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1. WO2020092807 - METHODS, COMPOSITIONS AND SYSTEMS FOR CALIBRATING EPIGENETIC PARTITIONING ASSAYS

Publication Number WO/2020/092807
Publication Date 07.05.2020
International Application No. PCT/US2019/059217
International Filing Date 31.10.2019
IPC
C12Q 1/6806 2018.01
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
6806Preparing nucleic acids for analysis, e.g. for polymerase chain reaction assay
C12Q 1/6869 2018.01
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
6869Methods for sequencing
C12Q 1/6886 2018.01
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
6886for cancer
CPC
C12Q 1/6806
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
6806Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
C12Q 1/682
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
6813Hybridisation assays
6816characterised by the detection means
682Signal amplification
C12Q 1/6827
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QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms
68involving nucleic acids
6813Hybridisation assays
6827for detection of mutation or polymorphism
C12Q 1/6832
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QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms
68involving nucleic acids
6813Hybridisation assays
6832Enhancement of hybridisation reaction
C12Q 1/6851
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
6844Nucleic acid amplification reactions
6851Quantitative amplification
C12Q 1/6855
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
6844Nucleic acid amplification reactions
6853using modified primers or templates
6855Ligating adaptors
Applicants
  • GUARDANT HEALTH, INC. [US]/[US]
Inventors
  • KENNEDY, Andrew
  • WESTESSON, Oscar
  • HE, Yupeng
  • SCHULTZ, Matthew
Agents
  • KANAKARAJ, Indhu
  • HOTT, Timothy A.
  • BORTNER, Scott R.
Priority Data
62/753,82631.10.2018US
Publication Language English (EN)
Filing Language English (EN)
Designated States
Title
(EN) METHODS, COMPOSITIONS AND SYSTEMS FOR CALIBRATING EPIGENETIC PARTITIONING ASSAYS
(FR) PROCÉDÉS, COMPOSITIONS ET SYSTÈMES POUR ÉTALONNER DES ESSAIS DE PARTITIONNEMENT ÉPIGÉNÉTIQUE
Abstract
(EN)
In an aspect, a method for evaluating the partitioning of nucleic acid molecules in a sample of polynucleotides based on epigenetic state, comprising: (a) adding a set of epigenetic-control nucleic acid molecules to the nucleic acid molecules in the sample of polynucleotides, whereby producing a spiked-in sample; (b) partitioning nucleic acid molecules of the spiked-in sample into plurality of partitioned sets; (c) enriching a subset of molecules from the plurality of partitioned sets to generate enriched molecules, wherein the enriched molecules comprises a group of epigenetic-control nucleic acid molecules and a group of nucleic acid molecules from the sample of polynucleotides; (d) sequencing the enriched molecules to produce sequencing reads; (e) analyzing the sequencing reads to generate one or more epigenetic partition scores of the epigenetic-control nucleic acid molecules; and (f) comparing the one or more epigenetic partition scores with one or more epigenetic partition cut-offs.
(FR)
Selon un aspect, l'invention concerne un procédé d'évaluation du partitionnement de molécules d'acide nucléique dans un échantillon de polynucléotides sur la base d'un état épigénétique, consistant à : (a) ajouter un ensemble de molécules d'acide nucléique à régulation épigénétique aux molécules d'acide nucléique dans l'échantillon de polynucléotides, ce qui permet de produire un échantillon dopé ; (b) partitionner les molécules d'acide nucléique de l'échantillon dopé en une pluralité d'ensembles partitionnés ; (c) enrichir un sous-ensemble de molécules de la pluralité d'ensembles partitionnés pour générer des molécules dopées, les molécules enrichies comprenant un groupe de molécules d'acide nucléique à régulation épigénétique et un groupe de molécules d'acide nucléique provenant de l'échantillon de polynucléotides ; (d) séquencer les molécules enrichies pour produire des lectures de séquençage ; (e) analyser les lectures de séquençage pour générer un ou plusieurs scores de partition épigénétique des molécules d'acide nucléique à régulation épigénétique ; et (f) comparer le ou les scores de partition épigénétiques à un ou plusieurs seuils de partition épigénétique.
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