Correct guideline abbreviation - AMP/ASCO/CAP

sigven · Jul 13, 2024 · 7a11279 · 7a11279
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diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@ The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for
 
 - Variant classification
   - according to *oncogenicity*: evaluating the oncogenic potential of somatic DNA aberrations (VICC/CGC/ClinGen guidelines)
-  - according to *actionability*: mapping the therapeutic, diagnostic, and prognostic implications of somatic DNA aberrations (ACMG/AMP guidelines)
+  - according to *actionability*: mapping the therapeutic, diagnostic, and prognostic implications of somatic DNA aberrations (AMP/ASCO/CAP guidelines)
 - Tumor mutational burden (TMB) estimation
 - Mutational signature analysis
 - Microsatellite instability (MSI) classification

diff --git a/pcgrr/R/acmg.R b/pcgrr/R/acmg.R
@@ -325,7 +325,7 @@ assign_acmg_tiers <- function(
     results_acmg[['biomarker_evidence']][['tier_classification']] <-
       tier_classification |>
       dplyr::rename(ACTIONABILITY_TIER = .data$ACMG_AMP_TIER) |>
-      dplyr::mutate(ACTIONABILITY_FRAMEWORK = "ACMG_AMP") |>
+      dplyr::mutate(ACTIONABILITY_FRAMEWORK = "AMP_ASCO_CAP") |>
       # dplyr::mutate(TIER_DESCRIPTION = dplyr::case_when(
       #   TIER == 1 ~ "Variants of strong clinical significance",
       #   TIER == 2 ~ "Variants of potential clinical significance",

diff --git a/pcgrr/R/input_data.R b/pcgrr/R/input_data.R
@@ -834,13 +834,13 @@ load_dna_variants <- function(
 
 
     ## Assign each variant a tier according to
-    ## ACMG/AMP guidelines for clinical actionability
+    ## AMP/ASCO/CAP guidelines for clinical actionability
     ## of somatic variants
     if (variant_origin == "Somatic") {
 
       pcgrr::log4r_info(
         paste0("Assigning variants to tiers of clinical significance",
-               " - somatic actionability guidelines (ACMG/AMP)"))
+               " - somatic actionability guidelines (AMP/ASCO/CAP)"))
       results <- pcgrr::assign_acmg_tiers(
         vartype = vartype,
         variants_df = results$variant,

diff --git a/pcgrr/inst/templates/pcgr_quarto_report/documentation.qmd b/pcgrr/inst/templates/pcgr_quarto_report/documentation.qmd
@@ -91,7 +91,7 @@ Note also that for somatic copy number aberrations, we showcase potential oncoge
 
 #### Actionability classificaton
 
-Clinical actionability assessment of SNVs/InDels and gene copy number aberrations found in the tumor sample follows recommendation guidelines by ACMG/AMP [@Li2017-ew]. Specifically, different levels  of actionability are implemented in the following manner:
+Clinical actionability assessment of SNVs/InDels and gene copy number aberrations found in the tumor sample follows recommendation guidelines by AMP/ASCO/CAP [@Li2017-ew]. Specifically, different levels  of actionability are implemented in the following manner:
 
 - **TIER 1: Variants of strong clinical significance** - constitutes aberrations linked to predictive, prognostic, or diagnostic biomarkers in the [CIViC database](http://civic.genome.wustl.edu) and the [Cancer Biomarkers Database](https://www.cancergenomeinterpreter.org/biomarkers) that are
 	 - Found within the same tumor type/class as specified by the user, **AND**

diff --git a/pcgrr/inst/templates/pcgr_quarto_report/snv_indel/actionability.qmd b/pcgrr/inst/templates/pcgr_quarto_report/snv_indel/actionability.qmd
@@ -1,9 +1,9 @@
 ### Variant classification - actionability
 
 Acquired SNVs and InDels in the tumor sample have been assessed for
-_clinical actionability_ through an implementation of ACMG/AMP guidelines [@Li2017-ew]. We use CIViC and CGI [@Griffith2017-do;@Tamborero2018-aj] as the underlying sources for actionable variants (versions indicated [below](#documentation)). 
+_clinical actionability_ through an implementation of AMP/ASCO/CAP guidelines [@Li2017-ew]. We use CIViC and CGI [@Griffith2017-do;@Tamborero2018-aj] as the underlying sources for actionable variants (versions indicated [below](#documentation)). 
 
-The tabset below indicates which variants have been classified into three distinct _tiers of clinical significance_ according to ACMG/AMP criteria.
+The tabset below indicates which variants have been classified into three distinct _tiers of clinical significance_ according to AMP/ASCO/CAP criteria.
 
 ::: {.callout-note}
 ## Note - biomarker matching

diff --git a/pcgrr/pkgdown/index.md b/pcgrr/pkgdown/index.md
@@ -11,7 +11,7 @@ The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for
 
 - Variant classification
   - according to *oncogenicity*: evaluating the oncogenic potential of somatic DNA aberrations (VICC/CGC/ClinGen guidelines)
-  - according to *actionability*: mapping the therapeutic, diagnostic, and prognostic implications of somatic DNA aberrations (ACMG/AMP guidelines)
+  - according to *actionability*: mapping the therapeutic, diagnostic, and prognostic implications of somatic DNA aberrations (AMP/ASCO/CAP guidelines)
 - Tumor mutational burden (TMB) estimation
 - Mutational signature analysis
 - Microsatellite instability (MSI) classification

diff --git a/pcgrr/vignettes/output.Rmd b/pcgrr/vignettes/output.Rmd
@@ -28,11 +28,11 @@ by the user. The following sections may be included in the report:
 	   variant types and consequences
 	* Variants are classified with respect to _oncogenicity_ (VICC/ClinGen/CGC operating procedures)
 	   - permits exploration of somatic mutations through interactive filtering according to several dimensions (variant sequencing depth/support, variant consequence etc.)
-	* Variants are classified with respect to _actionability_ (ACMG/AMP guidelines)
+	* Variants are classified with respect to _actionability_ (AMP/ASCO/CAP guidelines)
 	   - individual evidence items linked to actionable variants can be explored, indicating strength of evidence, tumor type and therapeutic context, and clinical significance
 
 3. __Somatic CNAs__
-	* Aberrations are classified with respect to _actionability_ (ACMG/AMP guidelines)
+	* Aberrations are classified with respect to _actionability_ (AMP/ASCO/CAP guidelines)
 	 - individual evidence items linked to actionable variants can be explored, indicating strength of evidence, tumor type and therapeutic context, and clinical significance
 	* Other potentially oncogenic aberrations are listed, pProto-oncogenes subject to copy number amplifications, and tumor suppressor genes subject to homozygous deletions
 
@@ -280,12 +280,12 @@ The following variables are included in the TSV file (VCF tags issued by the use
 | 19. `VAF_CONTROL` | Variant allele fraction at variant position in control sample |
 | 20. `MUTATION_HOTSPOT` | Mutation hotspot annotation |
 | 21. `MUTATION_HOTSPOT_CANCERTYPE` | Mutation hotspot-associated cancer types (from cancerhotspots.org) |
-| 22. `ACTIONABILITY_TIER` | Actionability tier - ACMG/AMP implementation |
-| 23. `ACTIONABILITY` | Actionability annotation - ACMG/AMP implementation |
-| 24. `ACTIONABILITY_FRAMEWORK` | Actionability framework - ACMG/AMP implementation |
-| 25. `ONCOGENICITY` | Oncogenicity annotation - VICC/ClinGen SOP implementation |
-| 26. `ONCOGENICITY_CODE` | Oncogenicity code - VICC/ClinGen SOP implementation |
-| 27. `ONCOGENICITY_SCORE` | Oncogenicity score - VICC/ClinGen SOP implementation |
+| 22. `ACTIONABILITY_TIER` | Actionability tier - AMP/ASCO/CAP implementation |
+| 23. `ACTIONABILITY` | Actionability annotation - AMP/ASCO/CAP implementation |
+| 24. `ACTIONABILITY_FRAMEWORK` | Actionability framework - AMP/ASCO/CAP implementation |
+| 25. `ONCOGENICITY` | Oncogenicity annotation - VICC/ClinGen/CGC SOP implementation |
+| 26. `ONCOGENICITY_CODE` | Oncogenicity code - VICC/ClinGen/CGC SOP implementation |
+| 27. `ONCOGENICITY_SCORE` | Oncogenicity score - VICC/ClinGen/CGC SOP implementation |
 | 28. `HGVSc` | HGVS coding sequence name |
 | 29. `HGVSp` | HGVS protein sequence name |
 | 30. `CANONICAL` | Flag indicating if transcript is canonical |

diff --git a/pcgrr/vignettes/variant_classification.Rmd b/pcgrr/vignettes/variant_classification.Rmd
@@ -28,9 +28,9 @@ The following criteria are currently used for oncogenicity classification in PCG
     
 ## Actionability
 
-PCGR prioritizes and evaluates variants according to clinical actionability. Currently, PCGR implements its tier classification framework along the proposed ACMG/AMP guidelines, as detailed below.
+PCGR prioritizes and evaluates variants according to clinical actionability. Currently, PCGR implements its tier classification framework along the proposed AMP/ASCO/CAP guidelines, as detailed below.
 
-This tier model attempts to adopt concensus recommendations by ACMG, as outlined in [Li et al., 2017](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5707196/):
+This tier model attempts to adopt concensus recommendations by AMP/ASCO/CAP, as outlined in [Li et al., 2017](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5707196/):
 
  - *Tier 1: Variants of strong clinical significance* - constitutes variants linked to predictive, prognostic, or diagnostic evidence items in the [CIViC database](http://civic.genome.wustl.edu) or the [Cancer Biomarkers Database](https://www.cancergenomeinterpreter.org/biomarkers) that are
 	 - A: found within the same tumor type/class as specified by the user, AND