diff --git a/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.nb.html b/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.nb.html
index 00e0aa76b8..78c3da71f6 100644
--- a/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.nb.html
+++ b/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.nb.html
@@ -3117,7 +3117,7 @@ Does seg.mean agree with status?
geom_jitter()
-
+
diff --git a/analyses/focal-cn-file-preparation/03-add-cytoband-status-consensus.nb.html b/analyses/focal-cn-file-preparation/03-add-cytoband-status-consensus.nb.html
index f9122021e6..b70fcef66e 100644
--- a/analyses/focal-cn-file-preparation/03-add-cytoband-status-consensus.nb.html
+++ b/analyses/focal-cn-file-preparation/03-add-cytoband-status-consensus.nb.html
@@ -3115,7 +3115,7 @@ Display and save final table
diff --git a/analyses/focal-cn-file-preparation/04-prepare-cn-file.R b/analyses/focal-cn-file-preparation/04-prepare-cn-file.R
index 28453dfec5..eabfbed61f 100644
--- a/analyses/focal-cn-file-preparation/04-prepare-cn-file.R
+++ b/analyses/focal-cn-file-preparation/04-prepare-cn-file.R
@@ -240,9 +240,10 @@ cnv_no_xy <- cnv_df %>%
# Merge and annotated no X&Y
autosome_annotated_cn <- process_annotate_overlaps(cnv_df = cnv_no_xy,
txdb_exons = tx_exons) %>%
- # mark possible amplifications in autosomes
+ # mark possible amplifications and deep loss in autosomes
dplyr::mutate(status = dplyr::case_when(
copy_number > (2 * ploidy) ~ "amplification",
+ copy_number == 0 ~ "deep deletion",
TRUE ~ status
))
@@ -264,7 +265,13 @@ if (xy_flag) {
# Merge and annotated no X&Y
sex_chrom_annotated_cn <- process_annotate_overlaps(cnv_df = cnv_sex_chrom,
- txdb_exons = tx_exons)
+ txdb_exons = tx_exons) %>%
+ # mark possible deep loss in sex chromosome
+ dplyr::mutate(status = dplyr::case_when(
+ copy_number == 0 ~ "deep deletion",
+ TRUE ~ status
+ ))
+
# Add germline sex estimate into this data.frame
sex_chrom_annotated_cn <- sex_chrom_annotated_cn %>%
diff --git a/analyses/focal-cn-file-preparation/05-define-most-focal-cn-units.nb.html b/analyses/focal-cn-file-preparation/05-define-most-focal-cn-units.nb.html
index 93693eef81..06fffed5a6 100644
--- a/analyses/focal-cn-file-preparation/05-define-most-focal-cn-units.nb.html
+++ b/analyses/focal-cn-file-preparation/05-define-most-focal-cn-units.nb.html
@@ -3172,7 +3172,7 @@ Determine cytoband status
@@ -3243,7 +3243,7 @@ Determine gene-level status
diff --git a/analyses/focal-cn-file-preparation/06-find-recurrent-calls.nb.html b/analyses/focal-cn-file-preparation/06-find-recurrent-calls.nb.html
index 0ab3d5bd9c..40918c762a 100644
--- a/analyses/focal-cn-file-preparation/06-find-recurrent-calls.nb.html
+++ b/analyses/focal-cn-file-preparation/06-find-recurrent-calls.nb.html
@@ -3064,7 +3064,7 @@ Tally the sample counts of each unique status call by region.
@@ -3093,7 +3093,7 @@ Tally the sample counts of each unique status call by region and short histo
@@ -3124,7 +3124,7 @@ Plot the distribution of counts
)
-
+
# Save plot
@@ -3158,7 +3158,7 @@ Plot the distribution of counts
)
-
+
# Save plot
@@ -3187,7 +3187,7 @@ All histologies represented
@@ -3207,7 +3207,7 @@ Separated by histology
@@ -3228,7 +3228,7 @@ Combine all histology recurrent data with the data separated by histology
diff --git a/analyses/focal-cn-file-preparation/README.md b/analyses/focal-cn-file-preparation/README.md
index 469720e8ac..af3ea82bee 100644
--- a/analyses/focal-cn-file-preparation/README.md
+++ b/analyses/focal-cn-file-preparation/README.md
@@ -45,7 +45,8 @@ See the notebook for more information. This notebook also prepares lists of copy
| biospecimen_id | status | copy_number | ploidy | ensembl | gene_symbol | cytoband |
|----------------|--------|-------------|--------|---------|-------------|---------|
- Any segment that is copy neutral is filtered out of this table. In addition, [any segments with copy number > (2 * ploidy) are marked as amplifications](https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/e2058dd43d9b1dd41b609e0c3429c72f79ff3be6/analyses/focal-cn-file-preparation/03-prepare-cn-file.R#L275) in the `status` column.
+ Any segment that is copy neutral is filtered out of this table. In addition, [any segments with copy number > (2 * ploidy) are marked as amplifications](https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/e2058dd43d9b1dd41b609e0c3429c72f79ff3be6/analyses/focal-cn-file-preparation/03-prepare-cn-file.R#L275) in the `status` column.
+Any segments with copy number == 0 are marked as deep deletions in the `status` column.
* `05-define-most-focal-cn-units.Rmd` - This notebook defines the _most focal_ recurrent copy number units by removing focal changes that are within entire chromosome arm losses and gains.
_Most focal_ here meaning if a chromosome arm is not clearly defined as a gain or loss (and is callable) we look to define the cytoband level status.
diff --git a/analyses/focal-cn-file-preparation/plots/all_histology_cn_counts.png b/analyses/focal-cn-file-preparation/plots/all_histology_cn_counts.png
index d588d527a3..afd7f347d3 100644
Binary files a/analyses/focal-cn-file-preparation/plots/all_histology_cn_counts.png and b/analyses/focal-cn-file-preparation/plots/all_histology_cn_counts.png differ
diff --git a/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_autosomes_stranded_loss_cor_plot.png b/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_autosomes_stranded_loss_cor_plot.png
index 3bac698a1a..587b262547 100644
Binary files a/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_autosomes_stranded_loss_cor_plot.png and b/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_autosomes_stranded_loss_cor_plot.png differ
diff --git a/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_autosomes_stranded_stacked_plot.png b/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_autosomes_stranded_stacked_plot.png
index 391fd47d51..3ae788f374 100644
Binary files a/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_autosomes_stranded_stacked_plot.png and b/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_autosomes_stranded_stacked_plot.png differ
diff --git a/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_loss_cor_plot.png b/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_loss_cor_plot.png
index 694eb0863f..c4f247d17b 100644
Binary files a/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_loss_cor_plot.png and b/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_loss_cor_plot.png differ
diff --git a/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_stacked_plot.png b/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_stacked_plot.png
index 8995dac4a3..2cf5a7d205 100644
Binary files a/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_stacked_plot.png and b/analyses/focal-cn-file-preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_stacked_plot.png differ
diff --git a/analyses/focal-cn-file-preparation/plots/separate_histology_cn_counts.png b/analyses/focal-cn-file-preparation/plots/separate_histology_cn_counts.png
index 054ecbfa26..91b46b4dcb 100644
Binary files a/analyses/focal-cn-file-preparation/plots/separate_histology_cn_counts.png and b/analyses/focal-cn-file-preparation/plots/separate_histology_cn_counts.png differ
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_autosomes.tsv.gz b/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_autosomes.tsv.gz
index b0cf3adf34..cab576171d 100644
Binary files a/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_autosomes.tsv.gz and b/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_autosomes.tsv.gz differ
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_x_and_y.tsv.gz b/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_x_and_y.tsv.gz
index f58ca6ca83..e659b414d9 100644
Binary files a/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_x_and_y.tsv.gz and b/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_x_and_y.tsv.gz differ
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_most_focal_cn_status.tsv.gz b/analyses/focal-cn-file-preparation/results/consensus_seg_most_focal_cn_status.tsv.gz
index e83cd496b6..a4a1ae7664 100644
Binary files a/analyses/focal-cn-file-preparation/results/consensus_seg_most_focal_cn_status.tsv.gz and b/analyses/focal-cn-file-preparation/results/consensus_seg_most_focal_cn_status.tsv.gz differ
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_recurrent_focal_cn_units.tsv b/analyses/focal-cn-file-preparation/results/consensus_seg_recurrent_focal_cn_units.tsv
index 60aef32e0d..6d28a9612a 100644
--- a/analyses/focal-cn-file-preparation/results/consensus_seg_recurrent_focal_cn_units.tsv
+++ b/analyses/focal-cn-file-preparation/results/consensus_seg_recurrent_focal_cn_units.tsv
@@ -2417,11 +2417,11 @@ ADM loss All 11 gene
ADM loss HGAT 5 gene
ADM2 loss All 4 gene
ADORA1 gain All 4 gene
-ADORA2A loss All 13 gene
-ADORA2A loss ATRT 6 gene
+ADORA2A loss All 12 gene
+ADORA2A loss ATRT 5 gene
ADORA2A loss LGAT 4 gene
-ADORA2A-AS1 loss All 14 gene
-ADORA2A-AS1 loss ATRT 6 gene
+ADORA2A-AS1 loss All 13 gene
+ADORA2A-AS1 loss ATRT 5 gene
ADORA2A-AS1 loss LGAT 4 gene
ADRA1D gain All 6 gene
ADRM1 gain All 16 gene
@@ -2434,7 +2434,6 @@ AEBP2 loss All 6 gene
AEBP2 loss HGAT 5 gene
AFAP1 gain All 4 gene
AFAP1-AS1 gain All 4 gene
-AFDN loss All 4 gene
AFG3L1P gain All 4 gene
AFG3L1P loss All 21 gene
AFG3L1P loss HGAT 10 gene
@@ -2458,10 +2457,10 @@ AGO2 gain HGAT 4 gene
AGPAT2 gain All 7 gene
AGPAT3 gain All 8 gene
AGPAT5 gain All 16 gene
-AGPAT5 loss All 13 gene
+AGPAT5 loss All 12 gene
AGPAT5 gain Medulloblastoma 4 gene
AGPAT5 loss HGAT 5 gene
-AGPAT5 loss Medulloblastoma 7 gene
+AGPAT5 loss Medulloblastoma 6 gene
AGRN loss All 14 gene
AGRN loss Meningioma 4 gene
AGRP gain All 7 gene
@@ -2469,12 +2468,12 @@ AGRP loss All 8 gene
AGRP loss HGAT 6 gene
AHCTF1 gain All 5 gene
AHCYL1 loss All 4 gene
-AHDC1 loss All 6 gene
+AHDC1 loss All 5 gene
AHNAK2 gain All 5 gene
AHNAK2 loss All 11 gene
AHNAK2 loss HGAT 7 gene
AHSP gain All 7 gene
-AHSP loss All 6 gene
+AHSP loss All 5 gene
AIFM3 gain All 7 gene
AIFM3 loss All 37 gene
AIFM3 gain HGAT 4 gene
@@ -2596,10 +2595,10 @@ ANAPC11 gain Medulloblastoma 8 gene
ANAPC2 gain All 7 gene
ANG gain All 5 gene
ANGPT2 gain All 16 gene
-ANGPT2 loss All 13 gene
+ANGPT2 loss All 12 gene
ANGPT2 gain Medulloblastoma 4 gene
ANGPT2 loss HGAT 5 gene
-ANGPT2 loss Medulloblastoma 7 gene
+ANGPT2 loss Medulloblastoma 6 gene
ANGPT4 loss All 6 gene
ANGPT4 loss HGAT 4 gene
ANGPTL8 gain All 4 gene
@@ -2689,8 +2688,8 @@ API5 loss Ependymoma 4 gene
APLNR gain All 4 gene
APOBEC1 gain All 6 gene
APOBEC3A loss All 9 gene
-APOBEC3B loss All 9 gene
-APOBEC3B-AS1 loss All 7 gene
+APOBEC3B loss All 8 gene
+APOBEC3B-AS1 loss All 6 gene
APOBEC3C loss All 4 gene
APOBEC3D loss All 4 gene
APOBEC3F loss All 4 gene
@@ -2784,7 +2783,7 @@ ARL8A gain HGAT 4 gene
ARMC10 gain All 17 gene
ARMC10 gain Medulloblastoma 6 gene
ARMC5 gain All 8 gene
-ARMC5 loss All 6 gene
+ARMC5 loss All 5 gene
ARMC9 gain All 6 gene
ARMS2 loss All 4 gene
ARPC1A gain All 12 gene
@@ -2847,11 +2846,9 @@ ASPSCR1 gain Medulloblastoma 8 gene
ASXL1 gain All 9 gene
ATAD3A loss All 15 gene
ATAD3A loss Meningioma 4 gene
-ATAD3B loss All 16 gene
-ATAD3B loss HGAT 4 gene
+ATAD3B loss All 15 gene
ATAD3B loss Meningioma 4 gene
-ATAD3C loss All 16 gene
-ATAD3C loss HGAT 4 gene
+ATAD3C loss All 15 gene
ATAD3C loss Meningioma 4 gene
ATAD5 gain All 5 gene
ATAD5 loss All 4 gene
@@ -2986,7 +2983,7 @@ BCCIP loss All 10 gene
BCCIP loss HGAT 4 gene
BCKDHB loss All 4 gene
BCKDK gain All 8 gene
-BCKDK loss All 6 gene
+BCKDK loss All 5 gene
BCL2L1 gain All 10 gene
BCL2L11 gain All 4 gene
BCL2L11 gain HGAT 4 gene
@@ -2999,9 +2996,9 @@ BCL6B loss All 4 gene
BCL7B gain All 13 gene
BCL7B gain HGAT 5 gene
BCL7C gain All 8 gene
-BCL7C loss All 6 gene
+BCL7C loss All 5 gene
BCL9 gain All 5 gene
-BCR loss All 8 gene
+BCR loss All 7 gene
BDNF loss All 4 gene
BDNF-AS loss All 4 gene
BDP1 gain All 5 gene
@@ -3029,9 +3026,8 @@ BISPR gain All 5 gene
BLACE gain All 9 gene
BLACE gain HGAT 4 gene
BLK gain All 12 gene
-BLK loss All 8 gene
+BLK loss All 7 gene
BLK gain HGAT 4 gene
-BLK loss Medulloblastoma 4 gene
BLMH gain All 5 gene
BLMH loss All 4 gene
BLOC1S4 gain All 4 gene
@@ -3153,7 +3149,7 @@ C14orf93 loss All 5 gene
C15orf40 gain All 4 gene
C15orf54 loss All 4 gene
C16orf58 gain All 8 gene
-C16orf58 loss All 6 gene
+C16orf58 loss All 5 gene
C16orf70 gain All 6 gene
C16orf70 loss All 8 gene
C16orf70 loss HGAT 6 gene
@@ -3249,8 +3245,8 @@ C21orf91 loss All 7 gene
C21orf91 loss HGAT 7 gene
C21orf91-OT1 loss All 6 gene
C21orf91-OT1 loss HGAT 6 gene
-C22orf15 loss All 14 gene
-C22orf15 loss ATRT 5 gene
+C22orf15 loss All 13 gene
+C22orf15 loss ATRT 4 gene
C22orf23 loss All 5 gene
C22orf31 loss All 6 gene
C22orf34 loss All 24 gene
@@ -3299,12 +3295,11 @@ C8G gain All 7 gene
C8orf31 gain All 11 gene
C8orf31 gain HGAT 4 gene
C8orf49 gain All 9 gene
-C8orf49 loss All 8 gene
-C8orf49 loss Medulloblastoma 4 gene
+C8orf49 loss All 7 gene
C8orf74 gain All 11 gene
-C8orf74 loss All 9 gene
+C8orf74 loss All 8 gene
C8orf74 gain HGAT 4 gene
-C8orf74 loss Medulloblastoma 5 gene
+C8orf74 loss Medulloblastoma 4 gene
C8orf82 loss All 5 gene
C8orf86 gain All 4 gene
C9orf116 gain All 7 gene
@@ -3330,8 +3325,8 @@ CA9 gain All 5 gene
CAAP1 loss All 6 gene
CAAP1 loss HGAT 5 gene
CAB39 gain All 7 gene
-CABIN1 loss All 14 gene
-CABIN1 loss ATRT 6 gene
+CABIN1 loss All 13 gene
+CABIN1 loss ATRT 5 gene
CABLES2 gain All 16 gene
CABLES2 gain HGAT 7 gene
CABP7 loss All 4 gene
@@ -3368,7 +3363,6 @@ CAMSAP1 gain All 8 gene
CAMSAP1 gain HGAT 4 gene
CAMSAP2 gain All 5 gene
CAMSAP2 gain HGAT 4 gene
-CAMTA1 loss All 4 gene
CANT1 gain All 16 gene
CANT1 gain Medulloblastoma 8 gene
CANX gain All 4 gene
@@ -3507,7 +3501,7 @@ CCDC188 loss Ependymoma 6 gene
CCDC188 loss LGAT 4 gene
CCDC188 loss Meningioma 5 gene
CCDC189 gain All 8 gene
-CCDC189 loss All 6 gene
+CCDC189 loss All 5 gene
CCDC194 gain All 5 gene
CCDC200 gain All 24 gene
CCDC200 loss All 4 gene
@@ -3575,13 +3569,13 @@ CCL3 gain All 22 gene
CCL3 loss All 5 gene
CCL3 gain Medulloblastoma 18 gene
CCL3L1 gain All 6 gene
-CCL3L1 loss All 6 gene
+CCL3L1 loss All 5 gene
CCL3L1 gain Medulloblastoma 4 gene
CCL4 gain All 22 gene
CCL4 loss All 5 gene
CCL4 gain Medulloblastoma 18 gene
CCL4L2 gain All 11 gene
-CCL4L2 loss All 6 gene
+CCL4L2 loss All 5 gene
CCL4L2 gain Medulloblastoma 9 gene
CCL5 gain All 22 gene
CCL5 loss All 6 gene
@@ -3619,9 +3613,9 @@ CD164L2 loss All 5 gene
CD27 gain All 8 gene
CD27-AS1 gain All 8 gene
CD2BP2 gain All 8 gene
-CD2BP2 loss All 5 gene
+CD2BP2 loss All 4 gene
CD2BP2-DT gain All 8 gene
-CD2BP2-DT loss All 5 gene
+CD2BP2-DT loss All 4 gene
CD300LG gain All 14 gene
CD300LG loss All 4 gene
CD300LG gain Medulloblastoma 10 gene
@@ -3714,15 +3708,21 @@ CDK5RAP3 gain All 8 gene
CDK5RAP3 gain Medulloblastoma 6 gene
CDK7 gain All 7 gene
CDK9 loss All 5 gene
+CDKN2A deep deletion All 4 gene
CDKN2A gain All 4 gene
-CDKN2A loss All 21 gene
-CDKN2A loss HGAT 12 gene
+CDKN2A loss All 18 gene
+CDKN2A deep deletion HGAT 4 gene
+CDKN2A loss HGAT 9 gene
+CDKN2B deep deletion All 4 gene
CDKN2B gain All 4 gene
-CDKN2B loss All 21 gene
-CDKN2B loss HGAT 12 gene
+CDKN2B loss All 18 gene
+CDKN2B deep deletion HGAT 4 gene
+CDKN2B loss HGAT 9 gene
+CDKN2B-AS1 deep deletion All 4 gene
CDKN2B-AS1 gain All 5 gene
-CDKN2B-AS1 loss All 22 gene
-CDKN2B-AS1 loss HGAT 12 gene
+CDKN2B-AS1 loss All 19 gene
+CDKN2B-AS1 deep deletion HGAT 4 gene
+CDKN2B-AS1 loss HGAT 9 gene
CDKN2B-AS1 loss LGAT 4 gene
CDKN2C loss All 7 gene
CDKN2D gain All 5 gene
@@ -3831,8 +3831,8 @@ CGN gain All 6 gene
CGN gain HGAT 4 gene
CHADL loss All 12 gene
CHADL loss Meningioma 5 gene
-CHCHD10 loss All 14 gene
-CHCHD10 loss ATRT 5 gene
+CHCHD10 loss All 13 gene
+CHCHD10 loss ATRT 4 gene
CHCHD2 gain All 18 gene
CHCHD2 gain HGAT 8 gene
CHCHD2 gain Medulloblastoma 4 gene
@@ -3923,9 +3923,9 @@ CLCC1 loss All 4 gene
CLDN15 gain All 9 gene
CLDN20 loss All 4 gene
CLDN23 gain All 12 gene
-CLDN23 loss All 8 gene
+CLDN23 loss All 7 gene
CLDN23 gain HGAT 4 gene
-CLDN23 loss Medulloblastoma 5 gene
+CLDN23 loss Medulloblastoma 4 gene
CLDN3 gain All 14 gene
CLDN3 gain HGAT 6 gene
CLDN4 gain All 14 gene
@@ -3980,7 +3980,7 @@ CLTCL1 loss LGAT 5 gene
CLTCL1 loss Meningioma 5 gene
CLUAP1 loss All 5 gene
CLUHP3 gain All 5 gene
-CLUHP3 loss All 6 gene
+CLUHP3 loss All 5 gene
CLUL1 loss All 5 gene
CMA1 loss All 4 gene
CMAS loss All 5 gene
@@ -4106,7 +4106,7 @@ CORO7-PAM16 loss All 5 gene
COX20 gain All 4 gene
COX4I2 gain All 10 gene
COX6A2 gain All 8 gene
-COX6A2 loss All 6 gene
+COX6A2 loss All 5 gene
CPD gain All 5 gene
CPD loss All 4 gene
CPEB4 gain All 4 gene
@@ -4246,7 +4246,7 @@ CTCF loss All 8 gene
CTCF loss HGAT 6 gene
CTDNEP1 loss All 4 gene
CTF1 gain All 8 gene
-CTF1 loss All 6 gene
+CTF1 loss All 5 gene
CTNNA3 loss All 9 gene
CTNNA3 loss HGAT 4 gene
CTNND1 gain All 4 gene
@@ -4257,8 +4257,7 @@ CTRL gain All 6 gene
CTRL loss All 8 gene
CTRL loss HGAT 6 gene
CTSB gain All 10 gene
-CTSB loss All 8 gene
-CTSB loss Medulloblastoma 4 gene
+CTSB loss All 7 gene
CTSD gain All 5 gene
CTSD loss All 5 gene
CTSD gain LGAT 4 gene
@@ -4358,7 +4357,7 @@ DCAF11 loss All 4 gene
DCAKD gain All 14 gene
DCAKD loss All 4 gene
DCAKD gain Medulloblastoma 10 gene
-DCBLD1 loss All 6 gene
+DCBLD1 loss All 5 gene
DCDC1 loss All 4 gene
DCDC2C gain All 5 gene
DCHS1 gain All 4 gene
@@ -4375,7 +4374,7 @@ DCTN5 loss All 5 gene
DCTN6 gain All 5 gene
DCTN6 loss All 6 gene
DCTPP1 gain All 8 gene
-DCTPP1 loss All 6 gene
+DCTPP1 loss All 5 gene
DCUN1D3 loss All 4 gene
DCUN1D4 gain All 5 gene
DCUN1D4 gain HGAT 5 gene
@@ -4389,10 +4388,8 @@ DDB2 loss All 7 gene
DDI1 loss All 4 gene
DDIAS loss All 6 gene
DDRGK1 gain All 7 gene
-DDT loss All 9 gene
-DDT loss ATRT 4 gene
-DDTL loss All 9 gene
-DDTL loss ATRT 4 gene
+DDT loss All 8 gene
+DDTL loss All 8 gene
DDX1 gain All 7 gene
DDX10 loss All 4 gene
DDX17 loss All 5 gene
@@ -4427,27 +4424,27 @@ DEFA1B loss All 6 gene
DEFA3 gain All 6 gene
DEFA3 loss All 6 gene
DEFA4 gain All 12 gene
-DEFA4 loss All 13 gene
+DEFA4 loss All 12 gene
DEFA4 loss HGAT 5 gene
-DEFA4 loss Medulloblastoma 7 gene
+DEFA4 loss Medulloblastoma 6 gene
DEFA5 gain All 6 gene
DEFA5 loss All 6 gene
DEFA6 gain All 12 gene
-DEFA6 loss All 13 gene
+DEFA6 loss All 12 gene
DEFA6 loss HGAT 5 gene
-DEFA6 loss Medulloblastoma 7 gene
+DEFA6 loss Medulloblastoma 6 gene
DEFA8P gain All 12 gene
-DEFA8P loss All 13 gene
+DEFA8P loss All 12 gene
DEFA8P loss HGAT 5 gene
-DEFA8P loss Medulloblastoma 7 gene
+DEFA8P loss Medulloblastoma 6 gene
DEFA9P gain All 12 gene
-DEFA9P loss All 13 gene
+DEFA9P loss All 12 gene
DEFA9P loss HGAT 5 gene
-DEFA9P loss Medulloblastoma 7 gene
+DEFA9P loss Medulloblastoma 6 gene
DEFB1 gain All 14 gene
-DEFB1 loss All 13 gene
+DEFB1 loss All 12 gene
DEFB1 loss HGAT 5 gene
-DEFB1 loss Medulloblastoma 7 gene
+DEFB1 loss Medulloblastoma 6 gene
DEFB115 gain All 8 gene
DEFB116 gain All 7 gene
DEFB118 gain All 9 gene
@@ -4456,17 +4453,13 @@ DEFB121 gain All 9 gene
DEFB122 gain All 9 gene
DEFB123 gain All 9 gene
DEFB124 gain All 9 gene
-DEFB130B loss All 4 gene
DEFB132 loss All 4 gene
DEFB134 gain All 9 gene
-DEFB134 loss All 8 gene
-DEFB134 loss Medulloblastoma 4 gene
+DEFB134 loss All 7 gene
DEFB135 gain All 9 gene
-DEFB135 loss All 8 gene
-DEFB135 loss Medulloblastoma 4 gene
+DEFB135 loss All 7 gene
DEFB136 gain All 9 gene
-DEFB136 loss All 8 gene
-DEFB136 loss Medulloblastoma 4 gene
+DEFB136 loss All 7 gene
DEFT1P gain All 6 gene
DEFT1P loss All 6 gene
DEFT1P2 gain All 6 gene
@@ -4490,8 +4483,8 @@ DENND6B loss All 8 gene
DEPP1 gain All 4 gene
DEPP1 loss All 5 gene
DERA loss All 4 gene
-DERL3 loss All 14 gene
-DERL3 loss ATRT 6 gene
+DERL3 loss All 12 gene
+DERL3 loss ATRT 4 gene
DESI1 loss All 13 gene
DESI1 loss Meningioma 4 gene
DESI2 gain All 4 gene
@@ -4592,8 +4585,8 @@ DLX5 gain All 4 gene
DLX6 gain All 4 gene
DMC1 loss All 6 gene
DMRTA1 gain All 5 gene
-DMRTA1 loss All 18 gene
-DMRTA1 loss HGAT 9 gene
+DMRTA1 loss All 17 gene
+DMRTA1 loss HGAT 8 gene
DMRTA2 loss All 5 gene
DMRTC2 loss All 4 gene
DNA2 loss All 4 gene
@@ -4690,8 +4683,8 @@ DRG2 loss All 38 gene
DRG2 gain Medulloblastoma 5 gene
DRG2 loss HGAT 12 gene
DRG2 loss Medulloblastoma 19 gene
-DRICH1 loss All 14 gene
-DRICH1 loss ATRT 5 gene
+DRICH1 loss All 13 gene
+DRICH1 loss ATRT 4 gene
DSTNP2 gain All 8 gene
DSTYK gain All 4 gene
DTX2 gain All 9 gene
@@ -4924,9 +4917,8 @@ ERC1 loss All 4 gene
ERF loss All 4 gene
ERFL loss All 4 gene
ERI1 gain All 13 gene
-ERI1 loss All 7 gene
+ERI1 loss All 6 gene
ERI1 gain HGAT 4 gene
-ERI1 loss Medulloblastoma 4 gene
ERI2 loss All 4 gene
ERICH1 gain All 6 gene
ERLNC1 gain All 4 gene
@@ -5030,13 +5022,13 @@ FAM166A gain All 8 gene
FAM166A gain HGAT 4 gene
FAM166B gain All 5 gene
FAM167A gain All 11 gene
-FAM167A loss All 9 gene
+FAM167A loss All 8 gene
FAM167A gain HGAT 4 gene
-FAM167A loss Medulloblastoma 5 gene
+FAM167A loss Medulloblastoma 4 gene
FAM167A-AS1 gain All 11 gene
-FAM167A-AS1 loss All 9 gene
+FAM167A-AS1 loss All 8 gene
FAM167A-AS1 gain HGAT 4 gene
-FAM167A-AS1 loss Medulloblastoma 5 gene
+FAM167A-AS1 loss Medulloblastoma 4 gene
FAM168B gain All 6 gene
FAM168B gain HGAT 4 gene
FAM169B gain All 12 gene
@@ -5086,11 +5078,10 @@ FAM230G loss Ependymoma 5 gene
FAM230G loss LGAT 4 gene
FAM230G loss Meningioma 5 gene
FAM230H loss All 8 gene
-FAM230I loss All 12 gene
-FAM230I loss ATRT 4 gene
+FAM230I loss All 11 gene
FAM25E loss All 4 gene
FAM27E5 gain All 9 gene
-FAM27E5 loss All 7 gene
+FAM27E5 loss All 6 gene
FAM27E5 gain Medulloblastoma 7 gene
FAM27E5 loss HGAT 5 gene
FAM30A loss All 5 gene
@@ -5117,8 +5108,8 @@ FAM83H-AS1 gain All 12 gene
FAM83H-AS1 loss All 4 gene
FAM83H-AS1 gain HGAT 6 gene
FAM86B3P gain All 10 gene
-FAM86B3P loss All 8 gene
-FAM86B3P loss Medulloblastoma 5 gene
+FAM86B3P loss All 7 gene
+FAM86B3P loss Medulloblastoma 4 gene
FAM86DP loss All 7 gene
FAM87B loss All 8 gene
FAM87B loss Meningioma 4 gene
@@ -5150,14 +5141,14 @@ FBLN1 loss All 4 gene
FBLN7 gain All 4 gene
FBLN7 gain HGAT 4 gene
FBRS gain All 8 gene
-FBRS loss All 6 gene
+FBRS loss All 5 gene
FBXL13 gain All 17 gene
FBXL13 gain Medulloblastoma 6 gene
FBXL14 gain All 6 gene
FBXL19 gain All 8 gene
-FBXL19 loss All 6 gene
+FBXL19 loss All 5 gene
FBXL19-AS1 gain All 8 gene
-FBXL19-AS1 loss All 6 gene
+FBXL19-AS1 loss All 5 gene
FBXL20 gain All 19 gene
FBXL20 gain Medulloblastoma 15 gene
FBXL6 gain All 11 gene
@@ -5177,7 +5168,7 @@ FBXW10 loss All 21 gene
FBXW10 loss HGAT 9 gene
FBXW10 loss Medulloblastoma 7 gene
FBXW12 loss All 4 gene
-FBXW4P1 loss All 7 gene
+FBXW4P1 loss All 6 gene
FBXW5 gain All 7 gene
FCGR1A gain All 6 gene
FCHO1 gain All 4 gene
@@ -5191,8 +5182,7 @@ FCN2 gain All 6 gene
FCN2 loss All 4 gene
FCN3 loss All 5 gene
FDFT1 gain All 9 gene
-FDFT1 loss All 8 gene
-FDFT1 loss Medulloblastoma 4 gene
+FDFT1 loss All 7 gene
FDX2 gain All 5 gene
FGF12 gain All 11 gene
FGF12 loss All 9 gene
@@ -5206,7 +5196,6 @@ FGL2 gain All 27 gene
FGL2 gain HGAT 6 gene
FGL2 gain LGAT 4 gene
FGL2 gain Medulloblastoma 9 gene
-FHIT loss All 4 gene
FHOD1 gain All 6 gene
FHOD1 loss All 8 gene
FHOD1 loss HGAT 6 gene
@@ -5246,7 +5235,7 @@ FLJ16779 gain All 15 gene
FLJ16779 gain HGAT 7 gene
FLJ34503 loss All 4 gene
FLJ36000 gain All 8 gene
-FLJ36000 loss All 5 gene
+FLJ36000 loss All 4 gene
FLJ36000 gain Medulloblastoma 7 gene
FLJ36000 loss HGAT 4 gene
FLJ40194 gain All 11 gene
@@ -5314,7 +5303,7 @@ FPGS loss All 5 gene
FPGT loss All 4 gene
FPGT-TNNI3K loss All 4 gene
FRG2KP gain All 6 gene
-FRG2KP loss All 6 gene
+FRG2KP loss All 5 gene
FRMPD2 loss All 8 gene
FSCN2 gain All 16 gene
FSCN2 gain Medulloblastoma 8 gene
@@ -5330,7 +5319,7 @@ FTCD-AS1 gain All 6 gene
FTCD-AS1 loss All 6 gene
FTCD-AS1 loss HGAT 5 gene
FUS gain All 8 gene
-FUS loss All 6 gene
+FUS loss All 5 gene
FUT7 gain All 7 gene
FXN gain All 4 gene
FXN loss All 10 gene
@@ -5397,8 +5386,7 @@ GAS8-AS1 loss All 21 gene
GAS8-AS1 loss HGAT 10 gene
GAS8-AS1 loss Medulloblastoma 7 gene
GATA4 gain All 10 gene
-GATA4 loss All 8 gene
-GATA4 loss Medulloblastoma 4 gene
+GATA4 loss All 7 gene
GATA5 gain All 16 gene
GATA5 gain HGAT 7 gene
GATAD2B gain All 15 gene
@@ -5436,13 +5424,13 @@ GGA2 gain All 6 gene
GGA2 loss All 5 gene
GGNBP2 gain All 12 gene
GGNBP2 gain Medulloblastoma 7 gene
-GGT1 loss All 14 gene
-GGT1 loss ATRT 5 gene
+GGT1 loss All 13 gene
+GGT1 loss ATRT 4 gene
GGT1 loss LGAT 4 gene
GGT2 loss All 10 gene
GGT2 loss ATRT 4 gene
-GGT5 loss All 14 gene
-GGT5 loss ATRT 7 gene
+GGT5 loss All 13 gene
+GGT5 loss ATRT 6 gene
GGTLC2 loss All 6 gene
GHET1 gain All 4 gene
GID4 gain All 12 gene
@@ -5547,7 +5535,7 @@ GOLGA8S gain All 4 gene
GOLGA8S loss All 4 gene
GOLT1A gain All 4 gene
GOLT1B loss All 5 gene
-GOPC loss All 6 gene
+GOPC loss All 5 gene
GOSR1 gain All 5 gene
GOSR1 loss All 4 gene
GP1BB gain All 7 gene
@@ -5653,9 +5641,9 @@ GS1-124K5.4 gain HGAT 10 gene
GS1-124K5.4 gain LGAT 6 gene
GS1-124K5.4 gain Medulloblastoma 8 gene
GS1-24F4.2 gain All 15 gene
-GS1-24F4.2 loss All 13 gene
+GS1-24F4.2 loss All 12 gene
GS1-24F4.2 loss HGAT 5 gene
-GS1-24F4.2 loss Medulloblastoma 7 gene
+GS1-24F4.2 loss Medulloblastoma 6 gene
GSAP gain All 28 gene
GSAP gain HGAT 6 gene
GSAP gain LGAT 4 gene
@@ -5678,12 +5666,10 @@ GSTM2 loss All 6 gene
GSTM3 loss All 4 gene
GSTM4 loss All 5 gene
GSTM5 loss All 4 gene
-GSTT2 loss All 9 gene
-GSTT2 loss ATRT 4 gene
-GSTT2B loss All 9 gene
-GSTT2B loss ATRT 4 gene
-GSTT4 loss All 11 gene
-GSTT4 loss ATRT 5 gene
+GSTT2 loss All 8 gene
+GSTT2B loss All 8 gene
+GSTT4 loss All 10 gene
+GSTT4 loss ATRT 4 gene
GSX2 gain All 12 gene
GSX2 gain HGAT 12 gene
GTF2H1 loss All 6 gene
@@ -5701,8 +5687,8 @@ GTF2IRD2 gain All 8 gene
GTF2IRD2B gain All 8 gene
GTPBP1 loss All 5 gene
GTPBP3 gain All 5 gene
-GUCD1 loss All 13 gene
-GUCD1 loss ATRT 5 gene
+GUCD1 loss All 12 gene
+GUCD1 loss ATRT 4 gene
GUCD1 loss LGAT 4 gene
GUCY1B2 loss All 4 gene
GUCY1B2 loss HGAT 4 gene
@@ -5716,8 +5702,8 @@ GUSBP1 gain All 7 gene
GUSBP1 loss All 12 gene
GUSBP1 loss HGAT 4 gene
GUSBP1 loss Medulloblastoma 6 gene
-GUSBP11 loss All 14 gene
-GUSBP11 loss ATRT 5 gene
+GUSBP11 loss All 13 gene
+GUSBP11 loss ATRT 4 gene
GVINP1 loss All 9 gene
GVINP1 loss HGAT 4 gene
GVQW3 loss All 4 gene
@@ -5741,9 +5727,11 @@ H3C13 gain All 8 gene
H3C14 gain All 10 gene
H3C15 gain All 10 gene
H3P28 loss All 5 gene
+H3P30 deep deletion All 4 gene
H3P30 gain All 4 gene
-H3P30 loss All 15 gene
-H3P30 loss HGAT 10 gene
+H3P30 loss All 12 gene
+H3P30 deep deletion HGAT 4 gene
+H3P30 loss HGAT 7 gene
H3P42 gain All 9 gene
H3P42 gain HGAT 4 gene
H4C14 gain All 10 gene
@@ -5825,7 +5813,6 @@ HEXIM1 gain Medulloblastoma 10 gene
HEXIM2 gain All 14 gene
HEXIM2 loss All 6 gene
HEXIM2 gain Medulloblastoma 10 gene
-HGC6.3 loss All 4 gene
HGH1 gain All 11 gene
HGH1 loss All 5 gene
HGH1 gain HGAT 6 gene
@@ -5944,7 +5931,7 @@ HSD17B12 loss HGAT 4 gene
HSD3B1 loss All 5 gene
HSD3B2 loss All 7 gene
HSD3B7 gain All 8 gene
-HSD3B7 loss All 6 gene
+HSD3B7 loss All 5 gene
HSF1 gain All 11 gene
HSF1 loss All 5 gene
HSF1 gain HGAT 6 gene
@@ -6011,51 +5998,65 @@ IFITM10 loss HGAT 4 gene
IFITM2 gain All 5 gene
IFITM3 gain All 5 gene
IFITM5 gain All 4 gene
+IFNA1 deep deletion All 4 gene
IFNA1 gain All 4 gene
-IFNA1 loss All 15 gene
-IFNA1 loss HGAT 10 gene
+IFNA1 loss All 12 gene
+IFNA1 deep deletion HGAT 4 gene
+IFNA1 loss HGAT 7 gene
IFNA10 gain All 4 gene
-IFNA10 loss All 12 gene
-IFNA10 loss HGAT 8 gene
+IFNA10 loss All 11 gene
+IFNA10 loss HGAT 7 gene
+IFNA13 deep deletion All 4 gene
IFNA13 gain All 4 gene
-IFNA13 loss All 15 gene
-IFNA13 loss HGAT 10 gene
+IFNA13 loss All 12 gene
+IFNA13 deep deletion HGAT 4 gene
+IFNA13 loss HGAT 7 gene
IFNA14 gain All 4 gene
-IFNA14 loss All 12 gene
-IFNA14 loss HGAT 8 gene
+IFNA14 loss All 11 gene
+IFNA14 loss HGAT 7 gene
IFNA16 gain All 4 gene
-IFNA16 loss All 12 gene
-IFNA16 loss HGAT 8 gene
+IFNA16 loss All 11 gene
+IFNA16 loss HGAT 7 gene
IFNA17 gain All 4 gene
-IFNA17 loss All 12 gene
-IFNA17 loss HGAT 8 gene
+IFNA17 loss All 11 gene
+IFNA17 loss HGAT 7 gene
+IFNA2 deep deletion All 4 gene
IFNA2 gain All 4 gene
-IFNA2 loss All 15 gene
-IFNA2 loss HGAT 10 gene
+IFNA2 loss All 12 gene
+IFNA2 deep deletion HGAT 4 gene
+IFNA2 loss HGAT 7 gene
IFNA21 gain All 4 gene
IFNA21 loss All 11 gene
IFNA21 loss HGAT 7 gene
IFNA4 gain All 4 gene
IFNA4 loss All 11 gene
IFNA4 loss HGAT 7 gene
+IFNA5 deep deletion All 4 gene
IFNA5 gain All 4 gene
-IFNA5 loss All 15 gene
-IFNA5 loss HGAT 10 gene
+IFNA5 loss All 12 gene
+IFNA5 deep deletion HGAT 4 gene
+IFNA5 loss HGAT 7 gene
+IFNA6 deep deletion All 4 gene
IFNA6 gain All 4 gene
-IFNA6 loss All 15 gene
-IFNA6 loss HGAT 10 gene
+IFNA6 loss All 12 gene
+IFNA6 deep deletion HGAT 4 gene
+IFNA6 loss HGAT 7 gene
IFNA7 gain All 4 gene
-IFNA7 loss All 12 gene
-IFNA7 loss HGAT 8 gene
+IFNA7 loss All 11 gene
+IFNA7 loss HGAT 7 gene
+IFNA8 deep deletion All 4 gene
IFNA8 gain All 4 gene
-IFNA8 loss All 15 gene
-IFNA8 loss HGAT 10 gene
+IFNA8 loss All 12 gene
+IFNA8 deep deletion HGAT 4 gene
+IFNA8 loss HGAT 7 gene
IFNB1 gain All 4 gene
IFNB1 loss All 11 gene
IFNB1 loss HGAT 7 gene
+IFNE deep deletion All 4 gene
IFNE gain All 4 gene
-IFNE loss All 15 gene
-IFNE loss HGAT 10 gene
+IFNE loss All 12 gene
+IFNE deep deletion HGAT 4 gene
+IFNE loss HGAT 7 gene
IFNK loss All 5 gene
IFNW1 gain All 4 gene
IFNW1 loss All 11 gene
@@ -6091,8 +6092,8 @@ IGFBPL1 loss All 4 gene
IGFBPL1 gain Ependymoma 4 gene
IGFN1 gain All 5 gene
IGFN1 gain HGAT 4 gene
-IGLL1 loss All 14 gene
-IGLL1 loss ATRT 5 gene
+IGLL1 loss All 13 gene
+IGLL1 loss ATRT 4 gene
IGLL5 loss All 8 gene
IGSF21 gain All 5 gene
IGSF21 loss All 14 gene
@@ -6207,13 +6208,13 @@ ITGA2B gain All 14 gene
ITGA2B loss All 4 gene
ITGA2B gain Medulloblastoma 10 gene
ITGAD gain All 8 gene
-ITGAD loss All 6 gene
+ITGAD loss All 5 gene
ITGAL gain All 8 gene
-ITGAL loss All 6 gene
+ITGAL loss All 5 gene
ITGAM gain All 8 gene
-ITGAM loss All 6 gene
+ITGAM loss All 5 gene
ITGAX gain All 8 gene
-ITGAX loss All 6 gene
+ITGAX loss All 5 gene
ITGB2 gain All 11 gene
ITGB2 loss All 9 gene
ITGB2 loss HGAT 7 gene
@@ -6251,7 +6252,7 @@ KANSL1 gain Medulloblastoma 7 gene
KANSL1-AS1 gain All 13 gene
KANSL1-AS1 gain Medulloblastoma 7 gene
KAT8 gain All 8 gene
-KAT8 loss All 6 gene
+KAT8 loss All 5 gene
KBTBD11 gain All 8 gene
KBTBD11-OT1 gain All 8 gene
KBTBD13 gain All 5 gene
@@ -6332,8 +6333,8 @@ KIAA1549 gain All 110 gene
KIAA1549 gain LGAT 107 gene
KIAA1614 loss All 5 gene
KIAA1614-AS1 loss All 5 gene
-KIAA1671 loss All 17 gene
-KIAA1671 loss ATRT 5 gene
+KIAA1671 loss All 16 gene
+KIAA1671 loss ATRT 4 gene
KIAA1671 loss Meningioma 5 gene
KIAA1671-AS1 loss All 15 gene
KIAA1671-AS1 loss ATRT 4 gene
@@ -6351,8 +6352,6 @@ KIF1A gain All 4 gene
KIF21B gain All 5 gene
KIF21B gain HGAT 4 gene
KIF22 loss All 4 gene
-KIF25 loss All 4 gene
-KIF25-AS1 loss All 4 gene
KIF26A gain All 5 gene
KIF26A loss All 12 gene
KIF26A loss HGAT 8 gene
@@ -6399,9 +6398,11 @@ KLHL22 loss Meningioma 5 gene
KLHL25 gain All 4 gene
KLHL33 gain All 5 gene
KLHL7 gain All 4 gene
+KLHL9 deep deletion All 4 gene
KLHL9 gain All 4 gene
-KLHL9 loss All 15 gene
-KLHL9 loss HGAT 10 gene
+KLHL9 loss All 12 gene
+KLHL9 deep deletion HGAT 4 gene
+KLHL9 loss HGAT 7 gene
KLRB1 gain All 5 gene
KLRF1 gain All 5 gene
KLRF2 gain All 5 gene
@@ -6641,8 +6642,8 @@ LIMS4 gain HGAT 4 gene
LIN28A loss All 6 gene
LIN7C loss All 4 gene
LINC00028 gain All 9 gene
-LINC00032 loss All 8 gene
-LINC00032 loss HGAT 6 gene
+LINC00032 loss All 6 gene
+LINC00032 loss HGAT 4 gene
LINC00051 gain All 10 gene
LINC00051 loss All 4 gene
LINC00051 gain HGAT 4 gene
@@ -6666,9 +6667,8 @@ LINC00205 gain All 11 gene
LINC00205 loss All 10 gene
LINC00205 loss HGAT 7 gene
LINC00208 gain All 12 gene
-LINC00208 loss All 8 gene
+LINC00208 loss All 7 gene
LINC00208 gain HGAT 4 gene
-LINC00208 loss Medulloblastoma 4 gene
LINC00244 gain All 9 gene
LINC00244 gain HGAT 4 gene
LINC002481 gain All 4 gene
@@ -6714,9 +6714,9 @@ LINC00567 loss HGAT 4 gene
LINC00589 gain All 5 gene
LINC00589 loss All 6 gene
LINC00599 gain All 12 gene
-LINC00599 loss All 9 gene
+LINC00599 loss All 8 gene
LINC00599 gain HGAT 4 gene
-LINC00599 loss Medulloblastoma 5 gene
+LINC00599 loss Medulloblastoma 4 gene
LINC00615 loss All 4 gene
LINC00615 loss HGAT 4 gene
LINC00619 gain All 4 gene
@@ -6815,12 +6815,12 @@ LINC01180 gain Medulloblastoma 10 gene
LINC01221 gain All 6 gene
LINC01221 gain HGAT 5 gene
LINC01239 gain All 5 gene
-LINC01239 loss All 17 gene
-LINC01239 loss HGAT 9 gene
+LINC01239 loss All 16 gene
+LINC01239 loss HGAT 8 gene
LINC01241 loss All 8 gene
LINC01241 loss HGAT 5 gene
-LINC01243 loss All 7 gene
-LINC01243 loss HGAT 5 gene
+LINC01243 loss All 6 gene
+LINC01243 loss HGAT 4 gene
LINC01250 gain All 5 gene
LINC01251 gain All 4 gene
LINC01251 loss All 6 gene
@@ -6917,8 +6917,7 @@ LINC01654 gain All 5 gene
LINC01654 loss All 14 gene
LINC01654 gain HGAT 5 gene
LINC01654 loss Meningioma 5 gene
-LINC01659 loss All 12 gene
-LINC01659 loss ATRT 4 gene
+LINC01659 loss All 11 gene
LINC01668 gain All 8 gene
LINC01668 loss All 4 gene
LINC01671 gain All 8 gene
@@ -6976,7 +6975,7 @@ LINC01929 loss All 4 gene
LINC01942 gain All 4 gene
LINC01942 loss All 8 gene
LINC01942 loss HGAT 5 gene
-LINC01947 loss All 5 gene
+LINC01947 loss All 4 gene
LINC01951 gain All 4 gene
LINC01951 loss All 8 gene
LINC01951 loss HGAT 5 gene
@@ -7097,7 +7096,7 @@ LINC02517 gain All 4 gene
LINC02545 loss All 4 gene
LINC02548 loss All 4 gene
LINC02552 loss All 6 gene
-LINC02556 loss All 8 gene
+LINC02556 loss All 7 gene
LINC02563 gain All 11 gene
LINC02563 gain HGAT 4 gene
LINC02563 gain Medulloblastoma 5 gene
@@ -7162,13 +7161,13 @@ LINC02810 gain HGAT 5 gene
LINC02810 loss Meningioma 5 gene
LINC02861 loss All 5 gene
LINCR-0001 gain All 11 gene
-LINCR-0001 loss All 9 gene
+LINCR-0001 loss All 8 gene
LINCR-0001 gain HGAT 4 gene
-LINCR-0001 loss Medulloblastoma 5 gene
+LINCR-0001 loss Medulloblastoma 4 gene
LINGO2 gain All 7 gene
-LINGO2 loss All 13 gene
+LINGO2 loss All 12 gene
LINGO2 gain HGAT 6 gene
-LINGO2 loss HGAT 7 gene
+LINGO2 loss HGAT 6 gene
LINGO4 gain All 7 gene
LINGO4 gain HGAT 4 gene
LINS1 gain All 10 gene
@@ -7214,9 +7213,9 @@ LOC100128398 gain All 9 gene
LOC100128398 gain Medulloblastoma 4 gene
LOC100128770 loss All 5 gene
LOC100129129 gain All 11 gene
-LOC100129129 loss All 9 gene
+LOC100129129 loss All 8 gene
LOC100129129 gain HGAT 4 gene
-LOC100129129 loss Medulloblastoma 5 gene
+LOC100129129 loss Medulloblastoma 4 gene
LOC100129215 loss All 5 gene
LOC100129503 gain All 16 gene
LOC100129503 gain Medulloblastoma 8 gene
@@ -7234,10 +7233,10 @@ LOC100130849 gain All 5 gene
LOC100131315 loss All 4 gene
LOC100133091 gain All 10 gene
LOC100287015 gain All 17 gene
-LOC100287015 loss All 13 gene
+LOC100287015 loss All 12 gene
LOC100287015 gain Medulloblastoma 4 gene
LOC100287015 loss HGAT 5 gene
-LOC100287015 loss Medulloblastoma 7 gene
+LOC100287015 loss Medulloblastoma 6 gene
LOC100287036 gain All 6 gene
LOC100287036 loss All 23 gene
LOC100287036 loss HGAT 11 gene
@@ -7366,13 +7365,13 @@ LOC101929141 loss HGAT 10 gene
LOC101929141 loss Medulloblastoma 8 gene
LOC101929240 gain All 4 gene
LOC101929269 gain All 11 gene
-LOC101929269 loss All 9 gene
+LOC101929269 loss All 8 gene
LOC101929269 gain HGAT 4 gene
-LOC101929269 loss Medulloblastoma 5 gene
+LOC101929269 loss Medulloblastoma 4 gene
LOC101929290 gain All 11 gene
-LOC101929290 loss All 9 gene
+LOC101929290 loss All 8 gene
LOC101929290 gain HGAT 4 gene
-LOC101929290 loss Medulloblastoma 5 gene
+LOC101929290 loss Medulloblastoma 4 gene
LOC101929331 loss All 5 gene
LOC101929415 gain All 5 gene
LOC101929415 gain HGAT 4 gene
@@ -7392,9 +7391,9 @@ LOC101930094 gain All 8 gene
LOC101930094 loss All 5 gene
LOC102546299 loss All 4 gene
LOC102723313 gain All 11 gene
-LOC102723313 loss All 9 gene
+LOC102723313 loss All 8 gene
LOC102723313 gain HGAT 4 gene
-LOC102723313 loss Medulloblastoma 5 gene
+LOC102723313 loss Medulloblastoma 4 gene
LOC102723335 gain All 10 gene
LOC102723335 gain HGAT 9 gene
LOC102723385 gain All 5 gene
@@ -7424,7 +7423,6 @@ LOC105370941 loss All 4 gene
LOC105370954 gain All 4 gene
LOC105371022 gain All 11 gene
LOC105371022 gain HGAT 10 gene
-LOC105371200 loss All 4 gene
LOC105371335 loss All 9 gene
LOC105371335 loss HGAT 5 gene
LOC105371414 gain All 6 gene
@@ -7489,7 +7487,7 @@ LOC107984813 gain All 6 gene
LOC107984813 loss All 8 gene
LOC107984813 loss HGAT 6 gene
LOC107984875 gain All 8 gene
-LOC107984875 loss All 6 gene
+LOC107984875 loss All 5 gene
LOC107984893 loss All 4 gene
LOC107984969 gain All 5 gene
LOC107984969 loss All 13 gene
@@ -7506,9 +7504,8 @@ LOC150776 gain All 6 gene
LOC150776 gain HGAT 4 gene
LOC155060 gain All 4 gene
LOC157273 gain All 13 gene
-LOC157273 loss All 7 gene
+LOC157273 loss All 6 gene
LOC157273 gain HGAT 4 gene
-LOC157273 loss Medulloblastoma 4 gene
LOC171391 gain All 7 gene
LOC171391 loss All 5 gene
LOC171391 gain LGAT 4 gene
@@ -7605,7 +7602,7 @@ LOC729732 loss All 13 gene
LOC729732 loss HGAT 4 gene
LOC729732 loss Medulloblastoma 6 gene
LOC730183 gain All 8 gene
-LOC730183 loss All 6 gene
+LOC730183 loss All 5 gene
LOC730668 loss All 4 gene
LOC93622 gain All 4 gene
LONRF1 gain All 9 gene
@@ -7695,8 +7692,8 @@ LRRC75A gain All 8 gene
LRRC75A loss All 47 gene
LRRC75A loss HGAT 10 gene
LRRC75A loss Medulloblastoma 31 gene
-LRRC75B loss All 13 gene
-LRRC75B loss ATRT 5 gene
+LRRC75B loss All 12 gene
+LRRC75B loss ATRT 4 gene
LRRC75B loss LGAT 4 gene
LRRC77P gain All 4 gene
LRRC8A loss All 5 gene
@@ -7911,10 +7908,10 @@ MCM7 gain All 12 gene
MCM7 gain LGAT 4 gene
MCM9 loss All 4 gene
MCPH1 gain All 17 gene
-MCPH1 loss All 13 gene
+MCPH1 loss All 12 gene
MCPH1 gain Medulloblastoma 4 gene
MCPH1 loss HGAT 5 gene
-MCPH1 loss Medulloblastoma 7 gene
+MCPH1 loss Medulloblastoma 6 gene
MCRIP1 gain All 16 gene
MCRIP1 gain Medulloblastoma 8 gene
MDFIC gain All 7 gene
@@ -7989,9 +7986,9 @@ MFAP4 gain Medulloblastoma 22 gene
MFAP4 loss HGAT 8 gene
MFAP4 loss Medulloblastoma 5 gene
MFHAS1 gain All 12 gene
-MFHAS1 loss All 8 gene
+MFHAS1 loss All 7 gene
MFHAS1 gain HGAT 4 gene
-MFHAS1 loss Medulloblastoma 5 gene
+MFHAS1 loss Medulloblastoma 4 gene
MFNG loss All 6 gene
MFSD3 loss All 5 gene
MFSD4A gain All 4 gene
@@ -8028,15 +8025,15 @@ MIEF2 loss Medulloblastoma 19 gene
MIEN1 gain All 19 gene
MIEN1 gain Medulloblastoma 15 gene
MIER2 loss All 4 gene
-MIF loss All 13 gene
-MIF loss ATRT 5 gene
+MIF loss All 12 gene
+MIF loss ATRT 4 gene
MIGA2 loss All 5 gene
MIMT1 gain All 8 gene
MIMT1 gain Medulloblastoma 4 gene
MINCR gain All 12 gene
MINCR gain HGAT 5 gene
-MINPP1 loss All 10 gene
-MINPP1 loss HGAT 7 gene
+MINPP1 loss All 9 gene
+MINPP1 loss HGAT 6 gene
MIOX loss All 4 gene
MIR1-1 gain All 16 gene
MIR1-1 gain HGAT 7 gene
@@ -8075,9 +8072,9 @@ MIR1234 loss All 5 gene
MIR1234 gain HGAT 5 gene
MIR1238 gain All 5 gene
MIR124-1 gain All 12 gene
-MIR124-1 loss All 9 gene
+MIR124-1 loss All 8 gene
MIR124-1 gain HGAT 4 gene
-MIR124-1 loss Medulloblastoma 5 gene
+MIR124-1 loss Medulloblastoma 4 gene
MIR124-3 gain All 15 gene
MIR124-3 gain HGAT 7 gene
MIR1244-1 gain All 7 gene
@@ -8136,9 +8133,9 @@ MIR130B loss HGAT 4 gene
MIR130B loss Meningioma 5 gene
MIR130B loss Schwannoma 4 gene
MIR1322 gain All 11 gene
-MIR1322 loss All 9 gene
+MIR1322 loss All 8 gene
MIR1322 gain HGAT 4 gene
-MIR1322 loss Medulloblastoma 5 gene
+MIR1322 loss Medulloblastoma 4 gene
MIR1323 gain All 5 gene
MIR133A2 gain All 16 gene
MIR133A2 gain HGAT 7 gene
@@ -8250,9 +8247,11 @@ MIR302E loss Ependymoma 4 gene
MIR302E loss HGAT 4 gene
MIR3065 gain All 17 gene
MIR3065 gain Medulloblastoma 9 gene
+MIR31 deep deletion All 4 gene
MIR31 gain All 4 gene
-MIR31 loss All 15 gene
-MIR31 loss HGAT 10 gene
+MIR31 loss All 12 gene
+MIR31 deep deletion HGAT 4 gene
+MIR31 loss HGAT 7 gene
MIR3121 loss All 5 gene
MIR3137 gain All 9 gene
MIR3137 loss All 6 gene
@@ -8288,9 +8287,11 @@ MIR3195 gain HGAT 7 gene
MIR3196 gain All 15 gene
MIR3196 gain HGAT 7 gene
MIR3198-1 loss All 8 gene
+MIR31HG deep deletion All 4 gene
MIR31HG gain All 4 gene
-MIR31HG loss All 15 gene
-MIR31HG loss HGAT 10 gene
+MIR31HG loss All 12 gene
+MIR31HG deep deletion HGAT 4 gene
+MIR31HG loss HGAT 7 gene
MIR324 loss All 4 gene
MIR328 gain All 6 gene
MIR328 loss All 8 gene
@@ -8394,9 +8395,9 @@ MIR4284 gain All 14 gene
MIR4284 gain HGAT 6 gene
MIR4285 gain All 5 gene
MIR4286 gain All 11 gene
-MIR4286 loss All 9 gene
+MIR4286 loss All 8 gene
MIR4286 gain HGAT 4 gene
-MIR4286 loss Medulloblastoma 5 gene
+MIR4286 loss Medulloblastoma 4 gene
MIR429 loss All 14 gene
MIR429 loss Meningioma 4 gene
MIR4292 gain All 7 gene
@@ -8474,9 +8475,9 @@ MIR4512 gain All 5 gene
MIR4512 gain HGAT 5 gene
MIR4515 gain All 4 gene
MIR4518 gain All 8 gene
-MIR4518 loss All 6 gene
+MIR4518 loss All 5 gene
MIR4519 gain All 8 gene
-MIR4519 loss All 6 gene
+MIR4519 loss All 5 gene
MIR4521 loss All 4 gene
MIR4522 gain All 4 gene
MIR4522 loss All 4 gene
@@ -8512,19 +8513,18 @@ MIR4653 gain All 9 gene
MIR4658 gain All 12 gene
MIR4658 gain LGAT 4 gene
MIR4659A gain All 16 gene
-MIR4659A loss All 13 gene
+MIR4659A loss All 12 gene
MIR4659A gain Medulloblastoma 4 gene
MIR4659A loss HGAT 5 gene
-MIR4659A loss Medulloblastoma 7 gene
+MIR4659A loss Medulloblastoma 6 gene
MIR4659B gain All 16 gene
-MIR4659B loss All 13 gene
+MIR4659B loss All 12 gene
MIR4659B gain Medulloblastoma 4 gene
MIR4659B loss HGAT 5 gene
-MIR4659B loss Medulloblastoma 7 gene
+MIR4659B loss Medulloblastoma 6 gene
MIR4660 gain All 13 gene
-MIR4660 loss All 7 gene
+MIR4660 loss All 6 gene
MIR4660 gain HGAT 4 gene
-MIR4660 loss Medulloblastoma 4 gene
MIR4661 gain All 4 gene
MIR4664 gain All 11 gene
MIR4664 loss All 4 gene
@@ -8534,8 +8534,8 @@ MIR4672 loss All 5 gene
MIR4673 gain All 7 gene
MIR4674 gain All 7 gene
MIR4677 gain All 4 gene
-MIR4678 loss All 10 gene
-MIR4678 loss HGAT 7 gene
+MIR4678 loss All 9 gene
+MIR4678 loss HGAT 6 gene
MIR4683 loss All 6 gene
MIR4683 loss HGAT 5 gene
MIR4686 loss All 5 gene
@@ -8730,13 +8730,13 @@ MIR590 gain HGAT 5 gene
MIR595 gain All 7 gene
MIR596 gain All 8 gene
MIR597 gain All 12 gene
-MIR597 loss All 9 gene
+MIR597 loss All 8 gene
MIR597 gain HGAT 4 gene
-MIR597 loss Medulloblastoma 5 gene
+MIR597 loss Medulloblastoma 4 gene
MIR598 gain All 11 gene
-MIR598 loss All 9 gene
+MIR598 loss All 8 gene
MIR598 gain HGAT 4 gene
-MIR598 loss Medulloblastoma 5 gene
+MIR598 loss Medulloblastoma 4 gene
MIR600 loss All 5 gene
MIR600HG loss All 5 gene
MIR601 loss All 5 gene
@@ -8933,9 +8933,9 @@ MIR7160 gain All 8 gene
MIR744 loss All 4 gene
MIR761 loss All 5 gene
MIR762 gain All 8 gene
-MIR762 loss All 6 gene
+MIR762 loss All 5 gene
MIR762HG gain All 8 gene
-MIR762HG loss All 6 gene
+MIR762HG loss All 5 gene
MIR765 gain All 4 gene
MIR7703 loss All 4 gene
MIR7847 gain All 5 gene
@@ -8944,10 +8944,10 @@ MIR7847 gain LGAT 4 gene
MIR7847 loss HGAT 4 gene
MIR7974 gain All 4 gene
MIR8055 gain All 16 gene
-MIR8055 loss All 13 gene
+MIR8055 loss All 12 gene
MIR8055 gain Medulloblastoma 4 gene
MIR8055 loss HGAT 5 gene
-MIR8055 loss Medulloblastoma 7 gene
+MIR8055 loss Medulloblastoma 6 gene
MIR8056 gain All 4 gene
MIR8056 loss All 8 gene
MIR8056 loss HGAT 5 gene
@@ -8962,13 +8962,11 @@ MIR8083 gain All 15 gene
MIR8083 gain HGAT 7 gene
MIR8087 loss All 4 gene
MIR873 gain All 7 gene
-MIR873 loss All 9 gene
+MIR873 loss All 8 gene
MIR873 gain HGAT 6 gene
-MIR873 loss HGAT 4 gene
MIR876 gain All 7 gene
-MIR876 loss All 9 gene
+MIR876 loss All 8 gene
MIR876 gain HGAT 6 gene
-MIR876 loss HGAT 4 gene
MIR9-2 gain All 4 gene
MIR920 gain All 5 gene
MIR920 gain HGAT 4 gene
@@ -9021,8 +9019,8 @@ MLLT6 gain Medulloblastoma 15 gene
MLXIPL gain All 14 gene
MLXIPL gain HGAT 6 gene
MMEL1 loss All 5 gene
-MMP11 loss All 16 gene
-MMP11 loss ATRT 7 gene
+MMP11 loss All 13 gene
+MMP11 loss ATRT 4 gene
MMP14 gain All 4 gene
MMP14 loss All 5 gene
MMP21 loss All 10 gene
@@ -9191,9 +9189,9 @@ MSL3P1 loss All 4 gene
MSMB loss All 4 gene
MSMP gain All 5 gene
MSRA gain All 12 gene
-MSRA loss All 9 gene
+MSRA loss All 8 gene
MSRA gain HGAT 4 gene
-MSRA loss Medulloblastoma 5 gene
+MSRA loss Medulloblastoma 4 gene
MST1 loss All 4 gene
MST1R loss All 4 gene
MSX2 gain All 4 gene
@@ -9202,9 +9200,11 @@ MSX2 loss HGAT 4 gene
MTA1 gain All 5 gene
MTA1 loss All 8 gene
MTA1 loss HGAT 5 gene
+MTAP deep deletion All 4 gene
MTAP gain All 4 gene
-MTAP loss All 21 gene
-MTAP loss HGAT 12 gene
+MTAP loss All 18 gene
+MTAP deep deletion HGAT 4 gene
+MTAP loss HGAT 9 gene
MTCH2 gain All 4 gene
MTCH2 loss All 8 gene
MTFMT gain All 5 gene
@@ -9217,13 +9217,13 @@ MTMR11 gain Ependymoma 4 gene
MTMR3 loss All 4 gene
MTMR4 gain All 4 gene
MTMR9 gain All 11 gene
-MTMR9 loss All 9 gene
+MTMR9 loss All 8 gene
MTMR9 gain HGAT 4 gene
-MTMR9 loss Medulloblastoma 5 gene
+MTMR9 loss Medulloblastoma 4 gene
MTNR1B gain All 7 gene
MTNR1B loss All 9 gene
MTRNR2L1 gain All 8 gene
-MTRNR2L1 loss All 5 gene
+MTRNR2L1 loss All 4 gene
MTRNR2L1 gain Medulloblastoma 7 gene
MTRNR2L1 loss HGAT 4 gene
MTRNR2L2 loss All 6 gene
@@ -9303,7 +9303,7 @@ MYLK3 loss All 13 gene
MYLK3 loss HGAT 5 gene
MYLK3 loss Medulloblastoma 4 gene
MYLPF gain All 8 gene
-MYLPF loss All 5 gene
+MYLPF loss All 4 gene
MYO15A gain All 12 gene
MYO15A loss All 37 gene
MYO15A gain Medulloblastoma 5 gene
@@ -9449,8 +9449,7 @@ NEFH loss All 5 gene
NEGR1 loss All 5 gene
NEGR1-IT1 loss All 5 gene
NEIL2 gain All 9 gene
-NEIL2 loss All 8 gene
-NEIL2 loss Medulloblastoma 4 gene
+NEIL2 loss All 7 gene
NEK3 loss All 4 gene
NEK3 loss HGAT 4 gene
NEK5 loss All 4 gene
@@ -9464,7 +9463,7 @@ NEURL4 loss All 4 gene
NEUROD2 gain All 19 gene
NEUROD2 gain Medulloblastoma 15 gene
NF1 loss All 4 gene
-NF2 loss All 5 gene
+NF2 loss All 4 gene
NFAM1 loss All 12 gene
NFAM1 loss Meningioma 4 gene
NFASC gain All 4 gene
@@ -9493,7 +9492,7 @@ NINJ2-AS1 gain All 4 gene
NIP7 gain All 6 gene
NIP7 loss All 8 gene
NIP7 loss HGAT 6 gene
-NIPSNAP1 loss All 6 gene
+NIPSNAP1 loss All 5 gene
NIPSNAP2 gain All 18 gene
NIPSNAP2 gain HGAT 8 gene
NIPSNAP2 gain Medulloblastoma 4 gene
@@ -9900,13 +9899,13 @@ OR52L1 loss All 9 gene
OR52L1 loss HGAT 4 gene
OR52M1 loss All 7 gene
OR52M1 loss HGAT 4 gene
-OR52N1 loss All 11 gene
+OR52N1 loss All 10 gene
OR52N1 loss HGAT 5 gene
OR52N2 loss All 9 gene
OR52N2 loss HGAT 4 gene
OR52N4 loss All 9 gene
OR52N4 loss HGAT 4 gene
-OR52N5 loss All 10 gene
+OR52N5 loss All 9 gene
OR52R1 loss All 7 gene
OR52R1 loss HGAT 4 gene
OR52W1 loss All 8 gene
@@ -9957,7 +9956,7 @@ OR9Q1 gain All 4 gene
OR9Q2 gain All 4 gene
ORAI2 gain All 5 gene
ORAI3 gain All 8 gene
-ORAI3 loss All 6 gene
+ORAI3 loss All 5 gene
ORC5 gain All 17 gene
ORC5 gain Medulloblastoma 6 gene
ORC6 loss All 13 gene
@@ -10052,8 +10051,8 @@ PANO1 gain All 7 gene
PANO1 loss All 5 gene
PANO1 gain LGAT 4 gene
PANX2 loss All 13 gene
-PAPSS2 loss All 11 gene
-PAPSS2 loss HGAT 8 gene
+PAPSS2 loss All 10 gene
+PAPSS2 loss HGAT 7 gene
PAQR4 loss All 4 gene
PAQR7 loss All 6 gene
PARD3 loss All 5 gene
@@ -10229,7 +10228,7 @@ PHKG1 gain All 18 gene
PHKG1 gain HGAT 8 gene
PHKG1 gain Medulloblastoma 4 gene
PHKG2 gain All 8 gene
-PHKG2 loss All 6 gene
+PHKG2 loss All 5 gene
PHLDA3 gain All 5 gene
PHLDA3 gain HGAT 4 gene
PHLPP2 loss All 10 gene
@@ -10296,9 +10295,9 @@ PILRB gain LGAT 4 gene
PIM3 loss All 19 gene
PIM3 loss Meningioma 5 gene
PINX1 gain All 11 gene
-PINX1 loss All 9 gene
+PINX1 loss All 8 gene
PINX1 gain HGAT 4 gene
-PINX1 loss Medulloblastoma 5 gene
+PINX1 loss Medulloblastoma 4 gene
PIP4K2B gain All 19 gene
PIP4K2B gain Medulloblastoma 15 gene
PIP4P1 gain All 5 gene
@@ -10309,8 +10308,8 @@ PIP5K1B loss HGAT 4 gene
PIP5KL1 loss All 5 gene
PIRT loss All 4 gene
PITPNM3 loss All 4 gene
-PIWIL3 loss All 17 gene
-PIWIL3 loss ATRT 5 gene
+PIWIL3 loss All 16 gene
+PIWIL3 loss ATRT 4 gene
PIWIL3 loss LGAT 4 gene
PIWIL3 loss Meningioma 4 gene
PKD1L3 loss All 10 gene
@@ -10468,8 +10467,8 @@ POLRMT loss All 4 gene
POM121 gain All 14 gene
POM121 gain LGAT 4 gene
POM121C gain All 10 gene
-POM121L9P loss All 15 gene
-POM121L9P loss ATRT 7 gene
+POM121L9P loss All 14 gene
+POM121L9P loss ATRT 6 gene
POM121L9P loss LGAT 4 gene
POMZP3 gain All 10 gene
POP7 gain All 12 gene
@@ -10529,9 +10528,8 @@ PPP1R35 gain All 12 gene
PPP1R35 gain LGAT 4 gene
PPP1R3A gain All 7 gene
PPP1R3B gain All 13 gene
-PPP1R3B loss All 7 gene
+PPP1R3B loss All 6 gene
PPP1R3B gain HGAT 4 gene
-PPP1R3B loss Medulloblastoma 4 gene
PPP1R3D gain All 14 gene
PPP1R3D gain HGAT 5 gene
PPP1R3E gain All 4 gene
@@ -10551,8 +10549,8 @@ PRAC1 gain Medulloblastoma 8 gene
PRAC2 gain All 11 gene
PRAC2 gain Medulloblastoma 8 gene
PRAG1 gain All 10 gene
-PRAG1 loss All 8 gene
-PRAG1 loss Medulloblastoma 5 gene
+PRAG1 loss All 7 gene
+PRAG1 loss Medulloblastoma 4 gene
PRAME loss All 6 gene
PRAMEF1 loss All 5 gene
PRAMEF10 loss All 5 gene
@@ -10634,7 +10632,7 @@ PRPSAP2 loss Medulloblastoma 8 gene
PRR11 gain All 5 gene
PRR11 gain HGAT 4 gene
PRR14 gain All 8 gene
-PRR14 loss All 6 gene
+PRR14 loss All 5 gene
PRR15L gain All 8 gene
PRR15L gain Medulloblastoma 6 gene
PRR5L loss All 6 gene
@@ -10655,18 +10653,18 @@ PRSS3 loss All 6 gene
PRSS30P loss All 4 gene
PRSS33 loss All 4 gene
PRSS36 gain All 8 gene
-PRSS36 loss All 6 gene
+PRSS36 loss All 5 gene
PRSS41 loss All 4 gene
PRSS53 gain All 8 gene
-PRSS53 loss All 6 gene
+PRSS53 loss All 5 gene
PRSS55 gain All 11 gene
-PRSS55 loss All 9 gene
+PRSS55 loss All 8 gene
PRSS55 gain HGAT 4 gene
-PRSS55 loss Medulloblastoma 5 gene
+PRSS55 loss Medulloblastoma 4 gene
PRSS57 gain All 4 gene
PRSS57 loss All 4 gene
PRSS8 gain All 8 gene
-PRSS8 loss All 6 gene
+PRSS8 loss All 5 gene
PRTN3 gain All 4 gene
PRTN3 loss All 4 gene
PRXL2B loss All 5 gene
@@ -10809,15 +10807,15 @@ PWRN2 loss HGAT 5 gene
PWWP2B loss All 4 gene
PXDN gain All 5 gene
PYCARD gain All 8 gene
-PYCARD loss All 6 gene
+PYCARD loss All 5 gene
PYCARD-AS1 gain All 8 gene
-PYCARD-AS1 loss All 6 gene
+PYCARD-AS1 loss All 5 gene
PYCR1 gain All 16 gene
PYCR1 gain Medulloblastoma 8 gene
PYCR3 gain All 11 gene
PYCR3 gain HGAT 5 gene
PYDC1 gain All 8 gene
-PYDC1 loss All 6 gene
+PYDC1 loss All 5 gene
PYGO2 gain All 16 gene
PYGO2 gain HGAT 8 gene
PYROXD1 loss All 5 gene
@@ -11017,8 +11015,8 @@ RFPL1 loss All 5 gene
RFX5 gain All 5 gene
RGL2 gain All 4 gene
RGL3 gain All 4 gene
-RGL4 loss All 14 gene
-RGL4 loss ATRT 5 gene
+RGL4 loss All 13 gene
+RGL4 loss ATRT 4 gene
RGP1 gain All 5 gene
RGPD6 gain All 4 gene
RGPD6 gain HGAT 4 gene
@@ -11152,7 +11150,7 @@ RNF31 loss All 4 gene
RNF32 gain All 9 gene
RNF32 gain HGAT 4 gene
RNF40 gain All 8 gene
-RNF40 loss All 6 gene
+RNF40 loss All 5 gene
RNF43 gain All 4 gene
RNH1 gain All 6 gene
RNH1 loss All 4 gene
@@ -11186,11 +11184,11 @@ ROBO2 loss All 4 gene
ROGDI loss All 6 gene
RORC gain All 7 gene
RORC gain HGAT 4 gene
-ROS1 loss All 6 gene
+ROS1 loss All 5 gene
RP1L1 gain All 11 gene
-RP1L1 loss All 9 gene
+RP1L1 loss All 8 gene
RP1L1 gain HGAT 4 gene
-RP1L1 loss Medulloblastoma 5 gene
+RP1L1 loss Medulloblastoma 4 gene
RPA1 loss All 4 gene
RPGRIP1 gain All 5 gene
RPH3AL loss All 4 gene
@@ -11500,9 +11498,9 @@ SEMA3F loss All 4 gene
SEMA3F-AS1 loss All 4 gene
SENP3 loss All 4 gene
SEPHS2 gain All 8 gene
-SEPHS2 loss All 6 gene
+SEPHS2 loss All 5 gene
SEPTIN1 gain All 8 gene
-SEPTIN1 loss All 5 gene
+SEPTIN1 loss All 4 gene
SEPTIN12 loss All 6 gene
SEPTIN14 gain All 18 gene
SEPTIN14 gain HGAT 8 gene
@@ -11547,7 +11545,7 @@ SERTAD4 loss All 4 gene
SET loss All 5 gene
SETBP1 loss All 4 gene
SETD1A gain All 8 gene
-SETD1A loss All 6 gene
+SETD1A loss All 5 gene
SETD2 loss All 4 gene
SEZ6L loss All 5 gene
SEZ6L2 loss All 5 gene
@@ -11566,8 +11564,8 @@ SGCD loss HGAT 4 gene
SGMS1 loss All 4 gene
SGSH gain All 16 gene
SGSH gain Medulloblastoma 8 gene
-SGSM1 loss All 15 gene
-SGSM1 loss ATRT 5 gene
+SGSM1 loss All 14 gene
+SGSM1 loss ATRT 4 gene
SGSM1 loss Meningioma 4 gene
SGSM2 gain All 4 gene
SH2B2 gain All 5 gene
@@ -11670,8 +11668,8 @@ SLC23A2 gain All 6 gene
SLC24A1 gain All 4 gene
SLC24A1 gain HGAT 4 gene
SLC24A2 gain All 5 gene
-SLC24A2 loss All 11 gene
-SLC24A2 loss HGAT 9 gene
+SLC24A2 loss All 10 gene
+SLC24A2 loss HGAT 8 gene
SLC25A1 gain All 5 gene
SLC25A1 loss All 35 gene
SLC25A1 loss ATRT 9 gene
@@ -11709,8 +11707,8 @@ SLC27A1 gain All 5 gene
SLC27A3 gain All 15 gene
SLC27A3 gain HGAT 7 gene
SLC27A4 loss All 5 gene
-SLC2A11 loss All 13 gene
-SLC2A11 loss ATRT 5 gene
+SLC2A11 loss All 12 gene
+SLC2A11 loss ATRT 4 gene
SLC2A14 gain All 6 gene
SLC2A14 loss All 4 gene
SLC2A3 gain All 6 gene
@@ -11742,9 +11740,9 @@ SLC35G4 loss All 19 gene
SLC35G4 gain Medulloblastoma 6 gene
SLC35G4 loss HGAT 9 gene
SLC35G5 gain All 11 gene
-SLC35G5 loss All 9 gene
+SLC35G5 loss All 8 gene
SLC35G5 gain HGAT 4 gene
-SLC35G5 loss Medulloblastoma 5 gene
+SLC35G5 loss Medulloblastoma 4 gene
SLC37A1 gain All 8 gene
SLC37A1 loss All 5 gene
SLC37A3 gain All 110 gene
@@ -11795,7 +11793,7 @@ SLC5A10 loss All 22 gene
SLC5A10 loss HGAT 10 gene
SLC5A10 loss Medulloblastoma 8 gene
SLC5A2 gain All 8 gene
-SLC5A2 loss All 6 gene
+SLC5A2 loss All 5 gene
SLC5A5 gain All 4 gene
SLC5A8 loss All 5 gene
SLC66A1 gain All 5 gene
@@ -11868,8 +11866,8 @@ SLX4 loss All 5 gene
SMAD6 gain All 5 gene
SMAD6 gain HGAT 5 gene
SMARCA4 gain All 4 gene
-SMARCB1 loss All 16 gene
-SMARCB1 loss ATRT 7 gene
+SMARCB1 loss All 13 gene
+SMARCB1 loss ATRT 4 gene
SMARCC1 loss All 4 gene
SMARCD3 gain All 11 gene
SMC1B loss All 4 gene
@@ -11892,7 +11890,7 @@ SMCR8 loss Medulloblastoma 19 gene
SMDT1 loss All 12 gene
SMDT1 loss Meningioma 4 gene
SMG1P5 gain All 8 gene
-SMG1P5 loss All 5 gene
+SMG1P5 loss All 4 gene
SMG6 gain All 4 gene
SMG8 gain All 5 gene
SMG8 gain HGAT 4 gene
@@ -11977,7 +11975,7 @@ SNORA24B gain HGAT 4 gene
SNORA26 gain All 9 gene
SNORA26 gain HGAT 9 gene
SNORA30 gain All 8 gene
-SNORA30 loss All 6 gene
+SNORA30 loss All 5 gene
SNORA30B gain All 4 gene
SNORA30B loss All 9 gene
SNORA30B loss HGAT 6 gene
@@ -12024,7 +12022,7 @@ SNORA77B loss LGAT 4 gene
SNORA77B loss Meningioma 5 gene
SNORA79B gain All 5 gene
SNORA80C gain All 8 gene
-SNORA80C loss All 5 gene
+SNORA80C loss All 4 gene
SNORD10 loss All 4 gene
SNORD107 gain All 6 gene
SNORD107 loss All 7 gene
@@ -12353,8 +12351,8 @@ SNPH loss HGAT 4 gene
SNRPA1 gain All 4 gene
SNRPB gain All 6 gene
SNRPB loss All 4 gene
-SNRPD3 loss All 14 gene
-SNRPD3 loss ATRT 5 gene
+SNRPD3 loss All 13 gene
+SNRPD3 loss ATRT 4 gene
SNRPD3 loss LGAT 4 gene
SNRPE gain All 4 gene
SNRPN gain All 6 gene
@@ -12396,9 +12394,9 @@ SOX6 gain All 5 gene
SOX6 loss All 8 gene
SOX6 loss HGAT 7 gene
SOX7 gain All 11 gene
-SOX7 loss All 9 gene
+SOX7 loss All 8 gene
SOX7 gain HGAT 4 gene
-SOX7 loss Medulloblastoma 5 gene
+SOX7 loss Medulloblastoma 4 gene
SP100 gain All 5 gene
SP110 gain All 5 gene
SP140 gain All 5 gene
@@ -12451,11 +12449,11 @@ SPECC1 loss All 17 gene
SPECC1 gain Medulloblastoma 24 gene
SPECC1 loss HGAT 8 gene
SPECC1 loss Medulloblastoma 5 gene
-SPECC1L loss All 15 gene
-SPECC1L loss ATRT 7 gene
+SPECC1L loss All 14 gene
+SPECC1L loss ATRT 6 gene
SPECC1L loss LGAT 4 gene
-SPECC1L-ADORA2A loss All 15 gene
-SPECC1L-ADORA2A loss ATRT 7 gene
+SPECC1L-ADORA2A loss All 14 gene
+SPECC1L-ADORA2A loss ATRT 6 gene
SPECC1L-ADORA2A loss LGAT 4 gene
SPEF1 gain All 7 gene
SPG21 gain All 5 gene
@@ -12513,7 +12511,7 @@ SQSTM1 gain All 4 gene
SQSTM1 loss All 9 gene
SQSTM1 loss HGAT 4 gene
SRCAP gain All 8 gene
-SRCAP loss All 6 gene
+SRCAP loss All 5 gene
SRCIN1 gain All 19 gene
SRCIN1 gain Medulloblastoma 15 gene
SRD5A3 gain All 7 gene
@@ -12621,10 +12619,10 @@ STT3A loss All 4 gene
STX1A gain All 14 gene
STX1A gain HGAT 6 gene
STX1B gain All 8 gene
-STX1B loss All 6 gene
+STX1B loss All 5 gene
STX3 gain All 4 gene
STX4 gain All 8 gene
-STX4 loss All 6 gene
+STX4 loss All 5 gene
STX6 loss All 5 gene
STXBP1 loss All 5 gene
STXBP3 loss All 4 gene
@@ -12644,8 +12642,8 @@ SUN2 loss All 5 gene
SUN5 gain All 9 gene
SUPT16H gain All 5 gene
SUPT4H1 gain All 4 gene
-SUSD2 loss All 13 gene
-SUSD2 loss ATRT 6 gene
+SUSD2 loss All 12 gene
+SUSD2 loss ATRT 5 gene
SV2A gain All 11 gene
SV2A gain Ependymoma 4 gene
SWAP70 gain All 4 gene
@@ -12750,7 +12748,7 @@ TAT loss HGAT 6 gene
TAT-AS1 loss All 10 gene
TAT-AS1 loss HGAT 6 gene
TBC1D10B gain All 8 gene
-TBC1D10B loss All 5 gene
+TBC1D10B loss All 4 gene
TBC1D13 loss All 5 gene
TBC1D14 gain All 4 gene
TBC1D16 gain All 16 gene
@@ -12824,9 +12822,9 @@ TCP10L loss All 4 gene
TCTA loss All 4 gene
TCTEX1D2 loss All 4 gene
TDH gain All 11 gene
-TDH loss All 9 gene
+TDH loss All 8 gene
TDH gain HGAT 4 gene
-TDH loss Medulloblastoma 5 gene
+TDH loss Medulloblastoma 4 gene
TDRD10 gain All 16 gene
TDRD10 gain HGAT 8 gene
TDRD9 gain All 5 gene
@@ -12894,7 +12892,7 @@ TFR2 gain All 12 gene
TFR2 gain LGAT 4 gene
TFRC loss All 4 gene
TGFB1I1 gain All 8 gene
-TGFB1I1 loss All 6 gene
+TGFB1I1 loss All 5 gene
TGM1 loss All 4 gene
TGM3 gain All 6 gene
TGM3 loss All 4 gene
@@ -13060,8 +13058,8 @@ TMEM208 gain All 6 gene
TMEM208 loss All 8 gene
TMEM208 loss HGAT 6 gene
TMEM210 gain All 7 gene
-TMEM211 loss All 16 gene
-TMEM211 loss ATRT 5 gene
+TMEM211 loss All 15 gene
+TMEM211 loss ATRT 4 gene
TMEM211 loss Meningioma 5 gene
TMEM215 loss All 4 gene
TMEM215 loss HGAT 4 gene
@@ -13100,7 +13098,7 @@ TMEM254 loss All 8 gene
TMEM254 loss HGAT 4 gene
TMEM259 loss All 4 gene
TMEM265 gain All 8 gene
-TMEM265 loss All 6 gene
+TMEM265 loss All 5 gene
TMEM268 gain All 5 gene
TMEM270 gain All 14 gene
TMEM270 gain HGAT 6 gene
@@ -13179,9 +13177,9 @@ TNFSF8 gain All 4 gene
TNK2 gain All 6 gene
TNK2 loss All 4 gene
TNKS gain All 12 gene
-TNKS loss All 9 gene
+TNKS loss All 8 gene
TNKS gain HGAT 4 gene
-TNKS loss Medulloblastoma 5 gene
+TNKS loss Medulloblastoma 4 gene
TNKS1BP1 gain All 4 gene
TNNI1 gain All 5 gene
TNNI1 gain HGAT 4 gene
@@ -13337,7 +13335,7 @@ TRIM66 loss HGAT 5 gene
TRIM68 loss All 7 gene
TRIM68 loss HGAT 4 gene
TRIM72 gain All 8 gene
-TRIM72 loss All 6 gene
+TRIM72 loss All 5 gene
TRIM73 gain All 10 gene
TRIM74 gain All 11 gene
TRIOBP loss All 5 gene
@@ -13531,7 +13529,7 @@ UBB loss All 47 gene
UBB loss HGAT 10 gene
UBB loss Medulloblastoma 31 gene
UBBP4 gain All 9 gene
-UBBP4 loss All 8 gene
+UBBP4 loss All 7 gene
UBBP4 gain Medulloblastoma 7 gene
UBBP4 loss HGAT 5 gene
UBE2D1 loss All 8 gene
@@ -13611,8 +13609,8 @@ UNC45B gain All 23 gene
UNC45B loss All 6 gene
UNC45B gain Medulloblastoma 19 gene
UNC5D gain All 4 gene
-UPB1 loss All 14 gene
-UPB1 loss ATRT 6 gene
+UPB1 loss All 13 gene
+UPB1 loss ATRT 5 gene
UPB1 loss LGAT 4 gene
UPK3B gain All 8 gene
UPK3BL1 gain All 4 gene
@@ -13701,7 +13699,7 @@ VEZF1 gain All 5 gene
VGF gain All 9 gene
VGLL4 gain All 4 gene
VKORC1 gain All 8 gene
-VKORC1 loss All 6 gene
+VKORC1 loss All 5 gene
VKORC1L1 gain All 33 gene
VKORC1L1 gain Ganglioglioma 4 gene
VKORC1L1 gain HGAT 9 gene
@@ -13710,13 +13708,13 @@ VKORC1L1 gain Medulloblastoma 7 gene
VN1R1 gain All 9 gene
VN1R1 gain Medulloblastoma 4 gene
VN1R3 gain All 5 gene
-VN1R3 loss All 6 gene
+VN1R3 loss All 5 gene
VN1R5 gain All 4 gene
VOPP1 gain All 19 gene
VOPP1 gain HGAT 8 gene
VOPP1 gain Medulloblastoma 5 gene
-VPREB3 loss All 14 gene
-VPREB3 loss ATRT 5 gene
+VPREB3 loss All 13 gene
+VPREB3 loss ATRT 4 gene
VPS13D loss All 5 gene
VPS16 gain All 7 gene
VPS28 gain All 8 gene
@@ -13821,13 +13819,13 @@ WWP2 loss All 8 gene
WWP2 loss HGAT 6 gene
XBP1 loss All 6 gene
XKR5 gain All 15 gene
-XKR5 loss All 13 gene
+XKR5 loss All 12 gene
XKR5 loss HGAT 5 gene
-XKR5 loss Medulloblastoma 7 gene
+XKR5 loss Medulloblastoma 6 gene
XKR6 gain All 11 gene
-XKR6 loss All 9 gene
+XKR6 loss All 8 gene
XKR6 gain HGAT 4 gene
-XKR6 loss Medulloblastoma 5 gene
+XKR6 loss Medulloblastoma 4 gene
XKR7 gain All 9 gene
Xp loss All 9 arm
Xp loss Medulloblastoma 4 arm
@@ -14219,7 +14217,7 @@ ZNF263 loss All 5 gene
ZNF264 gain All 8 gene
ZNF264 gain Medulloblastoma 4 gene
ZNF267 gain All 5 gene
-ZNF267 loss All 6 gene
+ZNF267 loss All 5 gene
ZNF273 gain All 20 gene
ZNF273 gain Ependymoma 4 gene
ZNF273 gain HGAT 5 gene
@@ -14324,7 +14322,7 @@ ZNF471 gain All 8 gene
ZNF471 gain Medulloblastoma 4 gene
ZNF479 gain All 4 gene
ZNF48 gain All 8 gene
-ZNF48 loss All 5 gene
+ZNF48 loss All 4 gene
ZNF480 gain All 5 gene
ZNF485 gain All 4 gene
ZNF485 loss All 6 gene
@@ -14404,9 +14402,9 @@ ZNF624 loss Medulloblastoma 31 gene
ZNF625 gain All 5 gene
ZNF627 gain All 4 gene
ZNF629 gain All 8 gene
-ZNF629 loss All 6 gene
+ZNF629 loss All 5 gene
ZNF646 gain All 8 gene
-ZNF646 loss All 6 gene
+ZNF646 loss All 5 gene
ZNF648 loss All 4 gene
ZNF652 gain All 11 gene
ZNF652 gain Medulloblastoma 8 gene
@@ -14418,7 +14416,7 @@ ZNF667 gain Medulloblastoma 4 gene
ZNF667-AS1 gain All 8 gene
ZNF667-AS1 gain Medulloblastoma 4 gene
ZNF668 gain All 8 gene
-ZNF668 loss All 6 gene
+ZNF668 loss All 5 gene
ZNF669 gain All 5 gene
ZNF670 gain All 5 gene
ZNF670-ZNF695 gain All 5 gene
@@ -14436,16 +14434,16 @@ ZNF683 loss All 6 gene
ZNF687 gain All 5 gene
ZNF687-AS1 gain All 5 gene
ZNF688 gain All 8 gene
-ZNF688 loss All 6 gene
+ZNF688 loss All 5 gene
ZNF689 gain All 8 gene
-ZNF689 loss All 6 gene
+ZNF689 loss All 5 gene
ZNF69 gain All 5 gene
ZNF695 gain All 5 gene
ZNF696 gain All 12 gene
ZNF696 gain HGAT 5 gene
ZNF697 loss All 5 gene
-ZNF70 loss All 14 gene
-ZNF70 loss ATRT 5 gene
+ZNF70 loss All 13 gene
+ZNF70 loss ATRT 4 gene
ZNF700 gain All 5 gene
ZNF702P loss All 4 gene
ZNF702P loss HGAT 4 gene
@@ -14460,7 +14458,7 @@ ZNF713 gain All 18 gene
ZNF713 gain HGAT 8 gene
ZNF713 gain Medulloblastoma 4 gene
ZNF720 gain All 5 gene
-ZNF720 loss All 6 gene
+ZNF720 loss All 5 gene
ZNF727 gain All 20 gene
ZNF727 gain Ependymoma 4 gene
ZNF727 gain HGAT 5 gene
@@ -14483,21 +14481,21 @@ ZNF74 loss LGAT 4 gene
ZNF74 loss Meningioma 5 gene
ZNF746 gain All 4 gene
ZNF747 gain All 8 gene
-ZNF747 loss All 6 gene
+ZNF747 loss All 5 gene
ZNF749 gain All 9 gene
ZNF749 gain Medulloblastoma 4 gene
ZNF75A loss All 4 gene
ZNF761 loss All 4 gene
ZNF763 gain All 5 gene
ZNF764 gain All 8 gene
-ZNF764 loss All 6 gene
+ZNF764 loss All 5 gene
ZNF765 loss All 4 gene
ZNF766 gain All 5 gene
ZNF767P gain All 4 gene
ZNF768 gain All 8 gene
-ZNF768 loss All 6 gene
+ZNF768 loss All 5 gene
ZNF771 gain All 8 gene
-ZNF771 loss All 6 gene
+ZNF771 loss All 5 gene
ZNF772 gain All 9 gene
ZNF772 gain Medulloblastoma 4 gene
ZNF773 gain All 9 gene
@@ -14512,7 +14510,7 @@ ZNF778 loss HGAT 11 gene
ZNF778 loss Medulloblastoma 8 gene
ZNF783 gain All 4 gene
ZNF785 gain All 8 gene
-ZNF785 loss All 6 gene
+ZNF785 loss All 5 gene
ZNF786 gain All 4 gene
ZNF787 gain All 8 gene
ZNF787 gain Medulloblastoma 4 gene
@@ -14539,7 +14537,7 @@ ZNF830 gain Medulloblastoma 19 gene
ZNF835 gain All 8 gene
ZNF835 gain Medulloblastoma 4 gene
ZNF843 gain All 8 gene
-ZNF843 loss All 6 gene
+ZNF843 loss All 5 gene
ZNF844 gain All 5 gene
ZNF845 loss All 4 gene
ZNF853 gain All 4 gene
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_with_ucsc_cytoband_status.tsv.gz b/analyses/focal-cn-file-preparation/results/consensus_seg_with_ucsc_cytoband_status.tsv.gz
index dded762652..ea4a8d5491 100644
Binary files a/analyses/focal-cn-file-preparation/results/consensus_seg_with_ucsc_cytoband_status.tsv.gz and b/analyses/focal-cn-file-preparation/results/consensus_seg_with_ucsc_cytoband_status.tsv.gz differ