receptor LILRB4 gene in a biological sample from the cancer patient; and a kit for predicting the prognosis of a cancer patient, said kit containing a reagent for measuring the expression level of the aforesaid biomarker.
8.WO/2023/004083COMPOSITIONS AND METHODS FOR DETECTION OF BILE DUCT CANCER
WO 26.01.2023
Int.Class C12Q 1/6886
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
6886for cancer
Appl.No PCT/US2022/037940 Applicant MERCY BIOANALYTICS, INC. Inventor SEDLAK, Joseph Charles
The present disclosure in one aspect provides technologies for detection of bile duct cancer, e.g., early detection of bile duct cancer. In another aspect, technologies provided herein are useful for selecting and/or monitoring and/or evaluating efficacy of, a treatment administered to a subject determined to have or susceptible to bile duct cancer. In some embodiments, technologies provided herein are useful for development of companion diagnostics, e.g., by measuring tumor burdens and changes in tumor burdens in conjunction with therapeutics. In some embodiments, technologies provided herein are useful for development of companion diagnostics, e.g., by identifying biomarkers in subjects' bodily fluid samples (e.g., blood samples) that are associated with therapeutic response.
9.WO/2023/004248DEPROTECTION-COUNTING PROBES FOR DETECTING AND QUANTIFYING SINGLE MOLECULAR ANALYTES
WO 26.01.2023
Int.Class C12Q 1/6876
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
Appl.No PCT/US2022/073707 Applicant THE REGENTS OF THE UNIVERSITY OF MICHIGAN Inventor JOHNSON-BUCK, Alexander, Edmund
A molecular architecture and method to better distinguish between specific and nonspecific binding events using molecular probes that possess an internal record of repeated binding of probes to the same analyte molecule, permitting the high-sensitivity, high-specificity detection of analytes (e.g., nucleic acids, proteins, or other biomolecules) is provided. The repeated binding of probes to the same analyte molecule (or to a probe bound to the analyte molecule) results in an accumulation of signal (e.g., fluorescence or chemiluminescence) dependent on the number and kinetics of probe binding events, yielding increased confidence in the presence of the analyte molecule as the number of independent binding events increases.
10.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.