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1. WO2018152487 - COMPOSITIONS AND METHODS FOR PREDICTING ANALYTIC SUCCESS OF T-CELL QUANTIFICATION AND T-CELL RECEPTOR SEQUENCING

Publication Number WO/2018/152487
Publication Date 23.08.2018
International Application No. PCT/US2018/018681
International Filing Date 20.02.2018
IPC
C12Q 1/68 2018.1
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
C12N 15/09 2006.1
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
15Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
09Recombinant DNA-technology
CPC
C12N 15/09
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
15Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
09Recombinant DNA-technology
C12Q 1/68
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
C12Q 1/6869
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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
6869Methods for sequencing
C12Q 1/6881
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
6881for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
C12Q 2535/122
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
2535Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
122Massive parallel sequencing
G16H 50/30
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
HHEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
50ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
30for calculating health indices; for individual health risk assessment
Applicants
  • UNIVERSITY OF SOUTHERN CALIFORNIA [US]/[US]
Inventors
  • GRUBER, Stephen B.
  • MELAS, Marilena
  • MCDONNELL, Kevin
Agents
  • EINHORN, Gregory P.
Priority Data
62/460,98320.02.2017US
Publication Language English (en)
Filing Language English (EN)
Designated States
Title
(EN) COMPOSITIONS AND METHODS FOR PREDICTING ANALYTIC SUCCESS OF T-CELL QUANTIFICATION AND T-CELL RECEPTOR SEQUENCING
(FR) COMPOSITIONS ET PROCÉDÉS DE PRÉDICTION DE RÉUSSITE ANALYTIQUE DE QUANTIFICATION DE LYMPHOCYTES T ET DE SÉQUENÇAGE DE RÉCEPTEUR DE LYMPHOCYTES T
Abstract
(EN) Provided are compositions, including products of manufacture and kits, and methods, for predicting the successful construction of a genomic T-Cell Receptor (TCR) library from a tissue sample; or predicting the successful sequencing of a TCR sequence from a tissue sample, wherein optionally the tissue sample comprises or is derived from a biopsy or a Formalin-Fixation and Paraffin Embedding (FFPE) sample, and optionally the tissue sample is a human or an animal sample. In alternative embodiments, provided herein are assays for predicting successful library construction and sequencing of a TCR chain. In alternative embodiments, the T cell is a tumor infiltrating lymphocyte (TIL). The results of methods provided herein can generate a prediction as to the success of assays used for quantifying T-cells and sequencing T-cell receptors, including any commercially available assay (e.g., ImmunoSeq, Adaptive Biotechnologies, Seattle, WA) to effectively assess TCR quantity and clonality.
(FR) L'invention concerne des compositions, comprenant des produits de fabrication et des kits, et des procédés, pour prédire la construction réussie d'une bibliothèque de récepteurs de lymphocytes T génomiques (TCR) à partir d'un échantillon de tissu biologique; ou prédire le séquençage réussi d'une séquence de TCR à partir d'un échantillon de tissu biologique, éventuellement l'échantillon de tissu comprenant une biopsie ou un échantillon fixé au formol et enrobé de paraffine (FFPE) ou étant dérivé de ceux-ci, et éventuellement l'échantillon de tissu biologique étant un échantillon humain ou animal. Dans d'autres modes de réalisation, l'invention concerne des dosages permettant de prédire la construction et le séquençage réussis d'une chaîne TCR. Dans d'autres modes de réalisation, le lymphocyte T est un lymphocyte infiltrant la tumeur (TIL). Les résultats des procédés selon la présente invention peuvent générer une prédiction quant à la résussite des dosages utilisés pour quantifier les lymphocytes T et séquencer les récepteurs des lymphocytes T, y compris tout dosage disponible dans le commerce (par exemple, ImmunoSeq, Adaptive Biotechnologies, Seattle, WA) pour évaluer efficacement la quantité et la clonalité de TCR.
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