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Analysis

1.WO/2022/127687METABOLIC PATHWAY PREDICTION METHOD, SYSTEM, TERMINAL DEVICE AND READABLE STORAGE MEDIUM
WO 23.06.2022
Int.Class G16B 5/00
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
5ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
Appl.No PCT/CN2021/136847 Applicant SHENZHEN INSTITUTES OF ADVANCED TECHNOLOGY Inventor JI, Chaojie
A metabolic pathway prediction method, a system, a terminal device and a readable storage medium, relating to the technical field of data analysis. The existing metabolic pathway prediction method cannot provide further explanation for the metabolic process. The metabolic pathway prediction method comprises: cutting a second substance according to a first substance to obtain a first structure, wherein the first structure is a common molecular structure of the first substance and the second substance; converting the second substance into a junction tree 1, wherein the junction tree 1 is represented by a junction tree having a non-common molecular substructure in the first substance; joining the junction tree 1 with the first structure to obtain the first substance having a definite structure; taking the first substance having the definite structure as the second substance 2, and repeating the process above according to the second substance 2 to obtain the second substance 2 having a definite structure; and obtaining the metabolic pathway. Possible biological interpretations are provided for the occurrence of metabolic reactions.
2.WO/2022/131691METHOD FOR DETERMINING TYPE OF HUMAN LEUKOCYTE ANTIGEN
WO 23.06.2022
Int.Class C12Q 1/6881
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
6881for tissue or cell typing, e.g. human leukocyte antigen probes
Appl.No PCT/KR2021/018723 Applicant NEOGENTC CORP. Inventor LEE, Hee Jin
According to an embodiment of the present disclosure, disclosed is a method for determining the type of a human leukocyte antigen (HLA), performed by a computing device comprising at least one processor. The method may comprise the steps of: acquiring a result of performing sequencing of DNA or RNA obtained from a biological sample from a subject; and determining an HLA type from the result of the sequencing, by using three or more tools from among OptiType, HLA-HD, PHLAT, HLAscan, and HLA*LA.
3.WO/2022/130041SYSTEM, APPARATUS, AND METHOD FOR AUTOMATED GENETIC INHERITANCE PATTERN IDENTIFICATION AND COUNSELLING
WO 23.06.2022
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/IB2021/058106 Applicant NAMBISON, Nisanth Km Inventor NAMBISON, Nisanth Km
The present disclosure provides an apparatus and method of automation of genetic inheritance pattern identification of monogenic disorders like Thalassemia, Sickle cell anemia etc in offspring, and counselling of prospective parents for making informed choice. These disorders are transmitted to the next generation via diseased allele from any one or both parents and the specific combination of alleles determines the disease phenotype. Thus, prevention of high-risk conception can prevent the disease transmission. With the apparatus and methods provided here, even lay persons, paramedics, prospective parents themselves not skilled in genetic or marriage counselling, can identify the genetic inheritance pattern and make an informed decision about childbearing. The apparatus representing one parent placed on the apparatus for another parent with assertive indicators (e.g., an opening/see through) at pre-determined places automatically reveals a single genetic inheritance pattern and counselling information for the prospective parents.
4.WO/2022/133131MACHINE LEARNING TECHNIQUES FOR IDENTIFYING MALIGNANT B-AND T-CELL POPULATIONS
WO 23.06.2022
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/US2021/063885 Applicant BOSTONGENE CORPORATION Inventor KUDRYASHOVA, Olga
Techniques for identifying malignant cell populations. The techniques include: obtaining sequencing data previously obtained from a biological sample from a subject; processing the sequencing data to identify: a plurality of cell population estimates for a cell of a first type, the plurality of cell population estimates including a first cell population estimate and a second cell population estimate associated respectively with largest and second largest cell population estimates from among the identified plurality of cell population estimates; and features associated with the plurality of cell population estimates, the features including: a first feature indicative of a size of the first cell population estimate; and a second feature indicative of a ratio between sizes of the first cell population estimate and the second cell population estimate; and determining, using the features and a trained machine learning model, whether the first cell population estimate includes malignant cells of the first type.
5.WO/2022/133315METHODS OF CANCER DETECTION USING EXTRAEMBRYONICALLY METHYLATED CPG ISLANDS
WO 23.06.2022
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/US2021/064210 Applicant PRESIDENT AND FELLOWS OF HARVARD COLLEGE Inventor SHI, Jiantao
The present invention relates to methods of characterizing cell-free DNA (cfDNA), detecting cancer, detecting the eradication of cancer, and determining a probability distribution of haplotypes. The methods use the data from genomic sequences from CpG Islands (CGI) methylated in the genome of extraembryonic ectoderm (ExE) to determine a proportion of fully methylated haplotypes in order to characterize the cfDNA sample and detect certain cancers.
6.WO/2022/126698SYNTHETIC GENE CIRCUIT MODEL AND CONSTRUCTION METHOD
WO 23.06.2022
Int.Class G16B 5/00
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
5ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
Appl.No PCT/CN2020/138716 Applicant SHENZHEN INSTITUTES OF ADVANCED TECHNOLOGY CHINESE ACADEMY OF SCIENCES Inventor FU, Xiongfei
A method for constructing a synthetic gene circuit model. The method comprises: establishing a gene circuit constrained resource allocation flux balance analysis method, and simulating a cell growth rate; constructing a growth rate regulated gene circuit model by combining the cell growth rate with a gene circuit dynamic model, and obtaining a dynamic behavior result of a gene circuit; and performing a quantitative experiment on the dynamic behavior of the gene circuit to obtain an experiment result, and correcting the model by means of a comparison result. According to the method, Escherichia coli is taken as a research object, the physiological state of cells is fully characterized using the method of combining flux balance analysis and a bacterial growth law on the basis of an Escherichia coli genome metabolic network model, the growth rate of the cells is simulated, and in conjunction with quantitative experiment data for standardizing a typical gene circuit, a gene circuit dynamic model depending on the cell growth rate is constructed, thereby accurately predicting the influence of the cell growth rate on the function of the synthetic gene circuit.
7.WO/2022/128918DIAGNOSTIC METHOD FOR CANCER EVOLUTION PREDICTION, AND USES THEREOF
WO 23.06.2022
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/EP2021/085491 Applicant INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE Inventor BENHADDOU, Ataaillah
] The present invention relates to the field of cancer diagnostic methods for classifying cancer patients using a measure of the distribution of markers of DNA structure alterations within tumor genomic DNA sequence. The inventors have observed, in sarcomas, such as leiomyosarcoma, that the distribution of breakpoints within a set of selected transcription-associated chromosomal instability elements and a set of selected replication-associated chromosomal instability elements can be used to classify patients in groups according to a level of genome instability, which may be representative of a cancer evolution, a risk of occurrence of metastasis, a survival rate, or a sensibility to a cancer treatment. The present invention also relates to machine learning and trained classifiers for classifying patients having a cancer based upon a distribution of genomic DNA structure alterations or variations.
8.WO/2022/131328METHOD FOR CALCULATING RELIABILITY VALUE OF SIGNAL OF POLYMORPHISM LOCI
WO 23.06.2022
Int.Class G16B 40/10
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
40ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
10Signal processing, e.g. from mass spectrometry or from PCR
Appl.No PCT/JP2021/046513 Applicant SEEDNA INC. Inventor KIM, Kibom
The present invention addresses the problem of providing a novel technique for evaluating the reliability of a signal indicating the presence of minor nucleic acid in analysis data of a mixed nucleic acid sample containing, in minute proportions, minor nucleic acids such as cffDNA, ctDNA, and ddcfDNA. The problem is solved by performing a regression analysis with respect to a synthetic variable and a reliability value obtained as the result of a linear combination performed with respect to a numerical value group including at least a minor constituent signal intensity and a minor constituent mixture rate included in analysis data, thereby determining a model function for calculating a reliability value.
9.WO/2022/132198COMPOSITIONS AND METHODS FOR IMPROVED IN VITRO ASSEMBLY OF POLYNUCLEOTIDES
WO 23.06.2022
Int.Class C12N 15/10
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
10Processes for the isolation, preparation or purification of DNA or RNA
Appl.No PCT/US2021/010063 Applicant NEW ENGLAND BIOLABS, INC. Inventor LOHMAN, Gregory
Ordered assembly of large numbers of fragments into a single large DN A have been improved in both frequency and fidelity of the assembled product. This has been achieved by novel compositions and methods that are utilized in a computer system that integrates comprehensive ligation data from multiple sources to provide optimized synthetic overhangs or overhangs from restriction endonuclease cleavage on DIMA fragments for assembly by ligation. Intragenic cut sites are avoided by the use of a novel restriction endonuclease which recognizes 7 nucleotides (bases) and cuts DNA to create 4-base overhangs with the help of a synthetic activator oligonucleotide. Variations in ligation preferences by different ligases provide extra precision in assembly reactions. The use of the improved methods are exemplified by the successful assembly from 52 fragments of a viral genome and also a 52 fragment ordered assembly of a bacteria operon.
10.WO/2022/132286BLOCK
WO 23.06.2022
Int.Class G06F 16/906
GPHYSICS
06COMPUTING; CALCULATING OR COUNTING
FELECTRIC DIGITAL DATA PROCESSING
16Information retrieval; Database structures therefor; File system structures therefor
90Details of database functions independent of the retrieved data types
906Clustering; Classification
Appl.No PCT/US2021/053143 Applicant THE JOHNS HOPKINS UNIVERSITY Inventor GRANT, Haley
A method for classifying data in blocks can include receiving a population of sample data, determining block sizes relative to the sample data, and grouping the sample data into blocks based on the determined block sizes. The method can further include selecting a block, determining a desired specificity for the block, assigning a score to each of the sample data, ranking the sample data according to the score associated with each of the sample data, identifying a positive threshold value for the block based on the desired specificity, and classifying the scored sample data based on the positive threshold value.