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Analysis

1.WO/2022/109267GENOTYPING BY SEQUENCING
WO 27.05.2022
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/US2021/060085 Applicant REGENERON PHARMACEUTICALS, INC. Inventor ABECASIS, Goncalo
The present disclosure provides methods for manufacturing nucleic acid probes for genotyping by sequencing, methods for genotyping a DNA sample by sequencing using a set of nucleic acid probes, and systems for carrying out such methods.
2.WO/2022/109462PROTEIN DATABASE SEARCH USING LEARNED REPRESENTATIONS
WO 27.05.2022
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/US2021/060533 Applicant NE47 BIO, INC. Inventor BEPLER, Tristan
A method for efficient search of protein sequence databases for proteins that have sequence, structural, and/or functional homology with respect to information derived from a search query. The method involves transforming the protein sequences into vector representations and searching in a vector space. Given a database of protein sequences and a learned embedding model, the embedding model is applied to each amino acid sequence to transform it into a sequence of vector representations. A query sequence is also transformed into a sequence of vector representations, preferably using the same learned embedding model. Once the query has been embedded in this manner, proteins are retrieved from the database based on distance between the query embedding and the protein embeddings contained within the database. Rapid and accurate search of the vector space is carried out using exact search using metric data structures, or approximate search using locality sensitive hashing.
3.WO/2022/107136METHODS AND BIOMARKERS FOR DIAGNOSTICS, DISEASE MONITORING, PERSONALIZED DRUG DISCOVERY AND TARGETED THERAPY IN GLIOMA PATIENTS
WO 27.05.2022
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/IL2021/051370 Applicant BAR-ILAN UNIVERSITY Inventor FRENKEL-MORGENSTERN, Milana
Novel powerful methods for identifying, monitoring, and treating conditions associated with omics-discoverable features in human subjects, and particularly conditions such as malignant tumors are provided.
4.WO/2022/109165METHODS FOR OBJECTIVE ASSESSMENT, RISK PREDICTION, MATCHING TO EXISTING MEDICATIONS AND NEW METHODS OF USING DRUGS, AND MONITORING RESPONSES TO TREATMENTS FOR MOOD DISORDERS
WO 27.05.2022
Int.Class A61B 5/16
AHUMAN NECESSITIES
61MEDICAL OR VETERINARY SCIENCE; HYGIENE
BDIAGNOSIS; SURGERY; IDENTIFICATION
5Measuring for diagnostic purposes; Identification of persons
16Devices for psychotechnics; Testing reaction times
Appl.No PCT/US2021/059935 Applicant INDIANA UNIVERSITY RESEARCH AND TECHNOLOGY CORPORATION Inventor NICULESCU, Alexander, B.
Methods for objective and precise assessment, risk prediction, monitoring of disease course and response to treatment, and precise matching to existing, and to new method of use repurposed drugs, in mood disorders, such as for patients with depression or bipolar disorder. These methods are based on an objective analysis of specific biomarker panels, as well as on the integration of the biomarker panel data with clinical measures of mood, life satisfaction, psycho-socio-demographic risk factors, and clinical history severity. These methods provide a foundation for precision medicine for mood disorders.
5.WO/2022/106074METHOD AND SYSTEM FOR QUANTIFYING CELLULAR ACTIVITY FROM HIGH THROUGHPUT SEQUENCING DATA
WO 27.05.2022
Int.Class G16B 40/20
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
40ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
20Supervised data analysis
Appl.No PCT/EP2021/066541 Applicant NEC LABORATORIES EUROPE GMBH Inventor PILEGGI, Giampaolo
The invention relates to a computer-implemented method and to a processing system for quantifying cellular activity from high throughput sequencing data. The method comprises generating a multimodal knowledge graph by combining a gene regulatory network, GRN, with gene annotations coming from domain knowledge, wherein the nodes of the multimodal knowledge graph are genes and wherein the gene annotations enrich the relations among the genes; creating a number of gene modules, GMs, by clustering the embeddings of the genes of the GRN; embedding the samples of the sequencing data into the multimodal knowledge graph; and generating, for each sample of the sequencing data, an activation vector in which the respective sample is expressed as the distances between the embedding and the centroids of each of the number of GMs.
6.WO/2022/106658Mass spectrometry system and method for providing an indication of integrity of a biological sample
WO 27.05.2022
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/EP2021/082375 Applicant OMICERA DIAGNOSTICS GMBH Inventor GEYER, Philipp Emanuel
A mass spectrometry system comprises a mass spectrometry apparatus configured to provide mass spectrometry data of a biological sample; and a computer system configured to process the mass spectrometry data to determine a characteristic of the biological sample as integrity data of the biological sample; and output an indication of the similarity to a predetermined sample characteristic as integrity data of the biological sample. A computerized method provides an indication of integrity of a biological sample from mass spectrometry data, the computerized method comprising: processing mass spectrometry data of a biological sample to determine a sample characteristic of the biological sample; and outputting an indication of the similarity to a predetermined sample characteristic as integrity data of the biological sample.
7.WO/2022/108965METHODS AND SYSTEMS FOR GENOMIC BASED PREDICTION OF VIRUS MUTATION
WO 27.05.2022
Int.Class G16H 50/80
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
50ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
80for detecting, monitoring or modelling epidemics or pandemics, e.g. flu
Appl.No PCT/US2021/059616 Applicant THE UNIVERSITY OF CHICAGO Inventor CHATTOPADHYAY, Ishanu
A method includes receiving a first plurality of aligned genomic sequences of a virus from a database. The aligned genomic sequences have a first common background. The method includes calculating a Qnet for each genomic sequence of the first plurality of aligned genomic sequences. The Qnet for each sequence is calculated by calculating a conditional inference tree for each index of the aligned genomic sequences using other indices in the aligned genomic sequences as predictive features, and calculating predictors for indices that were used as predictive features when calculating the conditional inference tree for each index.
8.WO/2022/108407METHOD FOR DIAGNOSING CANCER AND PREDICTING PROGNOSIS BY USING LENGTH RATIO OF NUCLEIC ACIDS
WO 27.05.2022
Int.Class G16B 35/10
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
35ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
10Design of libraries
Appl.No PCT/KR2021/017177 Applicant GREEN CROSS GENOME CORPORATION Inventor CHO, Eun-Hae
The present invention relates to a method for diagnosing cancer and predicting a prognosis by using a length ratio of nucleic acids and, more particularly, to a method for diagnosing cancer and predicting a prognosis by using a length ratio of nucleic acid fragments which are aligned after nucleic acids are extracted from a biological sample and sequence information thereof is acquired. The method for diagnosing cancer and predicting a prognosis, according to the present invention, is a detection method using a length ratio of nucleic acid fragments on the basis of aligned reads, unlike conventional methods using a step of determining the amount of chromosomes on the basis of read counts. While conventional methods reduce accuracy when read counts are reduced, the method of the present invention not only can increase detection accuracy even when read counts are reduced, but is also useful since detection accuracy is high even when using a length ratio of nucleic acid fragments of a certain section rather than all chromosome sections, and can also be applied to chromosomal abnormality samples that could not have been detected with conventional read counts.
9.WO/2022/105629METHOD FOR SCREENING SNP SITES FOR DETECTING CONTAMINATION LEVEL OF SAMPLE AND METHOD FOR DETECTING CONTAMINATION LEVEL OF SAMPLE
WO 27.05.2022
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/CN2021/129081 Applicant BERRY ONCOLOGY CO., LTD. Inventor LIU, Yan
A method for screening SNP sites for detecting the contamination level of a sample and a method for detecting the contamination level of a sample, which relate to the technical field of biological sequencing. The screening method comprises: obtaining SNP sites that have a population mutation frequency of 30% to 70% in a target region as candidate marker sites; dividing a region between a starting site and an terminating site among the candidate marker sites present on a single chromosome into a plurality of selection regions, the selection regions having a length of 0.7 to 1.3 Mb; and if there are two or more candidate marker sites in the selection regions, then selecting sites that have an allele frequency in the selection regions of 40% to 60% and different genotypes most in line with the Hardy-Weinberg equilibrium as marker sites, and removing other candidate markers within the regions. The marker sites screened on the basis of the screening method may be used to detect the contamination level of the sample, and has relatively low detection costs and relatively high detection accuracy.
10.WO/2022/108778DISEASE-ASSOCIATED ISOFORM IDENTIFIER
WO 27.05.2022
Int.Class G06N 3/08
GPHYSICS
06COMPUTING; CALCULATING OR COUNTING
NCOMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
3Computer systems based on biological models
02using neural network models
08Learning methods
Appl.No PCT/US2021/058436 Applicant KIROMIC BIOPHARMA, INC. Inventor MIRANDOLA, Leonardo
The technology relates in part to methods and systems for the identification of disease-associated transcript isoforms and peptides. In certain aspects, the technology relates to methods and systems for the identification of transcript isoforms and peptides preferentially expressed in tumor cells.