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Additional file 2: Table S1. Clinical features of 378 patients in the training and validation cohort whose DLBCL biopsies were sequenced and 290 patients whose sequencing results showed sufficient sequence reads. Table S2. Comparisons of clinicopathologic and molecular characteristics between patients with germinal-center B-cell–like (GCB) DLBCL with a low or high degree of somatic hypermutation (SHM) in immunoglobulin variable region genes. Table S3. Comparisons of clinicopathologic and molecular characteristics between patients with activated B-cell-like (ABC) subtype of DLBCL with a low or high degree of SHM in immunoglobulin variable region genes. Table S4. Significant prognostic effects of immunoglobulin molecular characteristics in DLBCL patients treated with R-CHOP by multivariate survival analysis. Table S5. Clinicopathologic and molecular characteristics of patients with DLBCL with a short or long immunoglobulin heavy/light chain CDR3 length. Table S6. Clinicopathologic and molecular characteristics of patients with DLBCL with ongoing SHM in immunoglobulin variable region genes. Table S7. Gene signatures associated with SHM in immunoglobulin sequences of DLBCL samples. Table S8. Multiple testing corrections for prognostic effects found in the overall cohort of DLBCL treated with R-CHOP by the Benjamini-Hochberg method with a false discovery rate of 0.10

Additional file 2: Table S1. Clinical features of 378 patients in the training and validation cohort whose DLBCL biopsies were sequenced and 290 patients whose sequencing results showed sufficient sequence reads. Table S2. Comparisons of clinicopathologic and molecular characteristics between patients with germinal-center B-cellâ like (GCB) DLBCL with a low or high degree of somatic hypermutation (SHM) in immunoglobulin variable region genes. Table S3. Comparisons of clinicopathologic and molecular characteristics between patients with activated B-cell-like (ABC) subtype of DLBCL with a low or high degree of SHM in immunoglobulin variable region genes. Table S4. Significant prognostic effects of immunoglobulin molecular characteristics in DLBCL patients treated with R-CHOP by multivariate survival analysis. Table S5. Clinicopathologic and molecular characteristics of patients with DLBCL with a short or long immunoglobulin heavy/light chain CDR3 length. Table S6. Clinicopathologic and molecular characteristics of patients with DLBCL with ongoing SHM in immunoglobulin variable region genes. Table S7. Gene signatures associated with SHM in immunoglobulin sequences of DLBCL samples. Table S8. Multiple testing corrections for prognostic effects found in the overall cohort of DLBCL treated with R-CHOP by the Benjamini-Hochberg method with a false discovery rate of 0.10

Table S1. Supplementary table. (PDF 37 kb)

Additional file 1: Fig S1.. Construction and clinical outcome of the diffuse large B-cell lymphoma (DLBCL) cohort. Fig. S2. Diagram showing numbers of cases in this mutation study that have been characterized by various biomarker studies, and survival rates of patients whose sequencing results were correlated with prognosis. Fig. S3. CONSORT flow diagram illustrating the number of cases performed for high-throughput IG sequencing and clonal sequence analysis. Fig. S4. Molecular characterization for immunoglobulin heavy chain (IGH) gene usage in the study cohort. Fig. S5. Immunoglobulin heavy chain V gene (IGHV) somatic hypermutation (SHM) analysis. Fig. S6. Analysis for length of heavy chain CDR3. Fig. S7. Prediction of MHC-binding peptides and frequency of T-cell exposed motifs (TCEM) for immunoglobulin diagnostic sequences in the training set and validation set. (a) Regional distribution of relatively rare neoantigens derived from heavy chain and light chain immunoglobulin genes in DLBCL patients in the training set (top) and validation set (bottom). (b) Cases with high degree of heavy chain or light chain IGV SHM compared with cases without had higher frequency of relatively rare TCEM in the training (left) and validation sets (right). (c) In ABC-DLBCL, high IGV SHM was associated with lower tissue cellularity of CD4+ T cells. Fig. S8. Moleclar analysis for immunoglobulin heavy chain ongoing SHM and light chain SHM. Fig. S9. Immunoglobulin light chain SHM and CDR3 analysis. Fig S10. Comparison between different subsets of DLBCL. Fig S11. Light chain IGK/LV ongoing SHM analysis.

Additional file 2: Table S1. Clinical features of 378 patients in the training and validation cohort whose DLBCL biopsies were sequenced and 290 patients whose sequencing results showed sufficient sequence reads. Table S2. Comparisons of clinicopathologic and molecular characteristics between patients with germinal-center B-cell–like (GCB) DLBCL with a low or high degree of somatic hypermutation (SHM) in immunoglobulin variable region genes. Table S3. Comparisons of clinicopathologic and molecular characteristics between patients with activated B-cell-like (ABC) subtype of DLBCL with a low or high degree of SHM in immunoglobulin variable region genes. Table S4. Significant prognostic effects of immunoglobulin molecular characteristics in DLBCL patients treated with R-CHOP by multivariate survival analysis. Table S5. Clinicopathologic and molecular characteristics of patients with DLBCL with a short or long immunoglobulin heavy/light chain CDR3 length. Table S6. Clinicopathologic and molecular characteristics of patients with DLBCL with ongoing SHM in immunoglobulin variable region genes. Table S7. Gene signatures associated with SHM in immunoglobulin sequences of DLBCL samples. Table S8. Multiple testing corrections for prognostic effects found in the overall cohort of DLBCL treated with R-CHOP by the Benjamini-Hochberg method with a false discovery rate of 0.10

Table S1. Supplementary table. (PDF 37 kb)

Additional file 1: Fig S1.. Construction and clinical outcome of the diffuse large B-cell lymphoma (DLBCL) cohort. Fig. S2. Diagram showing numbers of cases in this mutation study that have been characterized by various biomarker studies, and survival rates of patients whose sequencing results were correlated with prognosis. Fig. S3. CONSORT flow diagram illustrating the number of cases performed for high-throughput IG sequencing and clonal sequence analysis. Fig. S4. Molecular characterization for immunoglobulin heavy chain (IGH) gene usage in the study cohort. Fig. S5. Immunoglobulin heavy chain V gene (IGHV) somatic hypermutation (SHM) analysis. Fig. S6. Analysis for length of heavy chain CDR3. Fig. S7. Prediction of MHC-binding peptides and frequency of T-cell exposed motifs (TCEM) for immunoglobulin diagnostic sequences in the training set and validation set. (a) Regional distribution of relatively rare neoantigens derived from heavy chain and light chain immunoglobulin genes in DLBCL patients in the training set (top) and validation set (bottom). (b) Cases with high degree of heavy chain or light chain IGV SHM compared with cases without had higher frequency of relatively rare TCEM in the training (left) and validation sets (right). (c) In ABC-DLBCL, high IGV SHM was associated with lower tissue cellularity of CD4+ T cells. Fig. S8. Moleclar analysis for immunoglobulin heavy chain ongoing SHM and light chain SHM. Fig. S9. Immunoglobulin light chain SHM and CDR3 analysis. Fig S10. Comparison between different subsets of DLBCL. Fig S11. Light chain IGK/LV ongoing SHM analysis.

Figures S1 and S2. Supplementary figures. (PDF 1473 kb)