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更新数据库

master
chaopower 2024-02-01 17:43:01 +08:00
parent db1c34a59f
commit 4dff3bf0b0
9 changed files with 11535 additions and 10277 deletions
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26
codes/filter_snpindel.pl
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@ -262,14 +262,28 @@ while (<IN>) {
}
my $clisig;
if ($line[16] =~ /Likely_pathogenic|drug/i) {
$clisig = '2';
}
elsif ($line[16] =~ /pathogenic/i and $line[16] !~ /Conflicting/i) {
$clisig = '1';
# somatic 依据oncogenic改变等级
if (($pipeline eq 'somatic') | ($pipeline eq 'hotspot')) {
if ($oncogenic_col =~ /Likely Oncogenic/i) {
$clisig = '2';
}
elsif ($oncogenic_col =~ /Oncogenic/i) {
$clisig = '1';
}
else {
$clisig = '3';
}
}
else {
$clisig = '3';
if ($line[16] =~ /Likely_pathogenic|drug/i) {
$clisig = '2';
}
elsif ($line[16] =~ /pathogenic/i and $line[16] !~ /Conflicting/i) {
$clisig = '1';
}
else {
$clisig = '3';
}
}
my @genetags;

2
codes/public/blacklist.txt
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@ -19,3 +19,5 @@ chr6 31238909 31238910 GT TC HLA-C p.T187E
chr3 10088407 10088410 AGTA - FANCD2 p.V427Ffs*20
chr12 57112003 57112003 A G NACA p.M1104T
chr12 57112022 57112022 A G NACA p.S1098P
chr22 44324727 44324730 CCCC GCCT PNPLA3 p.I148M
chr7 116397716 116397716 C G MET p.P664A

13
database/cnv.csv
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@ -247,3 +247,16 @@ FLT3,Amplification,Likely Oncogenic,Gain-of-function,2
PRDM1,Deletion,Likely Oncogenic,Likely Loss-of-function,4
TLE1,Deletion,Likely Oncogenic,Likely Loss-of-function,2
TLE4,Deletion,Likely Oncogenic,Likely Loss-of-function,2
CCND2,Amplification,Likely Oncogenic,Likely Gain-of-function,3
FGFR3,Amplification,Likely Oncogenic,Likely Gain-of-function,.
MMS22L,Deletion,Likely Oncogenic,Likely Loss-of-function,.
CHEK2,Deletion,Likely Oncogenic,Likely Loss-of-function,.
DPAGT1,Amplification,Likely Oncogenic,Likely Gain-of-function,1
HGF,Amplification,Likely Oncogenic,Likely Gain-of-function,.
NTRK2,Amplification,Likely Oncogenic,Likely Gain-of-function,
NTRK3,Amplification,Likely Oncogenic,Likely Gain-of-function,
CSF1R,Amplification,Likely Oncogenic,Likely Gain-of-function,1
TLK2,Amplification,Likely Oncogenic,Likely Gain-of-function,1
RIT1,Amplification,Likely Oncogenic,Likely Gain-of-function,3
CRKL,Amplification,Likely Oncogenic,Likely Gain-of-function,2
FLT3,Amplification,Likely Oncogenic,Likely Gain-of-function,.

1 Gene Alteration Oncogenic Mutation_Effect Citations
247 PRDM1 Deletion Likely Oncogenic Likely Loss-of-function 4
248 TLE1 Deletion Likely Oncogenic Likely Loss-of-function 2
249 TLE4 Deletion Likely Oncogenic Likely Loss-of-function 2
250 CCND2 Amplification Likely Oncogenic Likely Gain-of-function 3
251 FGFR3 Amplification Likely Oncogenic Likely Gain-of-function .
252 MMS22L Deletion Likely Oncogenic Likely Loss-of-function .
253 CHEK2 Deletion Likely Oncogenic Likely Loss-of-function .
254 DPAGT1 Amplification Likely Oncogenic Likely Gain-of-function 1
255 HGF Amplification Likely Oncogenic Likely Gain-of-function .
256 NTRK2 Amplification Likely Oncogenic Likely Gain-of-function
257 NTRK3 Amplification Likely Oncogenic Likely Gain-of-function
258 CSF1R Amplification Likely Oncogenic Likely Gain-of-function 1
259 TLK2 Amplification Likely Oncogenic Likely Gain-of-function 1
260 RIT1 Amplification Likely Oncogenic Likely Gain-of-function 3
261 CRKL Amplification Likely Oncogenic Likely Gain-of-function 2
262 FLT3 Amplification Likely Oncogenic Likely Gain-of-function .

1
database/fusion.csv
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@ -337,3 +337,4 @@ NUP98,NSD1-NUP98 Fusion,Likely Oncogenic,Likely Gain-of-function,4
GTF2I,Fusion,Likely Oncogenic,Likely Gain-of-function,2
NRG1,SDC4-NRG1 Fusion,Likely Oncogenic,Likely Gain-of-function,
YY1,EWSR1-YY1 Fusion,Inconclusive,Inconclusive,1
TMPRSS2,TMPRSS2-ALPL Fusion,Resistance,Inconclusive,1

1 Gene Alteration Oncogenic Mutation_Effect Citations
337 GTF2I Fusion Likely Oncogenic Likely Gain-of-function 2
338 NRG1 SDC4-NRG1 Fusion Likely Oncogenic Likely Gain-of-function
339 YY1 EWSR1-YY1 Fusion Inconclusive Inconclusive 1
340 TMPRSS2 TMPRSS2-ALPL Fusion Resistance Inconclusive 1

1916
database/oncokbgene.txt
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32
database/oncotree.cancertype.20230801.txt
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@ -635,9 +635,27 @@ ST2101 SOLID-LUNG-LNET Lung Neuroendocrine Tumor 肺部神经内分泌肿瘤 Non
ST210101 SOLID-LUNG-LNET-SCLC Small Cell Lung Cancer 小细胞肺癌 Small Cell Lung Cancer 小细胞肺癌
ST210102 SOLID-LUNG-LNET-LUNE Large Cell Neuroendocrine Carcinoma 大细胞神经内分泌癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST210103 SOLID-LUNG-LNET-LUCA Lung Carcinoid 肺类癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST21010301 SOLID-LUNG-LNET-LUCA-ALUCA Atypical Lung Carcinoid 肺非典型类癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST210104 SOLID-LUNG-LNET-ALUCA Atypical Lung Carcinoid 肺非典型类癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2102 SOLID-LUNG-PPB Pleuropulmonary Blastoma 胸膜肺母细胞瘤 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2103 SOLID-LUNG-NSCLC Non-Small Cell Lung Cancer 非小细胞肺癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST21010101 SOLID-LUNG-LNET-SCLC-CSCLC Combined Small Cell Lung Carcinoma 复合性小细胞癌 Small Cell Lung Cancer 小细胞肺癌
ST2102 SOLID-LUNG-NSCLC Non-Small Cell Lung Cancer 非小细胞肺癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST210201 SOLID-LUNG-NSCLC-NSNSCLC Lung Non-Squamous Non-Small Cell Carcinoma 非鳞状非小细胞肺癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST21020101 SOLID-LUNG-NSCLC-NSNSCLC-CMPT Ciliated Muconodular Papillary Tumor of the Lung 肺纤毛黏液结节性乳头状肿瘤 Non-Small Cell Lung Cancer 非小细胞肺癌
ST21020102 SOLID-LUNG-NSCLC-NSNSCLC-LUAS Lung Adenosquamous Carcinoma 肺腺鳞癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST21020103 SOLID-LUNG-NSCLC-NSNSCLC-LCLC Large Cell Lung Carcinoma 大细胞肺癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2102010301 SOLID-LUNG-NSCLC-NSNSCLC-LCLC-CCLC Clear Cell Carcinoma of the Lung 肺透明细胞癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2102010302 SOLID-LUNG-NSCLC-NSNSCLC-LCLC-GCLC Giant Cell Carcinoma of the Lung 肺巨细胞癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2102010303 SOLID-LUNG-NSCLC-NSNSCLC-LCLC-BLCLC Basaloid Large Cell Carcinoma of the Lung 肺基底细胞样大细胞癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2102010304 SOLID-LUNG-NSCLC-NSNSCLC-LCLC-LECLC Lymphoepithelioma-like Carcinoma of the Lung 肺淋巴上皮瘤样癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2102010305 SOLID-LUNG-NSCLC-NSNSCLC-LCLC-RLCLC Large Cell Lung Carcinoma With Rhabdoid Phenotype 伴横纹肌样表型的大细胞肺癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST21020104 SOLID-LUNG-NSCLC-NSNSCLC-NSCLCPD Poorly Differentiated Non-Small Cell Lung Cancer 低分化非小细胞肺癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST21020105 SOLID-LUNG-NSCLC-NSNSCLC-LUAD Lung Adenocarcinoma 肺腺癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2102010501 SOLID-LUNG-NSCLC-NSNSCLC-LUAD-LAIS Lung Adenocarcinoma In Situ 原位肺腺癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST21020106 SOLID-LUNG-NSCLC-NSNSCLC-SARCL Sarcomatoid Carcinoma of the Lung 肺肉瘤样癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2102010601 SOLID-LUNG-NSCLC-NSNSCLC-SARCL-SPCC Spindle Cell Carcinoma of the Lung 肺梭形细胞癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2102010602 SOLID-LUNG-NSCLC-NSNSCLC-SARCL-LUPC Pleomorphic Carcinoma of the Lung 肺多形性癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST210202 SOLID-LUNG-NSCLC-LUSC Lung Squamous Cell Carcinoma 肺鳞状细胞癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2103 SOLID-LUNG-NUTCL NUT Carcinoma of the Lung 肺NUT癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST210301 SOLID-LUNG-NSCLC-CMPT Ciliated Muconodular Papillary Tumor of the Lung 肺纤毛黏液结节性乳头状肿瘤 Non-Small Cell Lung Cancer 非小细胞肺癌
ST210302 SOLID-LUNG-NSCLC-NUTCL NUT Carcinoma of the Lung 肺NUT癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST210303 SOLID-LUNG-NSCLC-NSCLCPD Poorly Differentiated Non-Small Cell Lung Cancer 低分化非小细胞肺癌 Non-Small Cell Lung Cancer 非小细胞肺癌
@ -655,10 +673,12 @@ ST21030804 SOLID-LUNG-NSCLC-LCLC-LECLC Lymphoepithelioma-like Carcinoma of the L
ST21030805 SOLID-LUNG-NSCLC-LCLC-RLCLC Large Cell Lung Carcinoma With Rhabdoid Phenotype 伴横纹肌样表型的大细胞肺癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST210309 SOLID-LUNG-NSCLC-LUAD Lung Adenocarcinoma 肺腺癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST210310 SOLID-LUNG-NSCLC-LUPC Pleomorphic Carcinoma of the Lung 肺多形性癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2104 SOLID-LUNG-LAM Pulmonary Lymphangiomyomatosis 肺淋巴管肌瘤病 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2105 SOLID-LUNG-LAIS Lung Adenocarcinoma In Situ 原位肺腺癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2106 SOLID-LUNG-CSCLC Combined Small Cell Lung Carcinoma 复合性小细胞癌 Small Cell Lung Cancer 小细胞肺癌
ST2107 SOLID-LUNG-SARCL Sarcomatoid Carcinoma of the Lung 肺肉瘤样癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2104 SOLID-LUNG-SGTTL Salivary Gland-Type Tumor of the Lung 肺涎腺型肿瘤 Non-Small Cell Lung Cancer 非小细胞肺癌
ST210401 SOLID-LUNG-SGTTL-LUMEC Mucoepidermoid Carcinoma of the Lung 肺黏液表皮样癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST210402 SOLID-LUNG-SGTTL-LUACC Adenoid Cystic Carcinoma of the Lung 肺腺腺样囊性癌 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2105 SOLID-LUNG-PPB Pleuropulmonary Blastoma 胸膜肺母细胞瘤 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2106 SOLID-LUNG-LAM Pulmonary Lymphangiomyomatosis 肺淋巴管肌瘤病 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2107 SOLID-LUNG-IMTL Inflammatory Myofibroblastic Lung Tumor 肺炎性肌纤维母细胞瘤 Non-Small Cell Lung Cancer 非小细胞肺癌
ST2108 SOLID-LUNG-IMTL Inflammatory Myofibroblastic Lung Tumor 肺炎性肌纤维母细胞瘤 Non-Small Cell Lung Cancer 非小细胞肺癌
ST22 SOLID-PENIS Penile Cancer 阴茎癌 Penile Cancer 阴茎癌
ST2201 SOLID-PENIS-PSCC Penile Squamous Cell Carcinoma 阴茎鳞状细胞癌 Penile Cancer 阴茎癌

36
database/snv_indel_mutation.csv
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@ -3763,7 +3763,7 @@ ERBB2,S310Y,Oncogenic,Gain-of-function,4,ENST00000269571,NM_004448.2,Yes,No
ERBB2,R677L,Likely Oncogenic,Likely Gain-of-function,4,ENST00000269571,NM_004448.2,Yes,No
ERBB2,R143G,Inconclusive,Inconclusive,4,ENST00000269571,NM_004448.2,Yes,No
ERBB2,V664F,Likely Oncogenic,Likely Gain-of-function,4,ENST00000269571,NM_004448.2,Yes,No
ERBB2,V842I,Likely Oncogenic,Gain-of-function,4,ENST00000269571,NM_004448.2,Yes,No
ERBB2,V842I ,Likely Oncogenic,Gain-of-function,6,ENST00000269571,NM_004448.2,Yes,No
ERBB2,D326G,Likely Neutral,Neutral,4,ENST00000269571,NM_004448.2,Yes,No
ERBB2,L663P,Oncogenic,Gain-of-function,4,ENST00000269571,NM_004448.2,Yes,No
ERBB2,V480A,Inconclusive,Inconclusive,4,ENST00000269571,NM_004448.2,Yes,No
@ -5297,8 +5297,7 @@ MET,M1250T,Oncogenic,Gain-of-function,4,ENST00000397752,NM_000245.2,Yes,No
MET,981_1028splice,Likely Oncogenic,Likely Gain-of-function,4,ENST00000397752,NM_000245.2,Yes,No
MET,H1094R,Oncogenic,Gain-of-function,4,ENST00000397752,NM_000245.2,Yes,No
MET,Y1230H,Oncogenic,Gain-of-function,4,ENST00000397752,NM_000245.2,Yes,No
MET,Exon 14 Skipping Mutation,Likely Oncogenic,Likely Gain-of-function,4,ENST00000397752,NM_000245.2,Yes,No
MET,Exon 14 skipping mutation,Likely Oncogenic,Likely Gain-of-function,4,ENST00000397752,NM_000245.2,Yes,No
MET,Exon 14 Deletion,Likely Oncogenic,Likely Gain-of-function,4,ENST00000397752,NM_000245.2,Yes,No
MET,Exon 14 deletions,Likely Oncogenic,Likely Gain-of-function,4,ENST00000397752,NM_000245.2,Yes,No
MET,D1228N,Likely Oncogenic,Likely Gain-of-function,4,ENST00000397752,NM_000245.2,Yes,No
MET,X1010_splice,Likely Oncogenic,Likely Gain-of-function,4,ENST00000397752,NM_000245.2,Yes,No
@ -6590,3 +6589,34 @@ KTT,Exon 17 mutation,Oncogenic,Gain-of-function,PMID: 30274985,,,,
KTT,Exon 9 mutation,Oncogenic,Gain-of-function,PMID: 30274985,,,,
ERBB2,G776L,Likely Oncogenic,Likely Gain-of-function,PMID: 22325357,ENST00000269571,NM_004448.2,Yes,No
TP53,A159fs,Likely Oncogenic,Likely Loss-of-function,PMID: 25669829,ENST00000269305,NM_000546.5,No,Yes
EGFR,I706T,Inconclusive,Inconclusive,4,ENST00000275493,NM_005228.3,Yes,No
EGFR,M766Q,Resistance,Inconclusive,.,ENST00000275493,NM_005228.3,Yes,No
EGFR,Q791L,Resistance,Inconclusive,.,ENST00000275493,NM_005228.3,Yes,No
EGFR,Q791H,Resistance,Inconclusive,.,ENST00000275493,NM_005228.3,Yes,No
EGFR,P794S,Resistance,Inconclusive,.,ENST00000275493,NM_005228.3,Yes,No
EGFR,P794R,Inconclusive,Inconclusive,1,ENST00000275493,NM_005228.3,Yes,No
RET,V804E,Resistance,Inconclusive,.,ENST00000355710,NM_020975.4,Yes,No
RET,L730I,Resistance,Inconclusive,.,ENST00000355710,NM_020975.4,Yes,No
RET,L730V,Resistance,Inconclusive,.,ENST00000355710,NM_020975.4,Yes,No
RET,E732K,Resistance,Inconclusive,.,ENST00000355710,NM_020975.4,Yes,No
FGFR2,N546K,Oncogenic,Gain-of-function,.,ENST00000358487,NM_000141.4,Yes,No
FGFR2,I291_Y308Del,Inconclusive,Inconclusive,.,ENST00000358487,NM_000141.4,Yes,No
FGFR2,Y376C,Likely Oncogenic,Likely Gain-of-function,.,ENST00000358487,NM_000141.4,Yes,No
FGFR2,L550F,Inconclusive,Inconclusive,.,ENST00000358487,NM_000141.4,Yes,No
ALK,G1202del,Resistance,Likely Gain-of-function,.,ENST00000389048,NM_004304.4,Yes,No
ALK,L1256F,Resistance,Inconclusive,.,ENST00000389048,NM_004304.4,Yes,No
FGFR3,A393E,Oncogenic,Gain-of-function,.,ENST00000260795,NM_000142.4,Yes,No
NTRK3,G623E,Resistance,Inconclusive,.,ENST00000360948,NM_001012338.2,Yes,No
ROS1,L2086F,Resistance,Inconclusive,.,ENST00000368508,NM_002944.2,Yes,No
FGFR1,K656E,Likely Oncogenic,Likely Gain-of-function,.,ENST00000425967,NM_001174067.1,Yes,No
ERBB2,V777_G778insGSP,Likely Oncogenic,Likely Gain-of-function,.,ENST00000269571,NM_004448.2,Yes,No
PIK3CB,L1049R,Likely Oncogenic,Likely Gain-of-function,1,ENST00000289153,NM_006219.2,Yes,No
MET,Exon 14 Skipping Mutation,Oncogenic,Gain-of-function,,ENST00000397752,NM_000245.2,Yes,No
MET,D1228V,Resistance,Inconclusive,.,ENST00000397752,NM_000245.2,Yes,No
PIK3R1,E451_Y452delinsD,Likely Oncogenic,Likely Gain-of-function,.,ENST00000274335,NM_181523.2,No,Yes
EPHA2,G391R,Likely Oncogenic,Likely Gain-of-function,.,ENST00000358432.8,NM_004431.5,Yes,No
POLE,A456P,Likely Oncogenic,Likely Loss-of-function,4,ENST00000320574,NM_006231.2,No,Yes
MMS22L,ENST00000683635.1,NM_001350599.2,来源于HGNC
DPAGT1,ENST00000354202.9,NM_001382.4,来源于HGNC
EPHA2,ENST00000358432.8,NM_004431.5,来源于HGNC
TLK2,ENST00000346027.10,NM_006852.6,来源于HGNC

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database/targetTherapy.txt
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database/target_drug.txt
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