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Update ashm - fix objects #116

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Merged
Kdreval merged 2 commits into from
May 20, 2025
Merged

Update ashm - fix objects #116

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0dcf7ec
update actual ashm objects
gillissierra May 20, 2025
6eb65df
Merge commit 'a0dbb96624006e638ba4e4a0209a18f164230391' into update_ashm
gillissierra May 20, 2025
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Binary file modified data/grch37_ashm_regions.rda
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Binary file modified data/hg38_ashm_regions.rda
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Binary file modified data/lymphoma_genes.rda
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391 changes: 391 additions & 0 deletions inst/extdata/lacy_genes.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,391 @@
Gene Feature Annotation as aSHM Included in statistical analysis
BCL11A Amplification NA Yes
MALT1 Amplification NA Yes
REL Amplification NA Yes
XPO1 Amplification NA Yes
CD58 Homozygous deletion NA Yes
CDKN2A Homozygous deletion NA Yes
DDX3X Homozygous deletion NA Yes
PRDM1 Homozygous deletion NA Yes
RB1 Homozygous deletion NA Yes
TNFAIP3 Homozygous deletion NA Yes
TNFRSF14 Homozygous deletion NA Yes
TP53 Homozygous deletion NA Yes
ARID1A Mutation Yes
ATM Mutation Yes
B2M Mutation Yes
BCL10 Mutation Yes
BCL2 Mutation Yes Yes
BCL6 Mutation Yes
BCL7A Mutation Yes
BCOR Mutation Yes
BLM Mutation Yes
BRAF Mutation Yes
BTG1 Mutation Yes Yes
BTG2 Mutation Yes Yes
BTK Mutation Yes
CARD11 Mutation Yes
CCND3 Mutation Yes
CD70 Mutation Yes
CD79A Mutation Yes
CD79B Mutation Yes
CD83 Mutation Yes Yes
CIITA Mutation Yes
CREBBP Mutation Yes
CXCR4 Mutation Yes
DNMT3A Mutation Yes
DTX1 Mutation Yes Yes
EBF1 Mutation Yes
EGR1 Mutation Yes
EP300 Mutation Yes
ETV6 Mutation Yes
EZH2_646 Mutation Yes
EZH2_noncan Mutation Yes
FAS Mutation Yes
FAT1 Mutation Yes
FAT3 Mutation Yes
FAT4 Mutation Yes
FBXO11 Mutation Yes
FOXO1 Mutation Yes
GNA13 Mutation Yes
HIST1H1B Mutation Yes Yes
HIST1H1C Mutation Yes Yes
HIST1H1D Mutation Yes Yes
HIST1H1E Mutation Yes Yes
HIST1H2AC Mutation Yes Yes
HIST1H2AG Mutation Yes Yes
HIST1H2AM Mutation Yes Yes
HIST1H2BC Mutation Yes Yes
HIST1H2BD Mutation Yes Yes
HIST1H2BG Mutation Yes Yes
HIST1H3B Mutation Yes Yes
HIST1H3G Mutation Yes Yes
ID3 Mutation Yes
IKZF1 Mutation Yes
IKZF3 Mutation Yes
IRF1 Mutation Yes
IRF4 Mutation Yes
IRF8 Mutation Yes
ITPKB Mutation Yes
KLF2 Mutation Yes
KLHL6 Mutation Yes
KMT2C Mutation Yes
KMT2D Mutation Yes
KRAS Mutation Yes
LTB Mutation Yes
MAP2K1 Mutation Yes
MEF2B Mutation Yes
MGA Mutation Yes
MPEG1 Mutation Yes
MYC Mutation Yes Yes
MYD88_265 Mutation Yes
MYD88_noncan Mutation Yes
NF1 Mutation Yes
NFKBIA Mutation Yes
NFKBIE Mutation Yes
NOTCH1 Mutation Yes
NOTCH2 Mutation Yes
P2RY8 Mutation Yes
PAX5 Mutation Yes
PDS5B Mutation Yes
PIK3CD Mutation Yes
PIK3R1 Mutation Yes
PIM1 Mutation Yes Yes
POU2AF1 Mutation Yes
POU2F2_239 Mutation Yes
POU2F2_noncan Mutation Yes
PRKCB Mutation Yes
PTEN Mutation Yes
PTPN6 Mutation Yes
PTPRC Mutation Yes
RASA2 Mutation Yes
RHOA Mutation Yes
ROBO1 Mutation Yes
SGK1 Mutation Yes Yes
SMARCA4 Mutation Yes
SOCS1 Mutation Yes Yes
SPEN Mutation Yes
SPIB Mutation Yes
SRSF2 Mutation Yes
STAT3 Mutation Yes
STAT6 Mutation Yes
TBL1XR1 Mutation Yes
TET2 Mutation Yes
TLR2 Mutation Yes
TMEM30A Mutation Yes
TNF Mutation Yes
XPO1 Mutation Yes
ZFP36L1 Mutation Yes
AKAP9 Amplification NA
BCL2 Amplification NA
BCL6 Amplification NA
CALR Amplification NA
CARD11 Amplification NA
CCND3 Amplification NA
CD274 Amplification NA
CD79A Amplification NA
CD79B Amplification NA
CDK4 Amplification NA
CXCR4 Amplification NA
ETNK1 Amplification NA
FGFR3 Amplification NA
IL7R Amplification NA
IRF4 Amplification NA
IRF8 Amplification NA
JAK2 Amplification NA
KDM4C Amplification NA
KMT2A Amplification NA
LCK Amplification NA
MYC Amplification NA
MYD88 Amplification NA
NFKBIZ Amplification NA
PDCD1LG2 Amplification NA
PIM1 Amplification NA
POU2AF1 Amplification NA
POU2F2 Amplification NA
PRKCB Amplification NA
PTPRD Amplification NA
SETBP1 Amplification NA
SETDB1 Amplification NA
SMC1A Amplification NA
SPIB Amplification NA
TLR2 Amplification NA
WHSC1 Amplification NA
ARID1A Homozygous deletion NA
ATRX Homozygous deletion NA
BCL7A Homozygous deletion NA
BCOR Homozygous deletion NA
BCORL1 Homozygous deletion NA
BIRC2 Homozygous deletion NA
BIRC3 Homozygous deletion NA
CD274 Homozygous deletion NA
CIITA Homozygous deletion NA
CUX1 Homozygous deletion NA
CYLD Homozygous deletion NA
EBF1 Homozygous deletion NA
ECT2L Homozygous deletion NA
EGR2 Homozygous deletion NA
ETV6 Homozygous deletion NA
FAS Homozygous deletion NA
FAT1 Homozygous deletion NA
FAT3 Homozygous deletion NA
FBXW10 Homozygous deletion NA
FBXW7 Homozygous deletion NA
FNDC3A Homozygous deletion NA
GATA1 Homozygous deletion NA
GATA3 Homozygous deletion NA
GNA13 Homozygous deletion NA
HLAA Homozygous deletion NA
HLAB Homozygous deletion NA
HLAC Homozygous deletion NA
IKZF1 Homozygous deletion NA
IRF1 Homozygous deletion NA
KDM6A Homozygous deletion NA
KLF2 Homozygous deletion NA
MLH1 Homozygous deletion NA
NFKBIA Homozygous deletion NA
PHF6 Homozygous deletion NA
PTEN Homozygous deletion NA
PTPN6 Homozygous deletion NA
RCOR1 Homozygous deletion NA
SGK1 Homozygous deletion NA
SPEN Homozygous deletion NA
STAG2 Homozygous deletion NA
TMEM30A Homozygous deletion NA
TNFAIP2 Homozygous deletion NA
TP73 Homozygous deletion NA
TRAF3 Homozygous deletion NA
ZFP36L1 Homozygous deletion NA
ZRSR2 Homozygous deletion NA
ABL1 Mutation
ACTG1 Mutation
AKAP9 Mutation
ALK Mutation
APC Mutation
ARAF Mutation
ARID1B Mutation
ARID2 Mutation
ASXL1 Mutation
ASXL2 Mutation
ATRX Mutation
BACH2 Mutation
BCL11A Mutation
BCORL1 Mutation
BCR Mutation
BIRC2 Mutation
BIRC3 Mutation
BLNK Mutation
CALR Mutation
CASP8 Mutation
CBFB Mutation
CBL Mutation
CCND1 Mutation
CD19 Mutation
CD22 Mutation
CD274 Mutation
CD58 Mutation
CDK4 Mutation
CDKN1B Mutation
CDKN2A Mutation
CDKN2B Mutation
CDKN2C Mutation
CEBPA Mutation
CHD2 Mutation
CHD4 Mutation
CHEK2 Mutation
CHUK Mutation
CSF2RB Mutation
CSF3R Mutation
CTCF Mutation
CTNNB1 Mutation
CUX1 Mutation
CYLD Mutation
DDX3X Mutation
DIS3 Mutation
DNMT3B Mutation
DTX1 Mutation
ECT2L Mutation
EED Mutation
EGFR Mutation
EGR2 Mutation
ERBB2 Mutation
ERCC4 Mutation
ETNK1 Mutation
ETV1 Mutation
FAM46C Mutation
FAT2 Mutation
FBXW10 Mutation
FBXW7 Mutation
FGFR2 Mutation
FGFR3 Mutation
FLT3 Mutation
FNDC3A Mutation
FYN Mutation
GATA1 Mutation
GATA2 Mutation
GATA3 Mutation
GCSAM Mutation
GMPS Mutation
GNAS Mutation
H3F3A Mutation
H3F3B Mutation
HIST1H2BO Mutation Yes
HLA-A Mutation
HLA-B Mutation
HLA-C Mutation
HRAS Mutation
IDH1 Mutation
IDH2 Mutation
IKBKG Mutation
IL2RG Mutation
IL7R Mutation
INTS12 Mutation
JAK1 Mutation
JAK2 Mutation
JAK3 Mutation
KDM4C Mutation
KDM6A Mutation
KDR Mutation
KIT Mutation
KMT2A Mutation
KMT2E Mutation
KSR2 Mutation
LCK Mutation
LYN Mutation
MALT1 Mutation
MAP2K4 Mutation
MAX Mutation
MECOM Mutation
MED1 Mutation
MET Mutation
MLH1 Mutation
MPL Mutation
MSH2 Mutation
MSH6 Mutation
MTOR Mutation
MYB Mutation
NBEAL2 Mutation
NF2 Mutation
NFE2 Mutation
NFKB1 Mutation
NFKB2 Mutation
NFKBIZ Mutation
NPM1 Mutation
NRAS Mutation
NTRK1 Mutation
PBRM1 Mutation
PDGFRA Mutation
PDGFRB Mutation
PDK1 Mutation
PEG3 Mutation
PHF6 Mutation
PIK3CA Mutation
PLCG1 Mutation
PLCG2 Mutation
PMS2 Mutation
POT1 Mutation
PPM1D Mutation
PRDM1 Mutation
PRPF40B Mutation
PTCH1 Mutation
PTPN1 Mutation
PTPN11 Mutation
PTPRD Mutation
RAD21 Mutation
RAD51 Mutation
RAG2 Mutation
RB1 Mutation
RCOR1 Mutation
REL Mutation
RELN Mutation
RET Mutation
ROS1 Mutation
RPL10 Mutation
RPL5 Mutation
RPN1 Mutation
RPS15 Mutation
RPS2 Mutation
RUNX1 Mutation
S1PR2 Mutation
SAMHD1 Mutation
SETBP1 Mutation
SETD2 Mutation
SETDB1 Mutation
SF1 Mutation
SF3A1 Mutation
SF3B1 Mutation
SH2B3 Mutation
SMARCB1 Mutation
SMC1A Mutation
SMC3 Mutation
SNX7 Mutation
SP140 Mutation
SPRY4 Mutation
STAG2 Mutation
STAT5B Mutation
STK11 Mutation
SUZ12 Mutation
SYK Mutation
TCF3 Mutation
TET1 Mutation
TET3 Mutation
TGDS Mutation
THPO Mutation
THRAP3 Mutation
TNFAIP2 Mutation
TNFAIP3 Mutation
TNFRSF14 Mutation
TNKS Mutation
TP53 Mutation
TP73 Mutation
TRAF2 Mutation
TRAF3 Mutation
TYK2 Mutation
U2AF1 Mutation
U2AF2 Mutation
USP29 Mutation
USP6 Mutation
WHSC1 Mutation
WT1 Mutation
XBP1 Mutation
ZRSR2 Mutation
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