Science Advances

Supplementary Materials

This PDF file includes:

  • Materials and Methods
  • Fig. S1. The 5′UTR lengths of mouse IGHV transcripts.
  • Fig. S2. Antibody synthetic spike-in genes.
  • Fig. S3. Nucleotide sequence logos of the primer-binding regions of selected spike-in clones.
  • Fig. S4. Precise library quantification by linking qPCR to ddPCR.
  • Fig. S5. Annotated example of biological sequence obtained from MAF library preparation.
  • Fig. S6. Design of experiments (DoE) for library preparation optimization.
  • Fig. S7. Response surface methodology analysis of clonal frequency bias with uncorrected data.
  • Fig. S8. Response surface methodology analysis of CDR3 diversity.
  • Fig. S9. Response surface methodology analysis of clonal frequency bias with MAF-corrected data.
  • Fig. S10. Comparison of V-gene coverage using new reduced primer set (TAK) and previously published primer set (Reddy-2010).
  • Fig. S11. Schematic of multistage error correction pipeline.
  • Fig. S12. Flow chart of multistage error correction pipeline.
  • Fig. S13. Error correction effects on various bias correction methods.
  • Fig. S14. Bias correction using MAF V-gene bias factor.
  • Fig. S15. Comparison of bias correction with a new reduced primer set (TAK) and a previously published primer set (Reddy-2010).
  • Fig. S16. Comparison of V-gene (germlines) before and after MAF correction.
  • Fig. S17. The MAF bias factor across V-genes.
  • Fig. S18. Correlation of MAF bias correction factor across data sets.
  • Fig. S19. Nominal logistic regression modeling based on Ig-seq clonotype measurements.
    Fig. S20. Comparison of the sensitivity and specificity of the nominal logistic regression models.
  • Fig. S21. Comparison of factor correlations with prediction probabilities of the nominal logistic regression models.
  • Fig. S22. Various immune profiling metrics from MAF-corrected Ig-seq data.
  • Fig. S23. Processing time of reads for MAF error and bias correction pipeline.
  • Fig. S24. Effect of the number of reads analyzed using final MAF sample preparation conditions.
  • Table S1. Ig-seq read count statistics for spike-ins following replicate library preparation by singleplex PCR (see fig. S2, B and C).
  • Table S2. Ig-seq read count statistics following MAF library preparation by multiplex PCR (see Fig. 2A).
  • Table S3. A comparison of the VDJ annotation tool used in this study (modified from Laserson et al. (12) with IMGT HighV-Quest.
  • Table. S4. Ig-seq read count statistics for DoE for library preparation optimization.
  • Table S5. A complete list of primers and sequences used in this study.
  • Table S6. Error correction statistics for spike in clones.
  • Table S7. Expanded Ig-seq processing statistics.
  • Table S8. Synthetic genes used in this study.

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