CSR junction analysis using CSreport

B-cells ensure humoral immune responses due to the production of antigen (Ag) -specific memory B-cells and antibody secreting plasma cells. In secondary lymphoïd organs, B-cell Ag-driven activation induces terminal maturation and the immunoglobulin (Ig) isotype class switch (class switch recombination, CSR). CSR create a virtually unique IgH locus in every B cell clone by intra-chromosomal recombination between two switch (S) regions upstream of each constant (C) segment encoding the Ig constant region. Amount and structural features of CSR junctions reveal precious information on CSR mechanism and analysis of CSR junctions is frequent in basic and clinical research studies of B-cell functions because. To overcome the lack of automatic tool able to analyze large data-sets of CSR junction sequences produced by high throughput sequencing (HTS) we designed CSReport, a computational program dedicated to support analysis of CSR recombination junctions sequenced with a HTS-based protocol (Ion Torrent technology). CSReport was assessed on a simulated dataset of CSR junctions and then used for analysis of Sµ-Sa or Sµ-S?1 junctions from CH12F3 cells or primary murine B-cells. CSReport provides definition of junction segment breakpoints on sequence reference and junction structure (blunt-ended junction or junction with insertion or microhomology). CSReport use will permit to reduce differences among CSR junction studies induced by several alignment methods and due to personal interpretation in the delineation of junction characteristics. Our results show CSReport is an accurate tool for analysis of sequences from our HTS based protocol for CSR junction, facilitating and accelerating the study of CSR junctions.