Measurement and monitoring of cell clonality
AssigneeThe Board of Trustees of the Leland Stanford Junior University
InventorsAndrew Fire, Scott D. Boyd, Jason Merker, Kyunga Seo, Eleanor M. Osborne
Life of this patent
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Abstract
Methods are provided for the detection and analysis of clonality in a cell population, where parallel sequencing is applied to a nucleic acid sample obtained from the cell population, optionally a population of lymphocytes. Replicate samples are amplified, and sequenced, where identification of coincident sequences in two or more replicates is indicative of clonal expansion.
Claims4
A method of determining the clonal expansion of B cells in response of an individual to a vaccine, the method comprising:
- obtaining a cell sample comprising B cells from said individual in a short defined time period following immunization with said vaccine;
- dividing said cell sample comprising B cells, or genomic DNA derived therefrom, into at least two distinct pools;
- amplifying genomic DNA sequences at an immunoglobulin heavy chain locus in said at least two distinct pools with a primer set that amplifies at least 50% of the known rearrangements at the locus;
- sequencing at least 103 reads of the amplified genomic DNA at the locus of interest from said at least two distinct pools;
- comparing sequences from said amplified genomic DNA to detect the presence of sequences that are coincident in said at least two distinct pools of nucleic acid;
- wherein the presence of coincident sequences is indicative of clonal expansion and responsiveness to said vaccine.
A method of determining the clonal expansion of B cells in response of an individual to a vaccine, the method comprising:
- obtaining a cell sample comprising B cells from said individual in a short defined time period following immunization with said vaccine wherein said short defined time period is less than about 14 days;
- dividing said cell sample comprising B cells, or genomic DNA derived therefrom, into at least two distinct pools;
- amplifying genomic DNA sequences at an immunoglobulin heavy chain locus in said at least two distinct pools with a primer set that amplifies at least 75% of the known rearrangements at the locus;
- sequencing at least 103 reads of the amplified genomic DNA at the locus of interest from said at least two distinct pools;
- comparing sequences from said amplified genomic DNA to detect the presence of sequences that are coincident in said at least two distinct pools of nucleic acid;
- wherein the presence of coincident sequences is indicative of clonal expansion and responsiveness to said vaccine.
Dependencies are inferred from the claim text.