From c1206abadd5a031c26ffcd45af8501e992b5f0bd Mon Sep 17 00:00:00 2001
From: msguixe <56801139+msguixe@users.noreply.github.com>
Date: Thu, 22 Jan 2026 15:25:26 +0100
Subject: [PATCH 1/3] Enhance GENIE dataset documentation

Added detailed description and notes about the GENIE dataset, including data sources, version, and important notes regarding synonymous mutations.
---
 docs/Datasets/General_datasets/GENIE.md | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/docs/Datasets/General_datasets/GENIE.md b/docs/Datasets/General_datasets/GENIE.md
index 4ee30b3fb..7121fe13c 100644
--- a/docs/Datasets/General_datasets/GENIE.md
+++ b/docs/Datasets/General_datasets/GENIE.md
@@ -1,5 +1,28 @@
 # GENIE
 
 ## Description
+A dataset of many panel sequencing samples (>170 000) from many institutions in many countries.  
+[Dataset website](https://genie.synapse.org/Explore/GENIE).  
+Data downloaded from [sypanspe.org](synapse.org).  
+[Here](https://docs.google.com/presentation/d/18MMDAOfSa3rRfApb8obhicyIU2n60aGcM9QA_2lMbao/edit?slide=id.p#slide=id.p) 
+you can find a Google Slides document with some details about the GENIE dataset.  
+GENIE contains panels from MSKCC IMPACT (>80%), DFCI, UCSC, VHIO, etc.
+Many of them are without a normal-matched control.
+Some panels are on hotspots instead of the whole gene.
+Overall, the MSKCC IMPACT panel data is the most complete one, 
+with a normal-match control and covering ~500 cancer-related genes.
+
+Downloaded data is in this path: ```/data/bbg/datasets/intogen/input/data/cancer/panels/GENIE/```  
+The latest version downloaded is GENIE v.15 (syn53210170).  
+Take into account that some IMPACT panel data could be duplicated in the cbioportal panel data download: 
+```/data/bbg/datasets/intogen/input/data/cancer/panels/cbioportal/```.
+The IMPACT panels from cbioportal have more clinical data.   
+
+**Important note**
+> This dataset has synonymous mutations filtered. It cannot be used for intOGen.
+
 
 ## Reference
+Mònica Sánchez Guixé  
+Santi Demajo  
+Abel González Perez

From 8e6d50360b507f8aa18f40ee3a85d0526d405c15 Mon Sep 17 00:00:00 2001
From: msguixe <56801139+msguixe@users.noreply.github.com>
Date: Thu, 22 Jan 2026 15:49:49 +0100
Subject: [PATCH 2/3] Change important note to a heading

Updated heading for important note section.
---
 docs/Datasets/General_datasets/GENIE.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/Datasets/General_datasets/GENIE.md b/docs/Datasets/General_datasets/GENIE.md
index 7121fe13c..b754e8e47 100644
--- a/docs/Datasets/General_datasets/GENIE.md
+++ b/docs/Datasets/General_datasets/GENIE.md
@@ -18,7 +18,7 @@ Take into account that some IMPACT panel data could be duplicated in the cbiopor
 ```/data/bbg/datasets/intogen/input/data/cancer/panels/cbioportal/```.
 The IMPACT panels from cbioportal have more clinical data.   
 
-**Important note**
+### Important note
 > This dataset has synonymous mutations filtered. It cannot be used for intOGen.
 
 

From ca02f1316a7d3814804ee95a448ed71eff203751 Mon Sep 17 00:00:00 2001
From: msguixe <56801139+msguixe@users.noreply.github.com>
Date: Thu, 22 Jan 2026 14:50:03 +0000
Subject: [PATCH 3/3] chore: fix linting issues

---
 docs/Datasets/General_datasets/GENIE.md | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/docs/Datasets/General_datasets/GENIE.md b/docs/Datasets/General_datasets/GENIE.md
index b754e8e47..353c7ac87 100644
--- a/docs/Datasets/General_datasets/GENIE.md
+++ b/docs/Datasets/General_datasets/GENIE.md
@@ -1,28 +1,30 @@
 # GENIE
 
 ## Description
+
 A dataset of many panel sequencing samples (>170 000) from many institutions in many countries.  
 [Dataset website](https://genie.synapse.org/Explore/GENIE).  
 Data downloaded from [sypanspe.org](synapse.org).  
-[Here](https://docs.google.com/presentation/d/18MMDAOfSa3rRfApb8obhicyIU2n60aGcM9QA_2lMbao/edit?slide=id.p#slide=id.p) 
+[Here](https://docs.google.com/presentation/d/18MMDAOfSa3rRfApb8obhicyIU2n60aGcM9QA_2lMbao/edit?slide=id.p#slide=id.p)
 you can find a Google Slides document with some details about the GENIE dataset.  
 GENIE contains panels from MSKCC IMPACT (>80%), DFCI, UCSC, VHIO, etc.
 Many of them are without a normal-matched control.
 Some panels are on hotspots instead of the whole gene.
-Overall, the MSKCC IMPACT panel data is the most complete one, 
+Overall, the MSKCC IMPACT panel data is the most complete one,
 with a normal-match control and covering ~500 cancer-related genes.
 
 Downloaded data is in this path: ```/data/bbg/datasets/intogen/input/data/cancer/panels/GENIE/```  
 The latest version downloaded is GENIE v.15 (syn53210170).  
-Take into account that some IMPACT panel data could be duplicated in the cbioportal panel data download: 
+Take into account that some IMPACT panel data could be duplicated in the cbioportal panel data download:
 ```/data/bbg/datasets/intogen/input/data/cancer/panels/cbioportal/```.
-The IMPACT panels from cbioportal have more clinical data.   
+The IMPACT panels from cbioportal have more clinical data.
 
 ### Important note
+>
 > This dataset has synonymous mutations filtered. It cannot be used for intOGen.
 
-
 ## Reference
+
 Mònica Sánchez Guixé  
 Santi Demajo  
 Abel González Perez