Qualifying high-throughput immune repertoire sequencing

•1,433,471 individual IGHV (B cell) and TCRβ (T cell) VDJ sequences of five healthy control and five CLL samples were compared.•Analysis strategy for diversity assessment of T and B cells.•Targeted resequencing with 454 next-generation sequencing of recombinant genomic DNA after multiplex PCR.•Systemic immunological activity finds its expression in significantly reduced clonality of CLL samples whereas mutation rate is comparable.