US 12,298,314 B2
Methods and compositions for analyzing target binding of molecules
Wyatt James McDonnell, Concord, CA (US); Michael John Terry Stubbington, Cambridge (GB); and Geoffrey McDermott, Livermore, CA (US)
Assigned to 10x Genomics, Inc., Pleasanton, CA (US)
Filed by 10x Genomics, Inc., Pleasanton, CA (US)
Filed on Oct. 8, 2021, as Appl. No. 17/497,135.
Claims priority of provisional application 63/090,143, filed on Oct. 9, 2020.
Prior Publication US 2022/0113318 A1, Apr. 14, 2022
This patent is subject to a terminal disclaimer.
Int. Cl. G01N 33/68 (2006.01); G01N 33/532 (2006.01)
CPC G01N 33/6857 (2013.01) [G01N 33/532 (2013.01)] 19 Claims
 
1. A method of analyzing the target binding specificity and/or affinity of an antibody or antigen-binding fragment thereof, comprising:
(a) providing a cell population, wherein the cell population comprises a mixture of:
(i) a first subset of cells comprising a candidate antigen or epitope and a nucleic acid molecule indicative of expression or presence of the candidate antigen or epitope, wherein the first subset of cells is engineered or otherwise modified to express the candidate antigen or epitope, and
(ii) a second subset of cells lacking the candidate antigen or epitope and the nucleic acid molecule indicative of expression or presence of the candidate antigen or epitope;
(b) contacting the cell population of (a) with at least one antibody or antigen-binding fragment thereof, wherein the at least one antibody or antigen-binding fragment thereof is coupled to an oligonucleotide comprising an antibody-specific barcode sequence, and wherein the antibody binds to the candidate antigen or epitope;
(c) partitioning the cells of the population of (b) into a plurality of partitions, wherein a partition of the plurality of partitions comprises a cell of the population and a plurality of nucleic acid molecules comprising a partition-specific barcode sequence;
(d) generating a first barcoded nucleic acid molecule using the oligonucleotide comprising the antibody-specific barcode sequence and a first nucleic acid molecule of the plurality of nucleic acid molecules wherein the first barcoded nucleic acid molecule comprises the:
(i) partition-specific barcode sequence or reverse complement thereof, and
(ii) antibody-specific barcode sequence or reverse complement thereof;
(e) generating a second barcoded nucleic acid molecule using the nucleic acid molecule indicative of expression or presence of the candidate antigen or epitope and a second nucleic acid molecule of the plurality of nucleic acid molecules, wherein the second barcoded nucleic acid molecule comprises the partition-specific barcode sequence or reverse complement thereof.