Nothing Special   »   [go: up one dir, main page]

Aganezov et al., 2021 - Google Patents

A complete human reference genome improves variant calling for population and clinical genomics

Aganezov et al., 2021

View PDF
Document ID
6073811956108864841
Author
Aganezov S
Yan S
Soto D
Kirsche M
Zarate S
Avdeyev P
Taylor D
Shafin K
Shumate A
Xiao C
Wagner J
McDaniel J
Olson N
Sauria M
Vollger M
Rhie A
Meredith M
Martin10 S
Koren S
Rosenfeld11 J
Paten B
Layer10 R
Chin12 C
Sedlazeck13 F
Hansen14 N
Miller D
Phillippy A
Miga K
McCoy R
Dennis M
Zook J
Schatz M
Publication year
Publication venue
bioRxiv (to appear)

External Links

Snippet

Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 Mbp of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the genome to clinical and functional study. Here we demonstrate how the new …
Continue reading at tsapps.nist.gov (PDF) (other versions)

Classifications

    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/22Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or SNP [Single-Nucleotide Polymorphism] discovery or sequence alignment
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/18Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/28Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/14Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for phylogeny or evolution, e.g. evolutionarily conserved regions determination or phylogenetic tree construction
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/24Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for machine learning, data mining or biostatistics, e.g. pattern finding, knowledge discovery, rule extraction, correlation, clustering or classification
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/16Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for molecular structure, e.g. structure alignment, structural or functional relations, protein folding, domain topologies, drug targeting using structure data, involving two-dimensional or three-dimensional structures
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/30286Information retrieval; Database structures therefor; File system structures therefor in structured data stores
    • G06F17/30289Database design, administration or maintenance
    • G06F17/30303Improving data quality; Data cleansing
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/20Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for hybridisation or gene expression, e.g. microarrays, sequencing by hybridisation, normalisation, profiling, noise correction models, expression ratio estimation, probe design or probe optimisation
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/12Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for modelling or simulation in systems biology, e.g. probabilistic or dynamic models, gene-regulatory networks, protein interaction networks or metabolic networks
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/26Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for data visualisation, e.g. graphics generation, display of maps or networks or other visual representations
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/70Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds
    • G06F19/706Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds for drug design with the emphasis on a therapeutic agent, e.g. ligand-biological target interactions, pharmacophore generation
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/30Medical informatics, i.e. computer-based analysis or dissemination of patient or disease data
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F11/00Error detection; Error correction; Monitoring
    • G06F11/07Error detection; Error correction; Monitoring responding to the occurence of a fault, e.g. fault tolerance
    • GPHYSICS
    • G06COMPUTING; CALCULATING; COUNTING
    • G06FELECTRICAL DIGITAL DATA PROCESSING
    • G06F21/00Security arrangements for protecting computers, components thereof, programs or data against unauthorised activity
    • G06F21/50Monitoring users, programs or devices to maintain the integrity of platforms, e.g. of processors, firmware or operating systems
    • G06F21/55Detecting local intrusion or implementing counter-measures
    • G06F21/56Computer malware detection or handling, e.g. anti-virus arrangements
    • G06F21/562Static detection
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES OR MICRO-ORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or micro-organisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or micro-organisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Hybridisation probes
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES OR MICRO-ORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or micro-organisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or micro-organisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869Methods for sequencing

Similar Documents

Publication Publication Date Title
Aganezov et al. A complete reference genome improves analysis of human genetic variation
Weisenfeld et al. Direct determination of diploid genome sequences
Jain et al. Nanopore sequencing and assembly of a human genome with ultra-long reads
DK2773954T3 (en) SYSTEMS AND PROCEDURES FOR GENOMIC ANNOTATION AND INTERPRETATION OF DISTRIBUTED VARIETIES
US20180107785A1 (en) Systems and methods for genomic annotation and distributed variant interpretation
US10235496B2 (en) Systems and methods for genomic annotation and distributed variant interpretation
Wu et al. Tangram: a comprehensive toolbox for mobile element insertion detection
US10741291B2 (en) Systems and methods for genomic annotation and distributed variant interpretation
Chimusa et al. A genomic portrait of haplotype diversity and signatures of selection in indigenous southern African populations
US20140163900A1 (en) Analyzing short tandem repeats from high throughput sequencing data for genetic applications
Mossotto et al. GenePy-a score for estimating gene pathogenicity in individuals using next-generation sequencing data
Szatkiewicz et al. Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation
US11342048B2 (en) Systems and methods for genomic annotation and distributed variant interpretation
Wang et al. Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data
Wang et al. Major sex differences in allele frequencies for X chromosomal variants in both the 1000 Genomes Project and gnomAD
Aganezov et al. A complete human reference genome improves variant calling for population and clinical genomics
Goncalves da Silva et al. SNP discovery in nonmodel organisms: strand bias and base‐substitution errors reduce conversion rates
Lin et al. MapCaller–An integrated and efficient tool for short-read mapping and variant calling using high-throughput sequenced data
DeGorter et al. Transcriptomics and chromatin accessibility in multiple African population samples
Niehus et al. PopDel identifies medium-size deletions jointly in tens of thousands of genomes
Kang et al. Inference of population mutation rate and detection of segregating sites from next-generation sequence data
Löytynoja Thousands of human mutation clusters are explained by short-range template switching
Decroly et al. Rewinding the ratchet: rare recombination locally rescues neo-W degeneration and generates plateaus of sex-chromosome divergence
Wang et al. VarSCAT: A computational tool for sequence context annotations of genomic variants
Aganezov et al. A complete reference genome improves long-read analysis of human genetic variation