Determining paired immune receptor chains from frequency matched subunits
AssigneeSequenta, Inc.
InventorsMalek Faham, Mark Klinger
Life of this patent
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Abstract
The invention is directed to methods for determining nucleic acids that encode immune receptor chains originating from the same cell, that is, paired immune receptor chains. Methods of the invention comprise high-throughput sequencing of rearranged nucleic acids encoding immune receptors from one or more samples of lymphocytes. In one aspect, from a plurality of subsets of a sample, nucleic acids encoding separate chains of a pair are separately sequenced, wherein the size of the sample and the number of subsets are selected so that the distribution of lymphocytes approximates a binomial model. Paired chains are determined by identifying pairs that appear together or that are entirely absent in the subsets.
Claims17
A method of determining paired immune receptor chains in a sample, the method comprising the steps of:
- (a) partitioning a sample into a plurality of subsets, the sample containing lymphocytes expressing pairs of immune receptor chains;
- (b) determining nucleotide sequences of a first chain of each pair of immune receptor chains of lymphocytes having such pairs in a portion of the plurality of subsets;
- (c) determining nucleotide sequences of a second chain of each pair of immune receptor chains of lymphocytes having such pairs in the same portion of the plurality of subsets;
- (d) identifying as paired immune receptor chains those pairs of first chains and second chains (i) that, for every subset of the portion, either occur together or do not occur and (ii) that occur together in at least one subset of the portion and do not occur in at least one subset of the portion.
The method of 6 wherein said plurality of subsets depends on said size of said population and said frequency of said lymphocytes whose paired immune receptor chains are to be determined.
A method of determining paired T cell receptor chains of T cells in a sample, the method comprising the steps of:
- obtaining a sample containing T cells, each T cell expressing a first immune receptor chain and a second immune receptor chain;
- determining nucleotide sequences of the first immune receptor chains of T cells of the sample, each first immune receptor chain having a frequency of occurrence in the sample;
- determining nucleotide sequences of the second immune receptor chains of T cells of the sample, each second immune receptor chain having a frequency of occurrence in the sample;
- identifying paired first immune receptor chains and second immune receptor chains as those having the same frequency within the sample.
A method of generating a profile of paired immune receptor chains, the method comprising the steps of:
- obtaining a sample containing T cells or B cells;
- determining nucleotide sequences of a first immune receptor chain of T cells or B cells of the sample;
- determining nucleotide sequences of a second immune receptor chain of T cells or B cells of the sample;
- pairing nucleotide sequences encoding first and second immune receptors chains expressed in the same T cell or B cell to form the profile of paired immune receptor chains.
Dependencies are inferred from the claim text.