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1. WO2018136888 - METHODS FOR NON-INVASIVE ASSESSMENT OF GENETIC ALTERATIONS

Publication Number WO/2018/136888
Publication Date 26.07.2018
International Application No. PCT/US2018/014726
International Filing Date 22.01.2018
IPC
G06F 19/18 2011.01
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 2011.01
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
CPC
C12Q 1/6816
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
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 25/00
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
25ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
G16B 30/00
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
30ICT specially adapted for sequence analysis involving nucleotides or amino acids
G16B 30/10
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
30ICT specially adapted for sequence analysis involving nucleotides or amino acids
10Sequence alignment; Homology search
Applicants
  • SEQUENOM, INC. [US]/[US]
Inventors
  • AZAB, Mostafa
  • SYKES, Michael
  • SUN, Youting
  • MAZLOOM, Amin
  • JENSEN, Taylor
  • EHRICH, Mathias
  • ELLISON, Christopher
Agents
  • ROTHSCHILD, Cynthia B.
  • ROTHWELL, Rodney H.
Priority Data
62/448,60020.01.2017US
62/448,60120.01.2017US
Publication Language English (EN)
Filing Language English (EN)
Designated States
Title
(EN) METHODS FOR NON-INVASIVE ASSESSMENT OF GENETIC ALTERATIONS
(FR) PROCÉDÉS D'ÉVALUATION NON INVASIVE D'ALTERATIONS GENETIQUE
Abstract
(EN)
Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of genetic alterations. In particular, a method is provided for that includes obtaining a set of sequence reads. The sequence reads each include a single molecule barcode (SMB) sequence that is a non-random oligonucleotide sequence. The method further includes assigning the sequence reads to read groups according to a read group signature. The read group signature comprises an SMB sequence and a start and end position of a nucleic acid fragment from the circulating cell free sample nucleic acid. The sequence reads comprising start and end positions and an SMB sequence similar to the read group signature are assigned to a read group. The method further includes generating a consensus for each read group, and determining the presence or absence of a genetic alteration based on the consensus for each read group.
(FR)
La technologie de la présente invention concerne, en partie, des méthodes, des procédés et des appareils pour l'évaluation non invasive d'altérations génétiques. En particulier, l'invention concerne un procédé qui consiste à obtenir un ensemble de lectures de séquence. Les lectures de séquence comprennent chacune une séquence de code à barres (SMB) à une seule molécule qui est une séquence d'oligonucléotide non aléatoire. Le procédé comprend en outre l'attribution des lectures de séquence à des groupes de lecture selon une signature de groupe de lecture. La signature de groupe de lecture comprend une séquence SMB et une position de début et de fin d'un fragment d'acide nucléique à partir de l'acide nucléique d'échantillon acellulaire circulant. Les lectures de séquence comprenant des positions de début et de fin et une séquence SMB similaire à la signature de groupe de lecture sont attribuées à un groupe de lecture. Le procédé comprend en outre la génération d'un consensus pour chaque groupe de lecture, et la détermination de la présence ou de l'absence d'une altération génétique sur la base du consensus pour chaque groupe de lecture.
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Latest bibliographic data on file with the International Bureau