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1.WO/2020/185725METHODS AND COMPOSITIONS FOR IMPUTING OR PREDICTING GENOTYPE OR PHENOTYPE
WO 17.09.2020
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/US2020/021790 Applicant PIONEER HI-BRED INTERNATIONAL, INC. Inventor BAUMGARTEN, Andrew
Methods and compositions to impute or predict genotype, haplotype, molecular phenotype, agronomic phenotypes, and/or coancestry are provided. Methods and compositions provided include using latent space to generate latent space representations or latent vectors that are independent of underlying genotypic or phenotypic data. The methods may include generating a universal latent space representation by encoding discrete or continuous variables derived from genotypic or phenotypic data into latent vectors through a machine learning-based encoder framework. Provided herein are universal methods of parametrically representing genotypic or phenotypic data obtained from one or more populations or sample sets to impute or predict a genotype or phenotype of interest.
2.WO/2020/181333INTRAGENIC ASSESSMENT AND METHODS THEREFOR
WO 17.09.2020
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/AU2020/050234 Applicant THE UNIVERSITY OF SYDNEY Inventor COOPER, Sandra
A method for determining the likelihood that a genetic variant of a genetic locus defines a genetic disease or cancer-associated allele. The method is based on the discovery that genetic variants that shorten the intragenic distance between a 5' splice-site and branch-point site below a critical threshold measure provide insufficient space for spliceosome assembly and intron lariat formation and/or excision. Such genetic variants that are more likely than not to be associated with disease, and in particular, more likely than not to result in abnormal pre-mRNA splicing.
3.WO/2020/182173METHOD AND SYSTEM FOR MERGING DUPLICATE MERGING MARKING TO OPTIMIZE COMPUTER OPERATIONS OF GENE SEQUENCING SYSTEM
WO 17.09.2020
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/CN2020/078903 Applicant HUAWEI TECHNOLOGIES CO., LTD. Inventor ROODI, Meysam
A processing unit performs alignment of a short read (SR) against a reference genome sequence. The processing unit determines whether the SR is aligned. If the SR is not aligned, the processing unit receives the next SR and processes the next SR by repeating. If the SR is aligned, in response to the determination that the SR is aligned with the reference genome sequence at a first position in the reference genome sequence, the processing unit generates a new SR metadata entry corresponding to the SR. The processing unit finds a linked list in a SR metadata collection. The first position of the linked list in the SR metadata collection corresponds to the first position of the reference genome sequence where the SR is aligned. The processing unit performs duplicate marking based on the SR and the linked list.
4.WO/2020/182172METHOD AND SYSTEM FOR MEMORY ALLOCATION TO OPTIMIZE COMPUTER OPERATIONS OF SEEDING FOR BURROWS WHEELER ALIGNMENT
WO 17.09.2020
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/CN2020/078900 Applicant HUAWEI TECHNOLOGIES CO., LTD. Inventor ROODI, Meysam
A processing unit receives a count table and an occurrence table for a reference sequence generated using a Burrows Wheeler Transform (BWT) algorithm. The reference sequence comprises a sequence of base pairs (bps). The processing unit stores a first part of the occurrence table in a first type of memory. The size of the first part of the occurrence table is determined based on a size of the first type of memory and a first number of bps of short reads (SRs) to be processed using the first type of memory. The processing unit receives a short read (SR) of a sample sequence. The SR comprises the first number of bps and a second number of bps. The processing unit performs alignment of the short read (SR) against the reference sequence using the count table and the occurrence table.
5.WO/2020/185411SYSTEM AND METHOD FOR VARIANT CALLING
WO 17.09.2020
Int.Class G06F 19/00
GPHYSICS
06COMPUTING; CALCULATING OR COUNTING
FELECTRIC DIGITAL DATA PROCESSING
19Digital computing or data processing equipment or methods, specially adapted for specific applications
Appl.No PCT/US2020/020047 Applicant NANTOMICS, LLC Inventor SANBORN, John, Zachary
A locus tester or locust database has stored therein DNA or RNA sequence information for one or more loci of interest. The sequence information may include a list of k-mers in a given DNA or RNA sequence, an identification of whether each k-mer in the list of k-mers appears in a reference sequence or in a variation of the reference sequence, and a count of how many times each k-mer in the list of k-mers has been identified in sequence information for the locus of interest in question. Sequence data for the locus in question received from a data source may be broken into fragments, with each fragment containing one or more k-mers. These k-mers may be quickly compared to the list of k-mers in the locust database to determine whether the sequence data corresponds to the reference sequence or to a variation of the reference sequence.
6.WO/2020/185010SYSTEM AND METHOD FOR PROVIDING NEOANTIGEN IMMUNOTHERAPY INFORMATION BY USING ARTIFICIAL-INTELLIGENCE-MODEL-BASED MOLECULAR DYNAMICS BIG DATA
WO 17.09.2020
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/KR2020/003464 Applicant SYNTEKABIO,INC. Inventor JUNG, Jongsun
The present invention relates to a system and method for predicting, based on molecular dynamics, a neoantigen and immune response induction, in which, by producing a neoantigen candidate group through genomic mutations, and then predicting MHC-antigen binding affinity for neoantigen candidates through molecular dynamics, the induction of immunity against a neoantigen with high binding potential can be verified. The present invention provides a method for providing neoantigen immunotherapy information for discovering a neoantigen by using AI-based molecular dynamics big data, the method comprising the steps of: (A) producing a neoantigen candidate group through genomic mutations; (B) filtering specificity of the neoantigen candidate group by tissues and diseases; (C) predicting in silico binding between a neoantigen and MHC; and (D) calculating and ranking TCR activities. According to such a present invention, precision medical technology combined with AI deep learning using big data of the present invention can contribute to medical industrialization of a specific neoantigen prediction technique customized for patients.
7.WO/2020/183428METHOD AND SYSTEM FOR MAPPING READ SEQUENCES USING A PANGENOME REFERENCE
WO 17.09.2020
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/IB2020/052294 Applicant TATA CONSULTANCY SERVICES LIMITED Inventor VADDADI, Kavya Naga Sai
There is a demand for low-cost efficient robust method for mapping read sequences with genome variation graph in genomic study. This disclosure herein relates to a method and system for mapping read sequences with genome variation graph by constructing a subgraph using a novel combination of graph embedding and graph winnowing techniques. The system processes the obtained plurality of read sequences and a genome variation graph for constructing the subgraph by computing an embedding for the genome variation graph utilizing a graph embedding technique. Further, graph index is generated for the genome variation graph based on the embedding and the genome variation graph utilizing the graph winnowing technique. Then computes gapped alignment score for read sequence (r) with its corresponding subgraph. Thus, enables a reliable method for read sequence with accurate, memory efficient and scalable system for mapping read sequences with genome variation graph.
8.WO/2020/181254SEQUENCE-GRAPH BASED TOOL FOR DETERMINING VARIATION IN SHORT TANDEM REPEAT REGIONS
WO 10.09.2020
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/US2020/021550 Applicant ILLUMINA, INC. Inventor DOLZHENKO, Egor
The disclosed embodiments concern methods, apparatus, systems and computer program products for genotyping repeat sequences such as medically significant short tandem repeats (STRs). The methods involve aligning reads to a repeat sequence represented by a sequence graph, and using the aligned reads to genotype the repeat sequence. The sequence graph is a directed graph each including at least one self-loop representing a repeat sub-sequence. In some implementations, the reads are paired end reads, and both mates of each read pair may be used to genotype the repeat sequences. Some implementations can be used to determine degenerate codon repeats. Some implementations can be used to genotype repeat sequences each including two or more repeat sub-sequences. Some implementations can be used to genotype nucleic acid sequences each including at least one repeat sub-sequence and another genetic variant such as an insertion, deletion, or substitution.
9.WO/2020/177943METHOD, DEVICE AND SYSTEM FOR DETECTION OF MICRO ORGANISMS
WO 10.09.2020
Int.Class C12Q 1/02
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
02involving viable microorganisms
Appl.No PCT/EP2020/051718 Applicant AGRICAM AKTIEBOLAG Inventor EINEREN, Ellinor
The present document discloses a method of processing a sample obtained from a livestock animal, comprising applying at least some of said milk to a test surface of a growth medium test plate, waiting for a time sufficient to allow microbial growth to form on said test surface, acquiring a visual spectrum image depicting at least part of the test surface, using an image capture device, and providing a computer-implemented pre-trained image classifier algorithm, said image classifier algorithm being pre-trained to determine a microorganism type based on a visible spectrum image depicting a growth pattern of a known microorganism, and applying said image to the pre-trained image classifier algorithm to determine a microorganism type based on a microorganism growth pattern visible on the image. The document also discloses a method of training an image classifier algorithm, an image capture support for use in acquiring the image, a system comprising the image capture support, a user device and a central processing device, and the use of a pre-trained image classifier algorithm for determining a microorganism type based on a visible spectrum image depicting a microorganism growth pattern on a growth medium containing test plate.
10.WO/2020/179962DNA CODING METHOD AND BIOMEDICAL ENGINEERING APPLICATION OF SAME CODING METHOD
WO 10.09.2020
Int.Class G16B 30/10
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
30ICT specially adapted for sequence analysis involving nucleotides or amino acids
10Sequence alignment; Homology search
Appl.No PCT/KR2019/003570 Applicant SON, In Sik Inventor SON, In Sik
The present invention relates to a method for code standardization of DNA, the method comprising: (a) assigning codes 00, 01, 10, and 11 to the four bases C, T, A, and G, respectively; and (b) coding base pairs between G and C and between A and T by providing 1100 for G and C, 0011 for C and G, 1001 for A and T, and 0110 for T and A in the 5' to 3' direction. The method for code standardization of DNA according to the present invention provides a method that makes it easy to detect specific patterns present in base sequences such as DNA fragments or aptamers, for example, a method that makes it easy to detect specific patterns and secondary structures in base sequences, mutations of base sequences, etc., and to predict a disease by using disease-specific sequence variations such as SNP, etc.