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1. (WO2018144782) METHODS OF DETECTING SOMATIC AND GERMLINE VARIANTS IN IMPURE TUMORS
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Pub. No.: WO/2018/144782 International Application No.: PCT/US2018/016522
Publication Date: 09.08.2018 International Filing Date: 01.02.2018
IPC:
G06F 19/10 (2011.01) ,G06F 19/18 (2011.01) ,G06F 19/22 (2011.01) ,G06F 19/28 (2011.01) ,G01N 33/574 (2006.01) ,C12Q 1/68 (2018.01)
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
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
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; 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
28
for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
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
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
Applicants:
THE TRANSLATIONAL GENOMICS RESEARCH INSTITUTE [US/US]; 445 N. Fifth Street Suite 600 Phoenix, Arizona 85004, US
Inventors:
HALPERIN, Rebecca; US
CRAIG, David; US
Agent:
FULLER, Rodney J.; US
Priority Data:
62/453,49201.02.2017US
Title (EN) METHODS OF DETECTING SOMATIC AND GERMLINE VARIANTS IN IMPURE TUMORS
(FR) PROCÉDÉS DE DÉTECTION DE VARIANTS SOMATIQUES ET DE LIGNÉE GERMINALE DANS DES TUMEURS IMPURES
Abstract:
(EN) A system is provided that considers allele fraction shifts as a function of copy number and clonal heterogeneity. The system leverages differences between allele frequencies to differentiate between somatic and normal variants in impure tumor samples. In solid tumors, stromal cells and infiltrating lymphocytes are typically interspersed among the tumor cells. The normal cell contamination in tumors can be leveraged to differentiate somatic from germline variants. We explicitly model allelic copy number and clonal sample fractions so that we can examine how these factors impact the power to detect somatic variants. The system models the copy number alterations, which can also affect the allele frequencies of both somatic and germline variants. The expected allele frequencies can be calculated. The expected allele frequencies for somatic and germline differ with tumor content for different copy number alterations.
(FR) L'invention concerne également un système qui considère des décalages de fractions d'allèles en fonction du nombre de copies et de l'hétérogénéité clonale. Le système tire profit de différences entre des fréquences d'allèle pour différencier des variants somatiques et normaux dans des échantillons de tumeur impure. Dans les tumeurs solides, les cellules stromales et les lymphocytes infiltrant sont typiquement intercalés parmi les cellules tumorales. La contamination cellulaire normale dans les tumeurs peut être exploitée pour différencier des somatique de variants de lignée germinale. Nous décrivons explicitement un nombre de copies alléliques et des fractions d'échantillons clonales de sorte que l'on puisse examiner la manière dont ces facteurs impactent la puissance pour détecter des variants somatiques. Le système modélise les altérations du nombre de copies, qui peuvent également affecter les fréquences d'allèle des variantes somatiques et germinales. Les fréquences d'allèle attendues peuvent être calculées. Les fréquences d'allèle attendues pour une somatique et une lignée germinale diffèrent par un contenu tumoral pour différentes modifications de nombre de copies.
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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, JO, JP, KE, KG, KH, 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)