Determining paired immune receptor chains from frequency matched subunits
First Claim
1. A method of determining a profile of likely paired immune receptor chains in a sample containing a plurality of lymphocytes, wherein the sample is obtained from a subject, and wherein the lymphocytes express a repertoire of immune receptor chain pairs, the method comprising the steps of:
- (a) partitioning the sample into a plurality of subsets such that each of the subsets comprises at least 1,000 T cells or at least 1,000 B cells;
(b) amplifying VDJ regions and VJ regions of CDR3 sequences of substantially all immune receptor chains in each of the subsets by a single multiplex polymerase chain reaction and sequencing the resulting amplicons to produce a subset list of VDJ regions and VJ regions nucleotide sequences for each of said subsets of step (a);
(c) determining, for each of said subsets, (i) whether or not a first nucleotide sequence encoding a first chain of a likely immune receptor pair in any of the subsets is present in each subset list of nucleotide sequences, and (ii) whether or not a second nucleotide sequence encoding a second chain of a likely immune receptor pair in any of the subsets is present in each subset list of nucleotide sequences; and
(d) producing a profile of a plurality of likely paired immune receptor chains by matching those first and second nucleotide sequences that are present together in at least one subset list and not present separately in other subset lists at all.
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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.
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Citations
9 Claims
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1. A method of determining a profile of likely paired immune receptor chains in a sample containing a plurality of lymphocytes, wherein the sample is obtained from a subject, and wherein the lymphocytes express a repertoire of immune receptor chain pairs, the method comprising the steps of:
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(a) partitioning the sample into a plurality of subsets such that each of the subsets comprises at least 1,000 T cells or at least 1,000 B cells; (b) amplifying VDJ regions and VJ regions of CDR3 sequences of substantially all immune receptor chains in each of the subsets by a single multiplex polymerase chain reaction and sequencing the resulting amplicons to produce a subset list of VDJ regions and VJ regions nucleotide sequences for each of said subsets of step (a); (c) determining, for each of said subsets, (i) whether or not a first nucleotide sequence encoding a first chain of a likely immune receptor pair in any of the subsets is present in each subset list of nucleotide sequences, and (ii) whether or not a second nucleotide sequence encoding a second chain of a likely immune receptor pair in any of the subsets is present in each subset list of nucleotide sequences; and (d) producing a profile of a plurality of likely paired immune receptor chains by matching those first and second nucleotide sequences that are present together in at least one subset list and not present separately in other subset lists at all. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9)
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Specification