WO2018009723 METHODS FOR FRAGMENTOME PROFILING OF CELL-FREE NUCLEIC ACIDS

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Publication Number WO/2018/009723

Publication Date 11.01.2018

International Application No. PCT/US2017/040986

International Filing Date 06.07.2017

IPC

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Applicants

GUARDANT HEALTH, INC. [US]/[US]

Inventors

ABDUEVA, Diana

Agents

SKUBATCH, Maya
ADVANI, Raj
ALEMOZAFAR, Ali
ALMEDA, Dariela
AGRAWAL, Trisha

Priority Data

62/359,151	06.07.2016	US
62/420,167	10.11.2016	US
62/437,172	21.12.2016	US
62/489,399	24.04.2017	US

Publication Language English (en)

Filing Language English (EN)

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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.

C	CHEMISTRY; METALLURGY
12	BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
Q	MEASURING 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
1	Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
68	involving nucleic acids

G	PHYSICS
06	COMPUTING; CALCULATING OR COUNTING
F	ELECTRIC DIGITAL DATA PROCESSING
19	Digital computing or data processing equipment or methods, specially adapted for specific applications
10	Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
18	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

G	PHYSICS
06	COMPUTING; CALCULATING OR COUNTING
F	ELECTRIC DIGITAL DATA PROCESSING
19	Digital computing or data processing equipment or methods, specially adapted for specific applications
10	Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
22	for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism discovery or sequence alignment

G	PHYSICS
06	COMPUTING; CALCULATING OR COUNTING
F	ELECTRIC DIGITAL DATA PROCESSING
19	Digital computing or data processing equipment or methods, specially adapted for specific applications
10	Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
24	for machine learning, data mining or biostatistics, e.g. pattern finding, knowledge discovery, rule extraction, correlation, clustering or classification

C	CHEMISTRY; METALLURGY
12	BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
Q	MEASURING 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
1	Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
68	involving nucleic acids

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

G	PHYSICS
16	INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
B	BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
20	ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations