ARTEMIS-DELFI samples detect 100% of samples with WGMAF>0.01
Last updated: 2025-03-27
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For each level of WGMAF, the fraction of samples detected by ARTEMIS-DELFI is indicated from .8-1 on the y axis.
library(cowplot)
library(here)
library(readxl)
library(tidyverse)suppl <- read_excel(here("data/supplementary_tables.xlsx"),
sheet = "Table S2", skip = 1)# Removing samples without WGMAF values
suppl <- suppl %>%
select(patient_id = Patient, sample_id = Sample, wgmaf = WGMAF, artemis_delfi_score = `ARTEMIS-DELFI Score`) %>%
filter(wgmaf != "-") %>%
mutate(wgmaf = as.numeric(wgmaf))
# Creating a column to indicate the post-tx samples from the exceptional responder to use as the ctDNA-free samples.
suppl <- suppl %>%
mutate(ctdna_free = case_when(patient_id == "CGPLPA223" & !(sample_id == "CGPLPA223P") ~ TRUE,
TRUE ~ FALSE))
# Counting the number of samples considered ctDNA-free
suppl %>%
filter(ctdna_free == TRUE) %>%
nrow[1] 14# Getting the maximum WGMAF of cfDNA-free samples. Samples with WGMAF above this level can be considered ctDNA+.
wgmaf_max_cancer_free <- suppl %>%
filter(ctdna_free == TRUE) %>%
.$wgmaf %>%
max
print(wgmaf_max_cancer_free) # Returns: 0.000283849. Anything above 0.001 would then easily test positive, using this threshold for the cumulative fraction detected figure.[1] 0.000283849# Getting the range of WGMAF of cfDNA-free samples. Samples with WGMAF above this level can be considered ctDNA+.
suppl %>%
filter(ctdna_free == TRUE) %>%
arrange(wgmaf)# A tibble: 14 × 5
patient_id sample_id wgmaf artemis_delfi_score ctdna_free
<chr> <chr> <dbl> <dbl> <lgl>
1 CGPLPA223 CGPLPA223P6 0 0.131 TRUE
2 CGPLPA223 CGPLPA223P10 0 0.0378 TRUE
3 CGPLPA223 CGPLPA223P12 0 0.0447 TRUE
4 CGPLPA223 CGPLPA223P16 0 0.0336 TRUE
5 CGPLPA223 CGPLPA223P14 0.0000526 0.0527 TRUE
6 CGPLPA223 CGPLPA223P7 0.0000632 0.0727 TRUE
7 CGPLPA223 CGPLPA223P8 0.0000679 0.0880 TRUE
8 CGPLPA223 CGPLPA223P15 0.0000712 0.0381 TRUE
9 CGPLPA223 CGPLPA223P11 0.0000829 0.0346 TRUE
10 CGPLPA223 CGPLPA223P3 0.0000872 0.0605 TRUE
11 CGPLPA223 CGPLPA223P2 0.0000933 0.0497 TRUE
12 CGPLPA223 CGPLPA223P18 0.000112 0.0278 TRUE
13 CGPLPA223 CGPLPA223P9 0.000118 0.0287 TRUE
14 CGPLPA223 CGPLPA223P17 0.000284 0.0307 TRUE # Getting the maximum ARTEMIS-DELFI score of cfDNA-free samples. Samples with ARTEMIS-DELFI score above this level can be considered ctDNA+.
artemis_delfi_max_cancer_free <- suppl %>%
filter(ctdna_free == TRUE) %>%
.$artemis_delfi_score %>%
max
# Computing the cumulative fraction of samples that test positive with ARTEMIS-DELFI across WGSMAF values from ~1 --> 0.001
suppl <- suppl %>%
mutate(wgmaf_positive = case_when(wgmaf > wgmaf_max_cancer_free ~ TRUE,
TRUE ~ FALSE)) %>%
mutate(artemis_delfi_positive = case_when(artemis_delfi_score > artemis_delfi_max_cancer_free ~ TRUE,
TRUE ~ FALSE)) %>%
filter(wgmaf_positive == TRUE) %>%
arrange(desc(wgmaf)) %>%
mutate(cumulative_eval = 1:n(),
cumulative_positive_artemis_delfi = cumsum(artemis_delfi_positive)) %>%
mutate(cumulative_frac_positive_artemis_delfi = cumulative_positive_artemis_delfi / cumulative_eval)# Plotting
ggplot(data = suppl, aes(x = wgmaf, y = cumulative_frac_positive_artemis_delfi)) +
geom_line() +
scale_x_continuous(trans = "log10",
breaks = c(0.1, 0.01, 0.001),
labels = c("0.1", "0.01", "0.001"),
guide = guide_axis_logticks()) +
theme_cowplot() +
xlab("WGMAF") +
ylab("Cumulative fraction of samples detected\nby ARTEMIS-DELFI")
# At least 95% of samples are detected above X WGMAF?
suppl %>% filter(cumulative_frac_positive_artemis_delfi >= 0.95) %>% .$wgmaf %>% tail(1)[1] 0.008297116# Get the cumulative fraction of positive samples with ARTEMIS-DELFI at WGMAF ≥ 0.001 (0.1%)
suppl %>% filter(wgmaf <= 0.001) %>% .$cumulative_frac_positive_artemis_delfi %>% head(1)[1] 0.8333333
sessionInfo()R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS 15.3.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[5] purrr_1.0.4 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[9] ggplot2_3.5.1 tidyverse_2.0.0 readxl_1.4.5 here_1.0.1
[13] cowplot_1.1.3 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] utf8_1.2.4 sass_0.4.9 generics_0.1.3 stringi_1.8.4
[5] hms_1.1.3 digest_0.6.37 magrittr_2.0.3 timechange_0.3.0
[9] evaluate_1.0.3 grid_4.4.1 fastmap_1.2.0 cellranger_1.1.0
[13] rprojroot_2.0.4 jsonlite_1.9.1 processx_3.8.6 whisker_0.4.1
[17] ps_1.9.0 promises_1.3.2 httr_1.4.7 scales_1.3.0
[21] jquerylib_0.1.4 cli_3.6.4 rlang_1.1.5 munsell_0.5.1
[25] withr_3.0.2 cachem_1.1.0 yaml_2.3.10 tools_4.4.1
[29] tzdb_0.4.0 colorspace_2.1-1 httpuv_1.6.15 vctrs_0.6.5
[33] R6_2.6.1 lifecycle_1.0.4 git2r_0.35.0 fs_1.6.5
[37] pkgconfig_2.0.3 callr_3.7.6 pillar_1.10.1 bslib_0.9.0
[41] later_1.4.1 gtable_0.3.6 glue_1.8.0 Rcpp_1.0.14
[45] xfun_0.51 tidyselect_1.2.1 rstudioapi_0.17.1 knitr_1.49
[49] farver_2.1.2 htmltools_0.5.8.1 labeling_0.4.3 rmarkdown_2.29
[53] compiler_4.4.1 getPass_0.2-4