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1. (WO2017065959) METHODS AND COMPOSITIONS THAT UTILIZE TRANSCRIPTOME SEQUENCING DATA IN MACHINE LEARNING-BASED CLASSIFICATION
Latest bibliographic data on file with the International Bureau    Submit observation

Pub. No.: WO/2017/065959 International Application No.: PCT/US2016/053578
Publication Date: 20.04.2017 International Filing Date: 23.09.2016
IPC:
C12Q 1/68 (2006.01) ,G01N 33/574 (2006.01) ,G06F 19/20 (2011.01) ,G06F 19/22 (2011.01) ,G06F 19/26 (2011.01) ,G06F 19/28 (2011.01) ,C40B 40/06 (2006.01) ,C40B 40/08 (2006.01)
C CHEMISTRY; METALLURGY
12
BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
Q
MEASURING OR TESTING PROCESSES INVOLVING ENZYMES OR MICRO-ORGANISMS; 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 or micro-organisms; Compositions therefor; Processes of preparing such compositions
68
involving nucleic acids
G PHYSICS
01
MEASURING; TESTING
N
INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
33
Investigating or analysing materials by specific methods not covered by groups G01N1/-G01N31/131
48
Biological material, e.g. blood, urine; Haemocytometers
50
Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
53
Immunoassay; Biospecific binding assay; Materials therefor
574
for cancer
G PHYSICS
06
COMPUTING; CALCULATING; 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
20
for hybridisation or gene expression, e.g. microarrays, sequencing by hybridisation, normalisation, profiling, noise correction models, expression ratio estimation, probe design or probe optimisation
G PHYSICS
06
COMPUTING; CALCULATING; 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 SNP [Single-Nucleotide Polymorphism] discovery or sequence alignment
G PHYSICS
06
COMPUTING; CALCULATING; 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
26
for data visualisation, e.g. graphics generation, display of maps or networks or other visual representations
G PHYSICS
06
COMPUTING; CALCULATING; 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
28
for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
C CHEMISTRY; METALLURGY
40
COMBINATORIAL TECHNOLOGY
B
COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICO LIBRARIES
40
Libraries per se, e.g. arrays, mixtures
04
Libraries containing only organic compounds
06
Libraries containing nucleotides or polynucleotides, or derivatives thereof
C CHEMISTRY; METALLURGY
40
COMBINATORIAL TECHNOLOGY
B
COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICO LIBRARIES
40
Libraries per se, e.g. arrays, mixtures
04
Libraries containing only organic compounds
06
Libraries containing nucleotides or polynucleotides, or derivatives thereof
08
Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
Applicants: VERACYTE, INC.[US/US]; 6000 Shoreline Court, Suite 300 South San Francisco, CA 94080, US
Inventors: WALSH, P., Sean; US
KENNEDY, Giulia, C.; US
TRAVERS, Kevin; US
HU, Zhanzhi; US
KIM, Su, Yeon; US
HUANG, Jing; US
Agent: ARONIN, Caren; US
ARMODEO, Gabriele; US
ADVANI, Raj; US
ALEMOZAFAR, Ali; US
AGRAWAL, Trisha; US
Priority Data:
62/233,20725.09.2015US
Title (EN) METHODS AND COMPOSITIONS THAT UTILIZE TRANSCRIPTOME SEQUENCING DATA IN MACHINE LEARNING-BASED CLASSIFICATION
(FR) PROCÉDÉS ET COMPOSITIONS QUI UTILISENT LES DONNÉES DE SÉQUENÇAGE DU TRANSCRIPTOME POUR LA CLASSIFICATION BASÉE SUR L'APPRENTISSAGE AUTOMATIQUE
Abstract:
(EN) Provided herein are methods and systems for producing a modified biological dataset by flagging or removing a nucleic acid sequence from the biological dataset that is assigned a noise-call to produce the modified biological dataset. The noise-call may be based on comparing a gene expression level, sequence information, or a combination thereof with a nucleic acid sequence of a control sample.
(FR) L'invention concerne des procédés et des systèmes de production d'un ensemble de données biologiques modifié par balisage ou élimination d'une séquence d'acide nucléique de l'ensemble de données biologiques auquel est affecté un bruit-appel pour générer l'ensemble de données biologiques modifié. Le bruit-appel peut se baser sur la comparaison d'un niveau d'expression génique, des informations de séquence, ou d'une combinaison des deux avec la séquence d'acide nucléique d'un échantillon témoin.
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Designated States: AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW
African Regional Intellectual Property Organization (ARIPO) (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW)
Eurasian Patent Office (AM, AZ, BY, KG, KZ, RU, TJ, TM)
European Patent Office (EPO) (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR)
African Intellectual Property Organization (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG)
Publication Language: English (EN)
Filing Language: English (EN)