Leucegene Validation
Last updated: 2020-06-11
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Knit directory: MINTIE-paper-analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | a166ab8 | Marek Cmero | 2020-05-08 | Build site. |
| html | a600688 | Marek Cmero | 2020-05-07 | Build site. |
| Rmd | 0fde0b8 | Marek Cmero | 2020-05-07 | Added RCH B-ALL analysis |
| html | 1c40e33 | Marek Cmero | 2020-05-07 | Build site. |
| Rmd | bbc278a | Marek Cmero | 2020-05-07 | Refactoring |
| html | 87b4e62 | Marek Cmero | 2020-05-07 | Build site. |
| Rmd | af503f2 | Marek Cmero | 2020-05-07 | Refactoring |
| html | 5c045b5 | Marek Cmero | 2020-05-07 | Build site. |
| Rmd | d8d5b96 | Marek Cmero | 2020-05-07 | Added Leucegene variant validation |
| html | 90c7fd9 | Marek Cmero | 2020-05-06 | Build site. |
| Rmd | 44d8c37 | Marek Cmero | 2020-05-06 | Build leucegene validation notebook. |
| Rmd | ff4b1dc | Marek Cmero | 2020-05-06 | Leucegene results |
# util
library(data.table)
library(dplyr)
library(here)
library(stringr)
# plotting/tables
library(ggplot2)
library(gt)options(stringsAsFactors = FALSE)source(here("code/leucegene_helper.R"))Leucegene Validation
Here we analyse the results of MINTIE run on a number of Leucegene samples, including the effect of controls on a cohort with KMT2A-PTD variants. We also check whether MINTIE has called known variants within the cohort.
# load SRX to patient ID lookup table
kmt2a_patient_lookup <- read.delim(here("data/leucegene/sample_info/KMT2A-PTD_samples.txt"),
header = FALSE,
col.names = c("sample", "patient"))
kmt2a_results_dir <- here("data/leucegene/KMT2A-PTD_results")
# load KMT2A cohort comparisons against all other controls
kmt2a_results <- load_controls_comparison(kmt2a_results_dir)
kmt2a_results <- inner_join(kmt2a_results, kmt2a_patient_lookup, by = "sample")
# load other validation reults and truth table
truth <- read.delim(here("data/leucegene/sample_info/variant_validation_table.tsv"), sep = "\t")
leucegene_results_dir <- here("data/leucegene/validation_results")
validation <- list.files(leucegene_results_dir, full.names = TRUE) %>%
lapply(., read.delim) %>%
rbindlist() %>%
filter(logFC > 5)KMT2A-PTD controls comparison
MINTIE paper Supplementary Figure 2. Shows the number of variant genes found in the Leucegene cohort containing KMT2A PTDs.
results_summary <- get_results_summary(mutate(kmt2a_results,
sample = patient,
group_var = controls),
group_var_name = "controls")
# build table
results_summary %>%
group_by(controls) %>%
summarise(min = min(V1), median = median(V1), max = max(V1)) %>%
data.frame() %>%
gt() %>%
tab_header(
title = md("**Total variant genes called using different controls**")
) %>%
cols_label(
controls = md("**Controls**"),
min = md("**Min**"),
median = md("**Median**"),
max = md("**Max**")
) | Total variant genes called using different controls | |||
|---|---|---|---|
| Controls | Min | Median | Max |
| AML_controls | 131 | 215.0 | 2151 |
| normal_controls | 268 | 525.5 | 2437 |
| normal_controls_reduced | 506 | 811.5 | 2637 |
ggplot(results_summary, aes(sample, V1, fill = controls)) +
geom_bar(position = position_dodge2(width = 0.9, preserve = "single"), stat = "identity") +
theme_bw() +
xlab("") +
ylab("Genes with variants") +
coord_flip() +
theme(legend.position = "bottom") +
scale_fill_brewer(palette="Dark2",
labels = c("AML_controls" = "13 AMLs",
"normal_controls" = "13 normals",
"normal_controls_reduced" = "3 normals"))
KMT2A variants found in cohort
MINTIE paper Supplementary Table 1. Shows whether MINITE found a KMT2A SV in each sample for the given control group. Coverage obtained from Audemard et al. spreadsheet containing the Leucegene results must be manually added to data/leucegene/sample_info to run the code.
# load results from km paper for coverage of KMT2A PTDs
kmt2a_lgene_km_results <- read.csv(here("data/leucegene/sample_info/KMT2A-PTD_8-2.fa.xls"), sep="\t") %>%
mutate(patient = Sample) %>%
group_by(patient) %>%
summarise(coverage = max(Min.coverage))
# check whether MINTIE found a KMT2A SV in each control set
found_using_cancon <- get_samples_with_kmt2a_sv(kmt2a_results, "AML_controls")
found_using_norcon <- get_samples_with_kmt2a_sv(kmt2a_results, "normal_controls")
found_using_redcon <- get_samples_with_kmt2a_sv(kmt2a_results, "normal_controls_reduced")
# make the table
kmt2a_control_comp <- inner_join(kmt2a_patient_lookup, kmt2a_lgene_km_results, by = "patient") %>%
arrange(desc(coverage))
kmt2a_control_comp$`13_AMLs` <- kmt2a_control_comp$sample %in% found_using_cancon
kmt2a_control_comp$`13_normals` <- kmt2a_control_comp$sample %in% found_using_norcon
kmt2a_control_comp$`3_normals` <- kmt2a_control_comp$sample %in% found_using_redcon
# build output table
kmt2a_control_comp %>%
gt() %>%
cols_label(
sample = md("**Sample**"),
patient = md("**Patient**"),
coverage = md("**Coverage**"),
`13_AMLs` = md("**13 AMLs**"),
`13_normals` = md("**13 Normals**"),
`3_normals` = md("**3 Normals**")
) %>%
tab_header(
title = md("**KMT2A PTDs found in Leucegene cohort**")
) %>%
tab_options(
table.font.size = 12
) %>%
tab_style(
style = cell_fill(color = "lightgreen"),
locations = cells_body(
columns = vars(`13_AMLs`),
rows = `13_AMLs`)
) %>%
tab_style(
style = cell_fill(color = "lightgreen"),
locations = cells_body(
columns = vars(`13_normals`),
rows = `13_normals`)
) %>%
tab_style(
style = cell_fill(color = "lightgreen"),
locations = cells_body(
columns = vars(`3_normals`),
rows = `3_normals`)
)| KMT2A PTDs found in Leucegene cohort | |||||
|---|---|---|---|---|---|
| Sample | Patient | Coverage | 13 AMLs | 13 Normals | 3 Normals |
| SRX958906 | 07H152 | 158 | TRUE | TRUE | TRUE |
| SRX332646 | 09H115 | 125 | TRUE | TRUE | TRUE |
| SRX957230 | 06H146 | 87 | TRUE | TRUE | TRUE |
| SRX957223 | 05H111 | 79 | TRUE | TRUE | TRUE |
| SRX332659 | 11H021 | 63 | TRUE | TRUE | TRUE |
| SRX332633 | 05H050 | 58 | TRUE | TRUE | TRUE |
| SRX959061 | 13H150 | 58 | TRUE | TRUE | TRUE |
| SRX959044 | 13H048 | 57 | TRUE | TRUE | TRUE |
| SRX958974 | 10H070 | 53 | TRUE | TRUE | TRUE |
| SRX958963 | 10H007 | 50 | TRUE | TRUE | TRUE |
| SRX958959 | 09H106 | 49 | TRUE | TRUE | TRUE |
| SRX959060 | 13H141 | 45 | TRUE | TRUE | TRUE |
| SRX958945 | 09H058 | 29 | TRUE | TRUE | TRUE |
| SRX958907 | 07H155 | 23 | TRUE | TRUE | TRUE |
| SRX381854 | 08H112 | 22 | TRUE | TRUE | TRUE |
| SRX332645 | 09H113 | 17 | TRUE | TRUE | TRUE |
| SRX959001 | 11H183 | 16 | FALSE | FALSE | FALSE |
| SRX381852 | 08H012 | 15 | FALSE | FALSE | FALSE |
| SRX958932 | 08H138 | 15 | FALSE | FALSE | FALSE |
| SRX381865 | 11H008 | 13 | FALSE | FALSE | FALSE |
| SRX958873 | 06H048 | 10 | FALSE | FALSE | FALSE |
| SRX958922 | 08H063 | 6 | FALSE | FALSE | FALSE |
| SRX958961 | 10H001 | 6 | FALSE | FALSE | FALSE |
| SRX958844 | 04H111 | 3 | FALSE | FALSE | FALSE |
Leucegene variants found by MINTIE
# add KMT2A results against AML controls as validation
validation <- validation %>% select(-logCPM) # remove logCPM col for backwards compatibility with older runs
validation <- filter(kmt2a_results, controls == "AML_controls") %>%
select(-c(controls, patient)) %>%
select(colnames(validation)) %>%
rbind(., validation)
rowwise(truth) %>%
mutate(found = is_variant_in_sample(Experiment, gene1, gene2, variant, validation)) %>%
data.frame() %>%
gt() %>%
tab_header(
title = md("**Variants found in Leucegene cohort**")
) %>%
cols_label(
patient_ID = md("**Patient**"),
Experiment = md("**Experiment**"),
gene1 = md("**Gene 1**"),
gene2 = md("**Gene 2**"),
variant = md("**Variant**"),
cohort = md("**Cohort**"),
found = md("**Found**")
) %>%
tab_options(
table.font.size = 12
) %>%
tab_style(
style = cell_fill(color = "lightgreen"),
locations = cells_body(
columns = vars(found),
rows = found)
)| Variants found in Leucegene cohort | ||||||
|---|---|---|---|---|---|---|
| Patient | Experiment | Gene 1 | Gene 2 | Variant | Cohort | Found |
| 03H065 | SRX729615 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 03H083 | SRX729616 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 03H095 | SRX729602 | CBFB | MYH11 | fusion | CBF | TRUE |
| 03H109 | SRX729580 | CBFB | MYH11 | fusion | CBF | TRUE |
| 03H112 | SRX729581 | CBFB | MYH11 | fusion | CBF | TRUE |
| 03H112 | SRX729581 | FLT3 | ITD | CBF | TRUE | |
| 04H030 | SRX729603 | CBFB | MYH11 | fusion | CBF | TRUE |
| 04H061 | SRX729582 | CBFB | MYH11 | fusion | CBF | TRUE |
| 04H091 | SRX729583 | CBFB | MYH11 | fusion | CBF | TRUE |
| 05H042 | SRX729617 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 05H099 | SRX958862 | CBFB | MYH11 | fusion | CBF | TRUE |
| 05H113 | SRX729604 | CBFB | MYH11 | fusion | CBF | TRUE |
| 05H118 | SRX729618 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 05H136 | SRX729605 | CBFB | MYH11 | fusion | CBF | TRUE |
| 05H184 | SRX729619 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 06H020 | SRX729606 | CBFB | MYH11 | fusion | CBF | TRUE |
| 06H035 | SRX729620 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 06H115 | SRX729607 | CBFB | MYH11 | fusion | CBF | TRUE |
| 07H099 | SRX381851 | CBFB | MYH11 | fusion | CBF | TRUE |
| 07H137 | SRX729621 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 07H144 | SRX729585 | CBFB | MYH11 | fusion | CBF | TRUE |
| 08H034 | SRX729622 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 08H042 | SRX729623 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 08H072 | SRX729624 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 08H072 | SRX729624 | FLT3 | ITD | CBF | TRUE | |
| 08H081 | SRX729586 | CBFB | MYH11 | fusion | CBF | TRUE |
| 08H099 | SRX729608 | CBFB | MYH11 | fusion | CBF | TRUE |
| 09H016 | SRX729587 | CBFB | MYH11 | fusion | CBF | FALSE |
| 09H040 | SRX729625 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 09H066 | SRX729588 | CBFB | MYH11 | fusion | CBF | TRUE |
| 10H008 | SRX729609 | CBFB | MYH11 | fusion | CBF | TRUE |
| 10H030 | SRX729626 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 10H119 | SRX729627 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 11H022 | SRX729610 | CBFB | MYH11 | fusion | CBF | TRUE |
| 11H022 | SRX729610 | FLT3 | ITD | CBF | FALSE | |
| 11H104 | SRX729589 | CBFB | MYH11 | fusion | CBF | TRUE |
| 11H107 | SRX729628 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 11H179 | SRX729611 | CBFB | MYH11 | fusion | CBF | TRUE |
| 12H042 | SRX729590 | CBFB | MYH11 | fusion | CBF | FALSE |
| 12H044 | SRX729591 | CBFB | MYH11 | fusion | CBF | TRUE |
| 12H045 | SRX729629 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 12H098 | SRX729630 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 12H165 | SRX729592 | CBFB | MYH11 | fusion | CBF | TRUE |
| 12H166 | SRX729631 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 12H180 | SRX729632 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 12H183 | SRX729633 | RUNX11 | RUNX1T1 | fusion | CBF | TRUE |
| 13H066 | SRX729612 | CBFB | MYH11 | fusion | CBF | TRUE |
| 13H120 | SRX959058 | CBFB | MYH11 | fusion | CBF | TRUE |
| 13H169 | SRX959064 | RUNX11 | RUNX1T1 | fusion | CBF | FALSE |
| 04H111 | SRX958844 | KMT2A | PTD | KMT2A-PTD | FALSE | |
| 05H050 | SRX332633 | KMT2A | PTD | KMT2A-PTD | TRUE | |
| 05H111 | SRX957223 | KMT2A | PTD | KMT2A-PTD | TRUE | |
| 06H048 | SRX958873 | KMT2A | PTD | KMT2A-PTD | FALSE | |
| 06H146 | SRX957230 | KMT2A | PTD | KMT2A-PTD | TRUE | |
| 07H152 | SRX958906 | KMT2A | PTD | KMT2A-PTD | FALSE | |
| 07H155 | SRX958907 | KMT2A | PTD | KMT2A-PTD | FALSE | |
| 08H012 | SRX381852 | KMT2A | PTD | KMT2A-PTD | FALSE | |
| 08H063 | SRX958922 | KMT2A | PTD | KMT2A-PTD | FALSE | |
| 08H112 | SRX381854 | KMT2A | PTD | KMT2A-PTD | TRUE | |
| 08H138 | SRX958932 | KMT2A | PTD | KMT2A-PTD | FALSE | |
| 09H058 | SRX958945 | KMT2A | PTD | KMT2A-PTD | TRUE | |
| 09H106 | SRX958959 | KMT2A | PTD | KMT2A-PTD | TRUE | |
| 09H113 | SRX332645 | KMT2A | PTD | KMT2A-PTD | TRUE | |
| 09H115 | SRX332646 | KMT2A | PTD | KMT2A-PTD | FALSE | |
| 10H001 | SRX958961 | KMT2A | PTD | KMT2A-PTD | FALSE | |
| 10H007 | SRX958963 | KMT2A | PTD | KMT2A-PTD | TRUE | |
| 10H070 | SRX958974 | KMT2A | PTD | KMT2A-PTD | TRUE | |
| 11H008 | SRX381865 | KMT2A | PTD | KMT2A-PTD | FALSE | |
| 11H021 | SRX332659 | KMT2A | PTD | KMT2A-PTD | FALSE | |
| 11H183 | SRX959001 | KMT2A | PTD | KMT2A-PTD | FALSE | |
| 13H048 | SRX959044 | KMT2A | PTD | KMT2A-PTD | TRUE | |
| 13H141 | SRX959060 | KMT2A | PTD | KMT2A-PTD | TRUE | |
| 13H150 | SRX959061 | KMT2A | PTD | KMT2A-PTD | FALSE | |
| 03H041 | SRX332627 | NUP98 | NSD1 | fusion | NUP98-NSD1 | TRUE |
| 03H041 | SRX332627 | FLT3 | ITD | NUP98-NSD1 | TRUE | |
| 05H034 | SRX958856 | NUP98 | NSD1 | fusion | NUP98-NSD1 | TRUE |
| 05H163 | SRX332635 | NUP98 | NSD1 | fusion | NUP98-NSD1 | TRUE |
| 08H049 | SRX958915 | NUP98 | NSD1 | fusion | NUP98-NSD1 | TRUE |
| 08H049 | SRX958915 | FLT3 | ITD | NUP98-NSD1 | TRUE | |
| 10H038 | SRX381861 | NUP98 | NSD1 | fusion | NUP98-NSD1 | TRUE |
| 11H027 | SRX958987 | NUP98 | NSD1 | fusion | NUP98-NSD1 | TRUE |
| 11H027 | SRX958987 | FLT3 | ITD | NUP98-NSD1 | TRUE | |
| 11H160 | SRX332667 | NUP98 | NSD1 | fusion | NUP98-NSD1 | TRUE |
| 11H160 | SRX332667 | FLT3 | ITD | NUP98-NSD1 | TRUE | |
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /config/RStudio/R/3.6.1/lib64/R/lib/libRblas.so
LAPACK: /config/RStudio/R/3.6.1/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] gt_0.2.1 ggplot2_3.3.1 stringr_1.4.0 here_0.1
[5] dplyr_1.0.0 data.table_1.12.6
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 RColorBrewer_1.1-2 pillar_1.4.4
[4] compiler_3.6.1 git2r_0.26.1 workflowr_1.4.0
[7] tools_3.6.1 digest_0.6.21 evaluate_0.14
[10] lifecycle_0.2.0 tibble_3.0.1 gtable_0.3.0
[13] checkmate_2.0.0 pkgconfig_2.0.3 rlang_0.4.6
[16] commonmark_1.7 yaml_2.2.0 xfun_0.10
[19] withr_2.1.2 knitr_1.25 generics_0.0.2
[22] fs_1.4.1 vctrs_0.3.1 sass_0.2.0
[25] rprojroot_1.3-2 grid_3.6.1 tidyselect_1.1.0
[28] glue_1.4.1 R6_2.4.0 rmarkdown_1.16
[31] farver_2.0.3 purrr_0.3.2 magrittr_1.5
[34] whisker_0.4 backports_1.1.4 scales_1.1.1
[37] ellipsis_0.3.0 htmltools_0.4.0 colorspace_1.4-1
[40] labeling_0.3 stringi_1.4.3 munsell_0.5.0
[43] crayon_1.3.4