ADAL02

Listing of Anti-Drug Antibody Data for Treatment Emergent ADA Positive Patients

Output

Standard Listing
Data Setup

Preview
Try this using WebR

Code

lsting <- as_listing(
  out,
  key_cols = "USUBJID",
  disp_cols = names(out),
  main_title = paste0(
    "Listing of Anti-", drugcd, " Antibody Data for Treatment Emergent ADA Positive Patients, PK Population",
    "\nProtocol: ", unique(adab$PARCAT1)[1]
  ),
  subtitles = paste("\nTreatment Group:", trt),
  
  main_footer = "Minimum reportable titer = 1.10 (example only)
--- = No sample evaluated
ADA = Anti-Drug Antibodies (is also referred to as ATA, or Anti-Therapeutic Antibodies)
Number of patients positive for Treatment Emergent ADA = the number of post-baseline evaluable patients determined to have treatment-induced ADA or treatment-enhanced ADA during the study period.
Treatment-induced ADA = a patient with negative or missing baseline ADA result(s) and at least one positive post-baseline ADA result.
Treatment-enhanced ADA = a patient with positive ADA result at baseline who has one or more post-baseline titer results that are at least 0.60 t.u. greater than the baseline titer result.
Transient ADA = ADA positive result detected (a) at only one post-baseline sampling timepoint (excluding last timepoint) OR (b) at 2 or more timepoints during treatment where the first and last ADA positive samples  are separated by a period of < 16 weeks, irrespective of any negative samples in between.
Persistent ADA =  ADA positive result detected (a) at the last post-baseline sampling timepoint, OR (b) at 2 or more time points during treatment where the first and last ADA positive samples are separated by a period ≥ 16 weeks, irrespective of any negative samples in between.
Asterisk denotes sample that tested positive for Neutralizing Antibodies."
  
)

head(lsting, 20)

Listing of Anti-R1800000 Antibody Data for Treatment Emergent ADA Positive Patients, PK Population
Protocol: A: Drug X Antibody

Treatment Group: A: Drug X

—————————————————————————————————————————————————————
                         Day 2     Patient Treatment 
     Subject ID         (Day 1)   Emergent ADA Status
—————————————————————————————————————————————————————
AB12345-BRA-1-id-105      ---          Enhanced      
AB12345-BRA-1-id-134      ---          Enhanced      
 AB12345-BRA-1-id-42      ---          Enhanced      
 AB12345-BRA-1-id-93      ---          Enhanced      
AB12345-BRA-11-id-217     ---          Enhanced      
AB12345-BRA-11-id-345     ---          Enhanced      
AB12345-BRA-11-id-397     ---          Enhanced      
AB12345-BRA-11-id-50      ---          Enhanced      
AB12345-BRA-13-id-177     ---          Enhanced      
AB12345-BRA-14-id-23      ---          Enhanced      
AB12345-BRA-15-id-36      ---          Enhanced      
AB12345-BRA-2-id-296      ---          Enhanced      
AB12345-BRA-6-id-369      ---          Enhanced      
 AB12345-CAN-1-id-18      ---          Enhanced      
AB12345-CAN-11-id-139     ---          Enhanced      
AB12345-CAN-14-id-104     ---          Enhanced      
AB12345-CHN-1-id-119      ---          Enhanced      
AB12345-CHN-1-id-123      ---          Enhanced      
AB12345-CHN-1-id-133      ---          Enhanced      
AB12345-CHN-1-id-199      ---          Enhanced      
—————————————————————————————————————————————————————

Minimum reportable titer = 1.10 (example only)
--- = No sample evaluated
ADA = Anti-Drug Antibodies (is also referred to as ATA, or Anti-Therapeutic Antibodies)
Number of patients positive for Treatment Emergent ADA = the number of post-baseline evaluable patients determined to have treatment-induced ADA or treatment-enhanced ADA during the study period.
Treatment-induced ADA = a patient with negative or missing baseline ADA result(s) and at least one positive post-baseline ADA result.
Treatment-enhanced ADA = a patient with positive ADA result at baseline who has one or more post-baseline titer results that are at least 0.60 t.u. greater than the baseline titer result.
Transient ADA = ADA positive result detected (a) at only one post-baseline sampling timepoint (excluding last timepoint) OR (b) at 2 or more timepoints during treatment where the first and last ADA positive samples  are separated by a period of < 16 weeks, irrespective of any negative samples in between.
Persistent ADA =  ADA positive result detected (a) at the last post-baseline sampling timepoint, OR (b) at 2 or more time points during treatment where the first and last ADA positive samples are separated by a period ≥ 16 weeks, irrespective of any negative samples in between.
Asterisk denotes sample that tested positive for Neutralizing Antibodies.

Experimental use!

WebR is a tool allowing you to run R code in the web browser. Modify the code below and click run to see the results. Alternatively, copy the code and click here to open WebR in a new tab.

Code

library(dplyr)
library(rlistings)

adab <- random.cdisc.data::cadab %>%
  filter(NFRLT %% 1 == 0 & NFRLT > 0)

trt <- "A: Drug X"
drug_a <- "A: Drug X Antibody"
drugcd <- unique(adab$PARAMCD[adab$PARAM == "Antibody titer units"])[1]
min_titer <- 1.10

adab_x <- adab %>%
  filter(
    ARM == trt,
    PARCAT1 == drug_a,
    ADPBLPFL == "Y"
  ) %>%
  select(-PARAMCD, -AVALC, -AVALU, -ARRLT, -NRRLT) %>%
  unique() %>%
  tidyr::pivot_wider(
    names_from = PARAM,
    values_from = AVAL
  ) %>%
  filter(if_any(matches("Treatment Emergent - Positive"), ~ .x == 1)) %>%
  # filter(`Treatment Emergent - Positive` == 1) %>%
  mutate(
    VISN = factor(paste0(
      VISIT, "\n(Day ",
      ifelse(
        NFRLT %% 1 == 0,
        NFRLT,
        as.character(format(round(NFRLT, 2), nsmall = 2))
      ),
      ")"
    )),
    PTES = ifelse(
      ifelse("Treatment induced ADA" %in% names(.), `Treatment induced ADA` == 1, FALSE),
      ifelse(
        "Transient ADA" %in% names(.) & `Transient ADA` == 1,
        "Induced (Transient)",
        "Induced (Persistent)"
      ),
      "Enhanced"
    )
  ) %>%
  mutate(
    AVAL = paste0(
      ifelse(
        ifelse("ADA interpreted per sample result" %in% names(.), `ADA interpreted per sample result` == 0, FALSE),
        "NEGATIVE",
        ifelse(
          ifelse("Antibody titer units" %in% names(.), !is.na(`Antibody titer units`), FALSE),
          ifelse(
            `Antibody titer units` < min_titer,
            paste0("<", format(min_titer, nsmall = 2)),
            as.character(format(round(`Antibody titer units`, 2), nsmall = 2))
          ),
          "---"
        )
      ),
      ifelse(
        ifelse("NAB interpreted per sample result" %in% names(.), `NAB interpreted per sample result` == 1, FALSE),
        "*",
        ""
      )
    )
  )

out <- adab_x %>%
  select(USUBJID, VISN, AVAL, PTES) %>%
  tidyr::pivot_wider(
    names_from = VISN,
    values_from = AVAL
  ) %>%
  select(USUBJID, unique(adab_x$VISN[order(adab_x$NFRLT)]), PTES)

var_labels(out) <- names(out)

out <- out %>%
  var_relabel(
    USUBJID = "Subject ID",
    PTES = "Patient Treatment\nEmergent ADA Status"
  )

Reproducibility

Timestamp

[1] "2024-12-21 18:02:56 UTC"

Session Info

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14)
 os       Ubuntu 22.04.5 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2024-12-21
 pandoc   3.4 @ /usr/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package           * version date (UTC) lib source
 backports           1.5.0   2024-05-23 [1] RSPM
 brio                1.1.5   2024-04-24 [1] RSPM
 checkmate           2.3.2   2024-07-29 [1] RSPM
 cli                 3.6.3   2024-06-21 [1] RSPM
 codetools           0.2-20  2024-03-31 [2] CRAN (R 4.4.1)
 curl                6.0.1   2024-11-14 [1] RSPM
 digest              0.6.37  2024-08-19 [1] RSPM
 dplyr             * 1.1.4   2023-11-17 [1] RSPM
 evaluate            1.0.1   2024-10-10 [1] RSPM
 fastmap             1.2.0   2024-05-15 [1] RSPM
 formatters        * 0.5.9   2024-09-12 [1] RSPM
 generics            0.1.3   2022-07-05 [1] RSPM
 glue                1.8.0   2024-09-30 [1] RSPM
 htmltools           0.5.8.1 2024-04-04 [1] RSPM
 htmlwidgets         1.6.4   2023-12-06 [1] RSPM
 jsonlite            1.8.9   2024-09-20 [1] RSPM
 knitr               1.49    2024-11-08 [1] RSPM
 lifecycle           1.0.4   2023-11-07 [1] RSPM
 magrittr            2.0.3   2022-03-30 [1] RSPM
 pillar              1.10.0  2024-12-17 [1] RSPM
 pkgcache            2.2.3   2024-09-12 [1] RSPM
 pkgconfig           2.0.3   2019-09-22 [1] RSPM
 processx            3.8.4   2024-03-16 [1] RSPM
 ps                  1.8.1   2024-10-28 [1] RSPM
 purrr               1.0.2   2023-08-10 [1] RSPM
 R6                  2.5.1   2021-08-19 [1] RSPM
 random.cdisc.data   0.3.16  2024-10-10 [1] RSPM
 rlang               1.1.4   2024-06-04 [1] RSPM
 rlistings         * 0.2.9   2024-06-20 [1] RSPM
 rmarkdown           2.29    2024-11-04 [1] RSPM
 sessioninfo         1.2.2   2021-12-06 [1] any (@1.2.2)
 stringi             1.8.4   2024-05-06 [1] RSPM
 stringr             1.5.1   2023-11-14 [1] RSPM
 testthat            3.2.2   2024-12-10 [1] RSPM
 tibble            * 3.2.1   2023-03-20 [1] RSPM
 tidyr               1.3.1   2024-01-24 [1] RSPM
 tidyselect          1.2.1   2024-03-11 [1] RSPM
 vctrs               0.6.5   2023-12-01 [1] RSPM
 withr               3.0.2   2024-10-28 [1] RSPM
 xfun                0.49    2024-10-31 [1] RSPM
 yaml                2.3.10  2024-07-26 [1] RSPM

 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library

──────────────────────────────────────────────────────────────────────────────

`.lock` file

Download the .lock file and use renv::restore() on it to recreate environment used to generate this website.

Download

Output

Reproducibility

Timestamp

Session Info

.lock file

`.lock` file