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1. US20190360040 - COMPOSITIONS AND METHODS FOR PREDICTING ANALYTIC SUCCESS OF T-CELL QUANTIFICATION AND T-CELL RECEPTOR SEQUENCING

Office
United States of America
Application Number 16487045
Application Date 20.02.2018
Publication Number 20190360040
Publication Date 28.11.2019
Publication Kind A1
IPC
C12Q 1/6869
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
6869Methods for sequencing
C12Q 1/6881
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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1Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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 probes
G16H 50/30
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
HHEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY 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
CPC
C12Q 2535/122
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12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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2535Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
122Massive parallel sequencing
C12Q 1/6869
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
6869Methods for 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
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
Applicants UNIVERSITY OF SOUTHERN CALIFORNIA
Inventors Stephen B. GRUBER
Marilena MELAS
Kevin MCDONNELL
Title
(EN) COMPOSITIONS AND METHODS FOR PREDICTING ANALYTIC SUCCESS OF T-CELL QUANTIFICATION AND T-CELL RECEPTOR SEQUENCING
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, Wash.) to effectively assess TCR quantity and clonality.


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