Abstract: The invention is directed to methods of measuring an immune response by comparing sequence-based clonotype frequency data from successively measured clonotype profiles. In particular, the invention includes immunotherapies of cancers, such as lymphomas, that include sensitive pre- and post-vaccination sequence-based measurements of changes in a patient's immune repertoire, thereby providing a sensitive measure of the likelihood of treatment success.

Abstract: In one aspect, the invention provides a method of enriching a pool of nucleic acid duplexes for heteroduplexes containing sequences that vary from those of a reference DNA population. A mixture of test sequences, that is, nucleic acids suspected of containing one or more mutations or rare alleles, and corresponding reference sequences are denatured and reassociated so that duplexes form comprising heteroduplexes and homoduplexes. In accordance with one aspect of the invention, whenever a subset of heteroduplexes contains mismatched sequences, the mismatches are corrected so that the sequences of strands from the test population are preserved, or selected. The preserved or selected sequences may then be denatured and reassociated with additional sequences from the reference population to once again form duplexes comprising homoduplexes and heteroduplexes, thereby generating an enriched population of variant sequences.