Diffuse Large B-cell Lymphoma Cohort (Rosenwald et al. 2002)

Patient-level survival data and gene-expression signature scores from the diffuse large-B-cell lymphoma (DLBCL) cohort of Rosenwald et al. (2002). Used in the Cox-regression vignettes to demonstrate distributed Cox estimation under threshold FHE with sites partitioned by molecular subgroup.

Usage

data(DLBCL)

Format

A data frame with 235 observations on the following 12 variables:

ID: LYM patient identifier (integer).
Set: Original analysis set assignment, either "Training" or "Validation".
Subgroup: Molecular subgroup, a factor with levels "GCB" (germinal-center B-cell-like), "ABC" (activated B-cell-like), and "Type III" (unclassified).
IPI: International Prognostic Index group ("Low", "Medium", "High", or NA).
time: Follow-up time in years.
status: Vital status at last follow-up coded as 1 for death and 0 for alive at follow-up.
GCB_sig: Germinal-center B-cell signature score.
LN_sig: Lymph-node signature score.
Prolif_sig: Proliferation signature score.
BMP6: BMP6 expression score.
MHC2_sig: MHC class II signature score.
Score: Outcome predictor score combining the four signatures and BMP6, as published.

Source

The Lymphoma/Leukemia Molecular Profiling Project release of the Rosenwald et al. (2002) study, file DLBCL_patient_data_NEW.txt at https://llmpp.ccr.cancer.gov/DLBCL/; processed by data-raw/DLBCL.R.

Details

Each row represents one patient. The four signature columns and BMP6 are carried over as published, without further scaling. GCB_sig, LN_sig, Prolif_sig and MHC2_sig are averages of median-centered log-ratio expression values over the genes of each signature; BMP6 is the median-centered log ratio of the single gene BMP6 (Rosenwald et al. 2002, Supplementary Appendix 1). Following Bayle, Fan and Lou (2025), the five patients with zero follow-up time are excluded, so the cohort spans 235 patients with 133 deaths (event rate 56.6%) over a median follow-up of 2.8 years. The molecular-subgroup partition gives three sites of unequal size: GCB (n=115, 54 deaths), ABC (n=71, 49 deaths), and Type III (n=49, 30 deaths).

The vignettes use Subgroup as the site boundary for distributed Cox estimation; the partition is a choice made for the demonstration. Stratified Cox regression with strata(Subgroup) factors the partial log-likelihood additively across the three subgroups, which is exactly the decomposition the master/worker protocol exploits.

References

Rosenwald, A., Wright, G., Chan, W. C., et al. (2002). The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. New England Journal of Medicine 346(25), 1937–1947. doi:10.1056/NEJMoa012914

Bayle, P., Fan, J., and Lou, Z. (2025). Communication-Efficient Distributed Estimation and Inference for Cox's Model. Journal of the American Statistical Association. doi:10.1080/01621459.2025.2516820

Examples

data(DLBCL)
table(DLBCL$Subgroup, DLBCL$status)
#>           
#>             0  1
#>   GCB      61 54
#>   ABC      22 49
#>   Type III 19 30

## Stratified Cox fit on the four signatures and BMP6
if (requireNamespace("survival", quietly = TRUE)) {
  fit <- survival::coxph(
    survival::Surv(time, status) ~ GCB_sig + LN_sig + Prolif_sig +
      BMP6 + MHC2_sig + survival::strata(Subgroup),
    data = DLBCL)
  print(fit)
}
#> Call:
#> survival::coxph(formula = survival::Surv(time, status) ~ GCB_sig + 
#>     LN_sig + Prolif_sig + BMP6 + MHC2_sig + survival::strata(Subgroup), 
#>     data = DLBCL)
#> 
#>                coef exp(coef) se(coef)      z        p
#> GCB_sig    -0.26387   0.76807  0.11940 -2.210 0.027112
#> LN_sig     -0.25436   0.77541  0.08515 -2.987 0.002816
#> Prolif_sig  0.30313   1.35408  0.14981  2.023 0.043036
#> BMP6        0.30364   1.35478  0.10728  2.830 0.004649
#> MHC2_sig   -0.31915   0.72677  0.09413 -3.391 0.000698
#> 
#> Likelihood ratio test=42.74  on 5 df, p=4.174e-08
#> n= 235, number of events= 133