Measurement and comparison of immune diversity by high-throughput sequencing

摘要

A precise measurement of the immunological receptor diversity present in a sample is obtained by sequence analysis. Samples of interest are generally complex, comprising more than 102, 103, 104, 105, 106, 107, 108, 109, 1010, 1011, 1012 or more different sequences for a receptor of interest. Immunological receptors of interest include immunoglobulins, T cell antigen receptors, and major histocompatibility receptors. The specific composition of immunological receptor sequence variations in the sample can be recorded and output. The composition is useful for predictive, diagnostic and therapeutic methods relating to the immune capabilities and history of an individual. Such predictions and diagnoses are used to guide clinical decisions.

主权项

1. A method of characterizing an immune repertoire of an organism, comprising:
a) obtaining mRNA from a biological sample comprising B cells of the organism; b) producing cDNA from the mRNA obtained in Step (a); c) producing amplicons from the cDNA produced in Step (b), wherein the amplicons are produced using a set of primers that amplify a plurality of immunoglobulin heavy chain VDJ exon sequences, wherein said amplicons comprise both the VD junction and the DJ junction; d) sequencing amplicons produced in Step (c) using massively-parallel sequencing to obtain at least 104 sequence reads of immunoglobulin heavy chain sequences, comprising sequences from a plurality of different genomic V segments, a plurality of different genomic D segments, and a plurality of different genomic J segments; e) comparing sequences obtained in Step (d) to known sequences associated with immune function, wherein said known sequences comprise a plurality of genomic heavy chain V-segment sequences of the organism, wherein said comparing step comprises compiling sequence data on a computer-readable medium and processing said data on said computer to identify regions of similarity and difference between said sequences obtained in Step (d) and said known sequences; f) grouping sequences obtained in Step (d) based on the comparison in Step (e) to identify a plurality of groups of heavy chain VDJ sequences; g) clustering heavy chain VDJ sequences within individual groups from Step (f) to define a plurality of clusters; h) determining consensus sequences for individual clusters, wherein the consensus sequences correspond to heavy chain VDJ segments of the organism's immune repertoire, and wherein the consensus sequences have reduced amplification bias and sequencing error compared to the sequence data of Step (d); and i) identifying somatic mutations in the heavy-chain VDJ exon sequences using the consensus sequences;
thereby to characterize the organism's immune repertoire.