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1. WO2018009723 - METHODS FOR FRAGMENTOME PROFILING OF CELL-FREE NUCLEIC ACIDS

Publication Number WO/2018/009723
Publication Date 11.01.2018
International Application No. PCT/US2017/040986
International Filing Date 06.07.2017
IPC
C12Q 1/68 2006.1
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
G06F 19/18 2011.1
GPHYSICS
06COMPUTING; CALCULATING OR COUNTING
FELECTRIC DIGITAL DATA PROCESSING
19Digital computing or data processing equipment or methods, specially adapted for specific applications
10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
18for 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
G06F 19/22 2011.1
GPHYSICS
06COMPUTING; CALCULATING OR COUNTING
FELECTRIC DIGITAL DATA PROCESSING
19Digital computing or data processing equipment or methods, specially adapted for specific applications
10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
22for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism discovery or sequence alignment
G06F 19/24 2011.1
GPHYSICS
06COMPUTING; CALCULATING OR COUNTING
FELECTRIC DIGITAL DATA PROCESSING
19Digital computing or data processing equipment or methods, specially adapted for specific applications
10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
24for machine learning, data mining or biostatistics, e.g. pattern finding, knowledge discovery, rule extraction, correlation, clustering or classification
CPC
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
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms
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
C12Q 2600/154
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
2600Oligonucleotides characterized by their use
154Methylation markers
G16B 20/00
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] 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
G16B 20/10
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] 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
10Ploidy or copy number detection
G16B 20/20
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] 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 [SNP] detection
G16B 25/10
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
25ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
10Gene or protein expression profiling; Expression-ratio estimation or normalisation
Applicants
  • GUARDANT HEALTH, INC. [US]/[US]
Inventors
  • ABDUEVA, Diana
Agents
  • SKUBATCH, Maya
  • ADVANI, Raj
  • ALEMOZAFAR, Ali
  • ALMEDA, Dariela
  • AGRAWAL, Trisha
Priority Data
62/359,15106.07.2016US
62/420,16710.11.2016US
62/437,17221.12.2016US
62/489,39924.04.2017US
Publication Language English (en)
Filing Language English (EN)
Designated States
Title
(EN) METHODS FOR FRAGMENTOME PROFILING OF CELL-FREE NUCLEIC ACIDS
(FR) PROCÉDÉS DE PROFILAGE D'UN FRAGMENTOME D'ACIDES NUCLÉIQUES SANS CELLULE
Abstract
(EN) The present disclosure contemplates various uses of cell-free DNA. Methods provided herein may use sequence information in a macroscale and global manner, with or without somatic variant information, to assess a fragmentome profile that can be representative of a tissue of origin, disease, progression, etc. In an aspect, disclosed herein is a method for determining a presence or absence of a genetic aberration in deoxyribonucleic acid (DNA) fragments from cell-free DNA obtained from a subject, the method comprising: (a) constructing a multi-parametric distribution of the DNA fragments over a plurality of base positions in a genome; and (b) without taking into account a base identity of each base position in a first locus, using the multi-parametric distribution to determine the presence or absence of the genetic aberration in the first locus in the subject.
(FR) La présente invention concerne diverses utilisations d'ADN sans cellule. Les procédés de l'invention peuvent utiliser l'information de séquence selon une manière type macro-échelle et globale, avec ou sans information de variant somatique, pour évaluer un profil de fragmentome qui peut être représentatif d'un tissu d'origine, d'une maladie, d'une progression, etc. Dans un aspect, la présente invention concerne un procédé de détermination d'une présence ou d'une absence d'une aberration génétique dans des fragments d'acide désoxyribonucléique (ADN) à partir d'ADN sans cellule obtenu auprès d'un sujet, le procédé comprenant : (a) la construction d'une distribution multi-paramétrique des fragments d'ADN sur une pluralité de positions de base dans un génome; et (b) sans prendre en compte une identité de base de chaque position de base dans un premier locus, l'utilisation de la distribution multi-paramétrique afin de déterminer la présence ou l'absence de l'aberration génétique dans le premier locus chez le sujet.
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