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1. WO2022047082 - SAMPLE VALIDATION FOR CANCER CLASSIFICATION

Publication Number WO/2022/047082
Publication Date 03.03.2022
International Application No. PCT/US2021/047822
International Filing Date 26.08.2021
IPC
G16B 20/00 2019.1
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY 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
CPC
C12Q 1/6879
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
6879for sex determination
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
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 20/20
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 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 40/00
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
40ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
Applicants
  • GRAIL, INC. [US]/[US]
Inventors
  • SAKARYA, Onur
  • YAKYM, Christopher-James, A., V.
Agents
  • JACOBSON, Anthony
  • LEM, Matthew
  • BECKER, Daniel
  • SEQUEIRA, Antonia, L.
Priority Data
63/071,95128.08.2020US
Publication Language English (en)
Filing Language English (EN)
Designated States
Title
(EN) SAMPLE VALIDATION FOR CANCER CLASSIFICATION
(FR) VALIDATION D'ÉCHANTILLON POUR UNE CLASSIFICATION DE CANCER
Abstract
(EN) Systems and methods for validating that a DNA sample is from a test subject are disclosed. The test subject reports one or more characteristics (biological sex, ethnicity, and/or age) that may be predicted from the DNA sample. The predictions are compared to the reported characteristics to validate the DNA sample. To validate according to biological sex, the system determines a Y-chromosome signal based on counts of sequence reads for a gene specific to the Y chromosome and, similarly, an X-chromosome signal using another gene specific to the X chromosome. The biological sex is predicted based on a comparison of the two signals. To validate according to ethnicity, the system predicts ethnicity based on detected allele frequencies for SNPs specific to each chromosome. To validate according to age, the system calculates the methylation densities for age-informative CpG sites. The system utilizes trained regression models to predict the age using the methylation densities.
(FR) L'invention concerne des systèmes et des procédés permettant de valider qu'un échantillon d'ADN provient d'un sujet de test. Le sujet de test rapporte une ou plusieurs caractéristiques (sexe biologique, origine ethnique et/ou âge) qui peuvent être prédites à partir de l'échantillon d'ADN. Les prédictions sont comparées aux caractéristiques rapportées pour valider l'échantillon d'ADN. Pour valider selon le sexe biologique, le système détermine un signal de chromosome Y sur la base de nombres de lectures de séquence pour un gène spécifique au chromosome Y et, de manière similaire, un signal de chromosome X à l'aide d'un autre gène spécifique au chromosome X. Le sexe biologique est prédit sur la base d'une comparaison des deux signaux. Pour valider selon l'origine ethnique, le système prédit l'origine ethnique sur la base de fréquences d'allèle détectées pour des SNP spécifiques à chaque chromosome. Pour valider selon l'âge, le système calcule les densités de méthylation pour des sites CpG informant sur l'âge. Le système utilise des modèles de régression formés pour prédire l'âge à l'aide des densités de méthylation.
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