diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml index bc3334d..9cff38f 100644 --- a/.github/workflows/lint-code.yml +++ b/.github/workflows/lint-code.yml @@ -19,7 +19,7 @@ jobs: # Run editor config check only on files not covered by a linter - name: Run ECLint check - run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile') + run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile\|.obo') Prettier: runs-on: ubuntu-latest diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 3470a7d..c51c119 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -28,7 +28,7 @@ jobs: - name: Install python dependencies run: | - python -m pip install --upgrade pip -r requirements-dev.txt + python -m pip install --upgrade pip -r requirements.txt pip install -e . - name: Test with pytest diff --git a/LICENSE b/LICENSE index 802fef8..2c6230a 100644 --- a/LICENSE +++ b/LICENSE @@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - diff --git a/README.rst b/README.rst index 69cf86b..822f9df 100644 --- a/README.rst +++ b/README.rst @@ -55,5 +55,3 @@ This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypack .. _Cookiecutter: https://github.com/audreyr/cookiecutter .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage - - diff --git a/example_files/cgi_test_out/cgi_test_out.cgi_results/biomarkers.tsv b/example_files/cgi_test_out/cgi_test_out.cgi_results/biomarkers.tsv new file mode 100644 index 0000000..7ea6e28 --- /dev/null +++ b/example_files/cgi_test_out/cgi_test_out.cgi_results/biomarkers.tsv @@ -0,0 +1,386 @@ +Sample ID Alterations Biomarker Drugs Diseases Response Evidence Match Source BioM Resist. Tumor type +input01 RET MUT* (FPEEEKCFC612-620-) RET fusion Pralsetinib (Tyrosine kinase inhibitor) Thyroid medullary Responsive A NO FDA:https://www.fda.gov/drugs/resources-information-approved-drugs/fda-approves-pralsetinib-ret-altered-thyroid-cancers;ASCO 2020 (abstr 109) only gene THM +input01 RET MUT* (FPEEEKCFC612-620-) RET fusion Selpercatinib (RET kinase inhibitor) Thyroid medullary Responsive A NO FDA:https://www.fda.gov/drugs/resources-information-approved-drugs/fda-approves-selpercatinib-lung-and-thyroid-cancers-ret-gene-mutations-or-fusions;ASCO 2020 (abstr 3594) only gene THM +input01 RET MUT* (FPEEEKCFC612-620-) RET fusion Cabozantinib (Kinase inhibitor ) Non-small cell lung Responsive C NO PMID:27825636 only gene NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR (S786I,G719., L861Q) Osimertinib (EGFR inhibitor 3d gen) Non-small cell lung Responsive A NO NCCN Non-Small Cell Lung Cancer guidlines 2022 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR (L858R,S768I,L861Q,G719.) Dacomitinib (EGFR inhibitor) Non-small cell lung Responsive A NO NCCN Non-Small Cell Lung Cancer guidlines 2022;FDA:https://www.fda.gov/drugs/drug-approvals-and-databases/fda-approves-dacomitinib-metastatic-non-small-cell-lung-cancer-0 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR (T790M) Gefitinib (EGFR inhibitor 1st gen) Non-small cell lung Resistant A NO PMID:26980062 only alteration type NSCLC +input01 ATM (N2875H) ATM oncogenic mutation Olaparib (PARP inhibitor) Prostate adenocarcinoma Responsive A NO FDA:https://www.fda.gov/drugs/resources-information-approved-drugs/fda-approves-olaparib-hrr-gene-mutated-metastatic-castration-resistant-prostate-cancer;PMID:32343890 complete PRAD +input01 KRAS wildtype KRAS wildtype Panitumumab (EGFR mAb inhibitor) Colorectal adenocarcinoma Responsive A NO PMID: 31268481 complete 621.0 COREAD +input01 KRAS wildtype KRAS wildtype Cetuximab (EGFR mAb inhibitor) Colorectal adenocarcinoma Responsive A NO PMID: 19339720 complete 246.0 COREAD +input01 EGFR (A289N), EGFR (A289D) EGFR exon 20 insertions Mobocertinib (EGFR inhibitor) Non-small cell lung Responsive A NO FDA:https://www.fda.gov/drugs/resources-information-approved-drugs/fda-grants-accelerated-approval-mobocertinib-metastatic-non-small-cell-lung-cancer-egfr-exon-20 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR exon 20 insertions Amivantamab (EGFR mAb inhibitor) Non-small cell lung Responsive A NO FDA:https://www.fda.gov/drugs/resources-information-approved-drugs/fda-grants-accelerated-approval-amivantamab-vmjw-metastatic-non-small-cell-lung-cancer only alteration type NSCLC +input01 RET MUT* (FPEEEKCFC612-620-) RET fusion Pralsetinib (Tyrosine kinase inhibitor) Non-small cell lung Responsive A NO FDA:https://www.fda.gov/drugs/resources-information-approved-drugs/fda-approves-pralsetinib-lung-cancer-ret-gene-fusions only gene NSCLC +input01 RET MUT* (FPEEEKCFC612-620-) RET fusion Selpercatinib (RET kinase inhibitor) Non-small cell lung Responsive A NO FDA:https://www.fda.gov/drugs/resources-information-approved-drugs/fda-approves-selpercatinib-lung-and-thyroid-cancers-ret-gene-mutations-or-fusions only gene NSCLC +input01 AKT1 (Q79K), AKT1 (E17K) AKT1 (Q79K,E17K) BRAF inhibitors Cutaneous melanoma Resistant C NO PMID:24265152 complete CM +input01 AKT1 (E17K) AKT1 (E17K) AKT inhibitors Any cancer type Responsive D YES PMID:21464312;PMID:17611497;PMID:23134728; ENA 2015 (abstr B109) complete CANCER +input01 AKT1 (E17K) AKT1 (E17K) allosteric AKT inhibitors Any cancer type Responsive C YES ENA 2015 (abstract B109);PMID:28489509 complete CANCER +input01 AKT1 (E17K) AKT1 (E17K) non-allosteric AKT inhibitors Any cancer type Responsive C YES ENA 2015 (abstract B109);PMID:28489509 complete CANCER +input01 AKT1 (E17K) AKT1 (E17K) PI3K pathway inhibitors Head an neck squamous Responsive C NO PMID:26763254 complete HNSC +input01 AKT1 (Q79K), AKT1 (E17K) AKT1 (H238Y) Everolimus (MTOR inhibitor) Fibrous histiocytoma Responsive C NO ASCO 2015 (abstr 11010) only alteration type FH +input01 AKT1 (E17K) AKT1 (E17K) Tensirolimus (MTOR inhibitor) Endometrium Responsive C NO PMID:27016228 complete ED +input01 EGFR (A289N), EGFR (A289D) EGFR inframe deletion (30-336) EGFR inhibitor 1st gens Glioma No Responsive C NO PMID:19204207 only alteration type G +input01 EGFR (A289N), EGFR (A289D) EGFR exon 20 insertions EGFR inhibitor 1st gens Lung Resistant B NO PMID:21764376;PMID:26773740;PMID:26051236 only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR amplification EGFR inhibitor 1st gens Glioma No Responsive C NO PMID:16282176;PMID:16278407 only gene G +input01 EGFR (A289N), EGFR (A289D) EGFR (D761Y) EGFR inhibitor 1st gens Non-small cell lung Resistant C NO PMID:19680293 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR (T790M) EGFR inhibitor 1st gens Non-small cell lung Resistant B NO PMID:19680293 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR inframe deletion (30-336) EGFR inhibitor 2nd gens Glioma No Responsive C NO PMID:19204207 only alteration type G +input01 EGFR (A289N), EGFR (A289D) EGFR amplification EGFR inhibitor 2nd gens Glioma No Responsive C NO PMID:16282176;PMID:16278407 only gene G +input01 EGFR (A289N), EGFR (A289D) EGFR (T790M) EGFR inhibitor 2nd gens Non-small cell lung Resistant B NO PMID:22452896 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR inframe deletion (30-336) EGFR inhibitor 3rd gens Glioma No Responsive C NO PMID:19204207 only alteration type G +input01 EGFR (A289N), EGFR (A289D) EGFR amplification EGFR inhibitor 3rd gens Glioma No Responsive C NO PMID:16282176;PMID:16278407 only gene G +input01 ATM (N2875H) ATM oncogenic mutation ATR inhibitors Colorectal adenocarcinoma Responsive C NO ENA 2015 (abstr A48) complete COREAD +input01 ATM (N2875H) ATM deletion ATR inhibitors Colorectal adenocarcinoma Responsive C NO ENA 2015 (abstr A48) only gene COREAD +input01 ATM (N2875H) ATM oncogenic mutation DNA-PKc inhibitors Lymphoma Responsive D NO PMID:23761041 complete LY +input01 ATM (N2875H) ATM deletion DNA-PKc inhibitors Lymphoma Responsive D NO PMID:23761041 only gene LY +input01 ATM (N2875H) ATM oncogenic mutation PARP inhibitors Stomach Responsive C NO ENA 2014 (abstr 8LBA) complete ST +input01 ATM (N2875H) ATM deletion PARP inhibitors Stomach Responsive C NO ENA 2014 (abstr 8LBA) only gene ST +input01 ATM (N2875H) ATM biallelic inactivation AZD6738 (ATR inhibitor) B cell lymphoma Responsive C NO NCT01955668;https://ash.confex.com/ash/2014/webprogram/Paper71027.html only alteration type BCL +input01 ATM (N2875H) ATM oncogenic mutation Cisplatin (Chemotherapy) Bladder Responsive C NO PMID:26238431 complete BLCA +input01 ATM (N2875H) ATM deletion Cisplatin (Chemotherapy) Bladder Responsive C NO PMID:26238431 only gene BLCA +input01 ATM (N2875H) ATM oncogenic mutation Olaparib (PARP inhibitor) Stomach Responsive C NO ENA 2014 (abstr 8LBA) complete ST +input01 ATM (N2875H) ATM oncogenic mutation Temozolomide (Chemotherapy) Glioma Responsive D NO PMID:23960094 complete G +input01 JAK1 (V658F), JAK1 (S646F), JAK1 (A634D) JAK1 oncogenic mutation PD1 inhibitors Colorectal adenocarcinoma Resistant C NO PMID:27903500 complete COREAD +input01 JAK1 (V658F), JAK1 (S646F), JAK1 (A634D) JAK1 oncogenic mutation PD1 inhibitors Cutaneous melanoma Resistant C NO PMID:27433843 complete CM +input01 NRAS (Q61H), NRAS (Q61H), NRAS MUT* (Q61L), NRAS MUT* (Q61R), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS MUT* (Q61R), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS (12,13,59,61,117,146) Cetuximab (EGFR mAb inhibitor) Colorectal adenocarcinoma Resistant A NO PMID:24024839;PMID:20619739;PMID:23325582 complete COREAD +input01 CSF3R (T618I), CSF3R (T615A) CSF3R frameshift variant (D771),frameshift variant (S783) Dasatinib (BCR-ABL inhibitor 2nd gen) Atypical chronic myeloid leukemia Responsive D NO PMID:23656643 only alteration type ACML +input01 EGFR (A289N), EGFR (A289D) EGFR (T790M) EGFR inhibitor 3rd gens Lung Responsive C NO ASCO 2014 (abstr 8009);ENA 2014 (abstr 10LBA);ENA 2014 (abstr 9LBA);ASCO 2015 (abstr 8001) only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR amplification EGFR inhibitors Head an neck squamous Responsive C NO PMID:26763254 only gene HNSC +input01 EGFR (A289N), EGFR (A289D) EGFR amplification EGFR mAb inhibitors Colorectal adenocarcinoma Responsive B NO PMID:18794099;PMID:17664472 only gene COREAD +input01 EGFR (A289N), EGFR (A289D) EGFR exon 19 insertions EGFR TK inhibitors Lung Responsive B NO PMID:22753918 only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR (L858R,L861Q,G719A,G719S,G719C,G719D,L747S,S768I,L861P,L861R) EGFR TK inhibitors Lung Responsive B NO PMID:22753918 only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR exon 19 insertions HSP90 inhibitors Lung Responsive C NO ESMO 2012 (abstr 4380) only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR exon 20 insertions HSP90 inhibitors Lung Responsive C NO ASCO 2014 (abstr 8015) only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR (L858R,L861Q,G719A,G719S,G719C,G719D,L747S,S768I,L861P,L861R) HSP90 inhibitors Lung Responsive C NO ESMO 2012 (abstr 4380) only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR (T790M) HSP90 inhibitors Lung Responsive C NO ESMO 2012 (abstr 4380) only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR exon 19 insertions MEK inhibitor (alone or in combination)s Lung Responsive D NO PMID:23102728 only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR (L858R,L861Q,G719A,G719S,G719C,G719D,L747S,S768I,L861P,L861R,T790M) MEK inhibitor (alone or in combination)s Lung Responsive D NO PMID:23102728 only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR (S492R) novel EGFR mAb inhibitors Colorectal adenocarcinoma Responsive C NO PMID:25962717 only alteration type COREAD +input01 EGFR (A289N), EGFR (A289D) EGFR (T790M) EGFR inhibitor 3rd gens (Rociletinib,HM61713,etc) Non-small cell lung Responsive B NO NCT02322281 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR exon 19 deletions Afatinib (ERBB2 inhibitor&EGFR inhibitor 2nd gen) Non-small cell lung Responsive A NO FDA only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR exon 19 insertions Afatinib (ERBB2 inhibitor&EGFR inhibitor 2nd gen) Lung Responsive B NO PMID:22753918;PMID:25589191 only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR (L858R,L861Q,G719A,G719S,G719C,G719D,L747S,S768I,L861P,L861Q,L861R) Afatinib (ERBB2 inhibitor&EGFR inhibitor 2nd gen) Non-small cell lung Responsive A NO FDA only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR (L861Q,G719A,G719S,G719C,G719D,L747S,S768I,L861P,L861Q,L861R) Afatinib (ERBB2 inhibitor&EGFR inhibitor 2nd gen) Non-small cell lung Responsive A NO FDA only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR exon 19 insertions Afatinib + Cetuximab (ERBB2 inhibitor&EGFR inhibitor 2nd gen + EGFR mAb inhibitor) Lung Responsive C NO ESMO 2012 (abstr 1289) only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR (L858R,L861Q,G719A,G719S,G719C,G719D,L747S,S768I,L861P,L861R) Afatinib + Cetuximab (ERBB2 inhibitor&EGFR inhibitor 2nd gen + EGFR mAb inhibitor) Lung Responsive C NO ESMO 2012 (abstr 1289) only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR (T790M) Afatinib + Cetuximab (ERBB2 inhibitor&EGFR inhibitor 2nd gen + EGFR mAb inhibitor) Lung Responsive C NO PMID:25074459 only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR (T790M) Afatinib + Nimotuzumab (ERBB2 inhibitor&EGFR inhibitor 2nd gen + EGFR mAb inhibitor) Lung Responsive C NO PMID:26667485 only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR overexpression Cetuximab (EGFR mAb inhibitor) Colorectal adenocarcinoma Responsive A NO FDA only gene 246.0 COREAD +input01 EGFR (A289N), EGFR (A289D) EGFR (P546S) Cetuximab (EGFR mAb inhibitor) Head an neck Responsive C NO PMID:23578570 only alteration type HNC +input01 EGFR (A289N), EGFR (A289D) EGFR (P753S) Cetuximab + Sirolimus (EGFR mAb inhibitor + MTOR inhibitor) Head an neck Responsive C NO PMID:24934779 only alteration type HNC +input01 EGFR (A289N), EGFR (A289D) EGFR-RAD51 fusion Erlotinib (EGFR inhibitor 1st gen) Non-small cell lung Responsive C NO PMID:27102076 only gene NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR-RAD51 fusion Erlotinib (EGFR inhibitor 1st gen) Lung Responsive C NO PMID:27102076 only gene L +input01 EGFR (A289N), EGFR (A289D) EGFR exon 19 deletions Erlotinib (EGFR inhibitor 1st gen) Non-small cell lung Responsive A NO FDA only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR exon 19 insertions Erlotinib (EGFR inhibitor 1st gen) Lung Responsive C NO PMID:22190593 only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR inframe insertion (769-770) Erlotinib (EGFR inhibitor 1st gen) Lung Responsive C NO PMID:26773740;PMID:23328547 only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR (A289V,R108K,G598V,T263P) Erlotinib (EGFR inhibitor 1st gen) Glioma Responsive D NO PMID:17177598 only alteration type G +input01 NRAS (Q61H), NRAS (Q61H), NRAS MUT* (Q61L), NRAS MUT* (Q61R), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS MUT* (Q61R), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K) NRAS (Q61) BRAF inhibitors Cutaneous melanoma Resistant C NO PMID:23569304;PMID:24265153 complete CM +input01 EGFR (A289N), EGFR (A289D) EGFR (K757R,E746G) Erlotinib (EGFR inhibitor 1st gen) Lung Responsive C NO PMID:26773740 only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR (L858R) Erlotinib (EGFR inhibitor 1st gen) Non-small cell lung Responsive A NO FDA only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR (L858R,L861,G719,S768I) Erlotinib (EGFR inhibitor 1st gen) Non-small cell lung Responsive A NO NCCN only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR exon 19 deletions Gefitinib (EGFR inhibitor 1st gen) Non-small cell lung Responsive A NO FDA only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR amplification Gefitinib (EGFR inhibitor 1st gen) Endometrium Responsive B NO PMID:24950987 only gene ED +input01 EGFR (A289N), EGFR (A289D) EGFR (L858R,L861Q,G719A,G719S,G719C,G719D,L747S,S768I,L861P,L861Q,L861R) Gefitinib (EGFR inhibitor 1st gen) Non-small cell lung Responsive A NO FDA only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR (L861Q,G719A,G719S,G719C,G719D,L747S,S768I,L861P,L861Q,L861R) Gefitinib (EGFR inhibitor 1st gen) Non-small cell lung Responsive A NO FDA only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR (E690K) Lapatinib (ERBB2 inhibitor) Endometrium Responsive C NO PMID:22885469 only alteration type ED +input01 EGFR (A289N), EGFR (A289D) EGFR exon 19 deletions Osimertinib (EGFR inhibitor 3rd gen) Lung Responsive C NO NCT02465060 only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR exon 20 insertions Osimertinib (EGFR inhibitor 3rd gen) Lung Responsive A NO PMID:26515464 only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR (L858R) Osimertinib (EGFR inhibitor 3rd gen) Non-small cell lung Responsive A NO NCCN Non-Small Cell Lung Cancer 2022;PMID:30659024 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR (T790M) Osimertinib (EGFR inhibitor 3rd gen) Non-small cell lung Responsive A NO FDA only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR (S492R) Panitumumab (EGFR mAb inhibitor) Colorectal adenocarcinoma Responsive C NO PMID:22270724 only alteration type 621.0 COREAD +input01 EGFR (A289N), EGFR (A289D) EGFR inframe deletion (6-273) Rindopepimut (Vaccine) Glioblastoma Responsive B NO NCT01480479 only alteration type GB +input01 EPHA2 (G391R), EPHA2 MUT* (G391R) EPHA2 (G391R) MTOR inhibitors Lung squamous cell Responsive D NO PMID:20360610 complete LUSC +input01 EPHA2 (G391R), EPHA2 MUT* (G391R) EPHA2 (G391R) MTOR inhibitors Lung squamous cell Responsive D NO PMID:20360610 complete LUSC +input01 EPHA2 (R721Q), EPHA2 (G391R), EPHA2 MUT* (G391R) EPHA2 amplification Dasatinib (BCR-ABL inhibitor 2nd gen) Any cancer type Responsive D YES PMID:18047674;PMID:19010823;PMID:19861960 only gene CANCER +input01 EPHA2 (R721Q), EPHA2 (G391R), EPHA2 MUT* (G391R) EPHA2 amplification Dasatinib (BCR-ABL inhibitor 2nd gen) Any cancer type Responsive D YES PMID:18047674;PMID:19010823;PMID:19861960 only gene CANCER +input01 EPHA2 (G391R), EPHA2 MUT* (G391R) EPHA2 (G391R) Dasatinib (BCR-ABL inhibitor 2nd gen) Lung squamous cell Responsive D NO PMID:20360610 complete LUSC +input01 EPHA2 (G391R), EPHA2 MUT* (G391R) EPHA2 (G391R) Dasatinib (BCR-ABL inhibitor 2nd gen) Lung squamous cell Responsive D NO PMID:20360610 complete LUSC +input01 STK11 (Q37*) STK11 oncogenic mutation BET inhibitors Lung Resistant D NO PMID:23129625;PMID:24045185 complete L +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 oncogenic mutation MDM2 inhibitors Liposarcoma Resistant C NO PMID:23084521;ASCO 2015 (abstr 10564) complete LIP +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 oncogenic mutation Abemaciclib (CDK4/CDK6 inhibitor) Breast adenocarcinoma Resistant C YES PMID:27217383 complete BRCA +input01 EGFR (A289N), EGFR (A289D) EGFR overexpression Panitumumab (EGFR mAb inhibitor) Colorectal adenocarcinoma Resistant A NO FDA guidelines only gene COREAD +input01 GNAQ (Q209R), GNAQ MUT* (Q209L) GNAQ (Q209) HDAC inhibitors Cutaneous melanoma Responsive D NO NCT01587352 complete CM +input01 GNAQ (Q209R), GNAQ MUT* (Q209L) GNAQ (Q209) PI3K pathway inhibitor + MEK inhibitors Cutaneous melanoma Responsive D NO PMID:22733540;PMID:22808163 complete CM +input01 GNAQ (Q209R), GNAQ MUT* (Q209L) GNAQ (Q209) PKC inhibitors Cutaneous melanoma Responsive D NO PMID:22653968;PMID:22253748 complete CM +input01 GNAQ (Q209R), GNAQ MUT* (Q209L) GNAQ (Q209) Selumetinib (MEK inhibitor) Cutaneous melanoma Responsive C NO ASCO 2013 (abstr CRA9003) complete CM +input01 GNAS (R844L), GNAS (Q870L) GNAS (R201) JAK inhibitors Any cancer type Responsive D YES PMID:21835143 only alteration type CANCER +input01 HRAS (G12S) HRAS oncogenic mutation MEK inhibitor +/- MTOR inhibitors Acute myeloid leukemia Responsive D NO PMID:22399013;PMID:22507781 complete AML +input01 HRAS (G12S) HRAS oncogenic mutation MTOR inhibitors Cervix squamous cell Responsive D NO PMID:22345164 complete CESC +input01 HRAS (G12S) HRAS oncogenic mutation PI3K pathway inhibitor + MEK inhibitors Cervix Responsive D NO PMID:15950068 complete CER +input01 HRAS (G12S) HRAS oncogenic mutation Tipifarnib (Farnesyltransferase inhibitor) Any cancer type Responsive C YES NCT02383927 complete CANCER +input01 HRAS (G12S) HRAS oncogenic mutation Tipifarnib (Farnesyltransferase inhibitor) Any cancer type Responsive C YES NCT02383927 complete CANCER +input01 EGFR (A289N), EGFR (A289D) EGFR (S464L,G465R,I491M) Cetuximab (EGFR mAb inhibitor) Colorectal adenocarcinoma Resistant D NO PMID:25623215 only alteration type COREAD +input01 EGFR (A289N), EGFR (A289D) EGFR (S492R,G465R,R451C,K467T) Cetuximab (EGFR mAb inhibitor) Colorectal adenocarcinoma Resistant C NO PMID:22270724;PMID:26059438;PMID:25623215;PMID:22270724;PMID:26888827 only alteration type COREAD +input01 JAK1 (S646F) JAK1 (S646F;R683) Ruxolitinib (JAK inhibitor) Acute lymphoblastic leukemia Responsive D NO PMID:22955920;PMID:18805579 complete ALL +input01 NRAS (Q61H), NRAS (Q61H), NRAS MUT* (Q61L), NRAS MUT* (Q61R), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS MUT* (Q61R), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS (12,13,59,61,117,146) Panitumumab (EGFR mAb inhibitor) Colorectal adenocarcinoma Resistant A NO FDA guidelines complete COREAD +input01 KIT wildtype KIT wildtype Dasatinib (BCR-ABL inhibitor 2nd gen) Gastrointestinal stromal Responsive D NO PMID:16397263 complete GIST +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 oncogenic mutation Cisplatin (Chemotherapy) Female germ cell tumor, Male germ cell tumor Resistant C NO PMID:27646943 complete FGCT, MGCT +input01 KIT wildtype KIT wildtype Sorafenib (Pan-TK inhibitor) Gastrointestinal stromal Responsive C NO ASCO 2011 (abstr 10009) complete GIST +input01 KIT wildtype KIT wildtype Sunitinib (Pan-TK inhibitor) Gastrointestinal stromal Responsive B NO PMID:18955458 complete GIST +input01 EGFR (A289N), EGFR (A289D) EGFR amplification Erlotinib (EGFR inhibitor 1st gen) Lung No Responsive C NO ASCO2015(abstre19028) only gene L +input01 EGFR (A289N), EGFR (A289D) EGFR (S720) Erlotinib (EGFR inhibitor 1st gen) Lung No Responsive C NO PMID:26773740 only alteration type L +input01 MTOR (F2108L) MTOR (F2108L) Everolimus (MTOR inhibitor) Thyroid carcinoma Resistant C NO PMID:25295501 complete THCA +input01 EGFR (A289N), EGFR (A289D) EGFR inframe deletion (L747),inframe insertion (P753PS) Gefitinib (EGFR inhibitor 1st gen) Head an neck No Responsive C NO PMID:21274259 only alteration type HNC +input01 EGFR (A289N), EGFR (A289D) EGFR amplification Gefitinib (EGFR inhibitor 1st gen) Head an neck No Responsive C NO PMID:21274259;PMID:22261807 only gene HNC +input01 EGFR (A289N), EGFR (A289D) EGFR (V843I) Gefitinib (EGFR inhibitor 1st gen) Head an neck No Responsive C NO PMID:21274259 only alteration type HNC +input01 BTK MUT* (C515S) BTK (C481) Ibrutinib (BTK inhibitor) Mantle cell lymphoma Resistant C NO PMID:25082755 only alteration type MCL +input01 BTK MUT* (C515S) BTK (C481S) Ibrutinib (BTK inhibitor) Chronic lymphocytic leukemia Resistant C NO PMID:24869598;PMID:27199251 only alteration type CLL +input01 PLCG2 (R665W), PLCG2 (L845F), PLCG2 (L845F) PLCG2 (R665W,L845F) Ibrutinib (BTK inhibitor) Chronic lymphocytic leukemia Resistant C NO PMID:24869598 complete CLL +input01 KIT wildtype KIT wildtype Imatinib (BCR-ABL inhibitor 1st gen&KIT inhibitor) Gastrointestinal stromal Resistant B NO PMID:18955458 complete GIST +input01 MPL (S505C), MPL (S505N), MPL (W515L) MPL (W515F) JAK inhibitors Myelodisplasic proliferative syndrome Responsive D NO PMID:16834459 only alteration type MDPS +input01 MTOR (F2108L) MTOR (F2108L) MTOR kinase inhibitors Any cancer type Responsive D YES PMID:25295501 complete CANCER +input01 MTOR (E2419K), MTOR (E2014K) MTOR (E2014K,E2419K,N1421D) Everolimus (MTOR inhibitor) Bladder Responsive C NO PMID:24625776 complete BLCA +input01 MTOR (R2505P), MTOR (I2500M), MTOR (I2500F), MTOR (E2419K), MTOR (Q2223K), MTOR (S2215F), MTOR (S2215Y), MTOR (S2215T), MTOR (P2213S), MTOR (F2108L), MTOR (E2014K), MTOR (H1968Y), MTOR (C1483W), MTOR (C1483F), MTOR (C1483Y), MTOR (C1483R), MTOR (L1460P) MTOR (I1973F) Everolimus (MTOR inhibitor) Angiosarcoma, Renal Responsive C NO ASCO 2015 (abstr 11010);PMID:26859683 only alteration type AS, R +input01 MTOR (R2505P), MTOR (I2500M), MTOR (I2500F), MTOR (E2419K), MTOR (Q2223K), MTOR (S2215F), MTOR (S2215Y), MTOR (S2215T), MTOR (P2213S), MTOR (F2108L), MTOR (E2014K), MTOR (H1968Y), MTOR (C1483W), MTOR (C1483F), MTOR (C1483Y), MTOR (C1483R), MTOR (L1460P) MTOR (K1771R) Everolimus (MTOR inhibitor) Stomach, Adrenal gland Responsive C NO ASCO 2015 (abstr 11010);PMID:26859683 only alteration type ST, AG +input01 MTOR (R2505P), MTOR (I2500M), MTOR (I2500F), MTOR (E2419K), MTOR (Q2223K), MTOR (S2215F), MTOR (S2215Y), MTOR (S2215T), MTOR (P2213S), MTOR (F2108L), MTOR (E2014K), MTOR (H1968Y), MTOR (C1483W), MTOR (C1483F), MTOR (C1483Y), MTOR (C1483R), MTOR (L1460P) MTOR (N1421D) Everolimus (MTOR inhibitor) Stomach Responsive C NO PMID:26859683 only alteration type ST +input01 MTOR (Q2223K) MTOR (Q2223K) Everolimus (MTOR inhibitor) Renal Responsive C NO PMID:24622468 complete R +input01 MTOR (R2505P), MTOR (S2215Y), MTOR (L1460P) MTOR (L1460P,S2215Y,R2505P) Sirolimus (MTOR inhibitor) Any cancer type Responsive D YES PMID:24631838 complete CANCER +input01 PDGFRA wildtype PDGFRA wildtype Imatinib (BCR-ABL inhibitor 1st gen&KIT inhibitor) Gastrointestinal stromal Resistant B NO PMID:14645423;PMID:18955458 complete GIST +input01 EGFR (A289N), EGFR (A289D) EGFR (C797S) Osimertinib (EGFR inhibitor 3rd gen) Lung Resistant C NO PMID:25939061 only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR (L718) Osimertinib (EGFR inhibitor 3rd gen) Lung Resistant C NO ASCO 2017 (abstr 2572) only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR (L792) Osimertinib (EGFR inhibitor 3rd gen) Lung Resistant C NO ASCO 2017 (abstr 2572) only alteration type L +input01 EGFR (A289N), EGFR (A289D) EGFR (G465R) Panitumumab (EGFR mAb inhibitor) Colorectal adenocarcinoma Resistant C NO PMID:26059438 only alteration type COREAD +input01 EGFR (A289N), EGFR (A289D) EGFR (T790M) Afatinib (ERBB2 inhibitor&EGFR inhibitor 2nd gen) Lung Resistant A NO NCCN only alteration type L +input01 NRAS (Q61H), NRAS (Q61H), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS oncogenic mutation CDK4/6 inhibitor + MEK inhibitors Cutaneous melanoma Responsive C NO PMID:26658964;NCT01781572;NCT02065063;NCT02022982;ASCO 2014 (abstr 9009) complete CM +input01 NRAS (Q61H), NRAS (Q61H), NRAS MUT* (Q61L), NRAS MUT* (Q61R), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS MUT* (Q61R), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS (G12C) ERK inhibitors Any cancer type Responsive D YES PMID:23614898 only alteration type CANCER +input01 NRAS (Q61H), NRAS (Q61H), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS oncogenic mutation ERK inhibitors Cutaneous melanoma Responsive C NO ASCO 2017 (abstr 2508) complete CM +input01 NRAS (Q61H), NRAS (Q61H), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS oncogenic mutation HSP90 inhibitors Cutaneous melanoma Responsive D NO PMID:23538902 complete CM +input01 NRAS (Q61H), NRAS (Q61H), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS oncogenic mutation MEK inhibitor +/- PI3K pathway inhibitors Colorectal adenocarcinoma Responsive D NO PMID:23274911;PMID:22392911 complete COREAD +input01 NRAS (Q61H), NRAS (Q61H), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS oncogenic mutation MEK inhibitors Acute myeloid leukemia, Lung adenocarcinoma, Acute lymphoblastic leukemia Responsive D NO PMID:22507781;PMID:23515407;PMID:18701506 complete AML, LUAD, ALL +input01 NRAS (Q61H), NRAS (Q61H), NRAS MUT* (Q61L), NRAS MUT* (Q61R), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS MUT* (Q61R), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K) NRAS (Q61) MEK inhibitors Cutaneous melanoma Responsive B NO PMID:23414587,ASCO 2016 (abstr 9500) complete CM +input01 NRAS (Q61H), NRAS (Q61H), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS oncogenic mutation Pan-RAF inhibitors Cutaneous melanoma Responsive C NO ESMO 2015 (abstract 300);AACR 2017 (abstr CT002) complete CM +input01 NRAS (Q61H), NRAS (Q61H), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS oncogenic mutation PI3K pathway inhibitor + MEK inhibitors Myeloma Responsive D NO PMID:22985491 complete MYMA +input01 NRAS (Q61H), NRAS (Q61H), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS oncogenic mutation Sorafenib + MEK inhibitor (Pan-TK inhibitor + MEK inhibitor) Hepatic carcinoma Responsive C NO PMID:25294897 complete HC +input01 PDGFRA wildtype PDGFRA wildtype Dasatinib (BCR-ABL inhibitor 2nd gen) Gastrointestinal stromal Responsive D NO PMID:16397263 complete GIST +input01 RET MUT* (FPEEEKCFC612-620-) RET (I788N) Ponatinib (BCR-ABL inhibitor 3rd gen&Pan-TK inhibitor) Lung adenocarcinoma Resistant D NO PMID:28615362 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR (T790M) Erlotinib (EGFR inhibitor 1st gen) Lung Resistant A NO NCCN only alteration type L +input01 PDGFRA wildtype PDGFRA wildtype Sorafenib (Pan-TK inhibitor) Gastrointestinal stromal Responsive C NO ASCO 2011 (abstr 10009) complete GIST +input01 PDGFRA wildtype PDGFRA wildtype Sunitinib (Pan-TK inhibitor) Gastrointestinal stromal Responsive B NO PMID:18955458 complete GIST +input01 EGFR (A289N), EGFR (A289D) EGFR (L798I) Rociletinib (EGFR inhibitor) Lung adenocarcinoma Resistant C NO PMID:27283993 only alteration type LUAD +input01 RB1 (R556*), RB1 (R579*), RB1 (C706F), RB1 (E748*) RB1 oncogenic mutation HDAC inhibitors Retinoblastoma Responsive D NO PMID:18483379 complete RB +input01 RB1 (R556*), RB1 (R579*), RB1 (C706F), RB1 (E748*) RB1 deletion HDAC inhibitors Retinoblastoma Responsive D NO PMID:18483379 only gene RB +input01 RB1 (R556*), RB1 (R579*), RB1 (C706F), RB1 (E748*) RB1 oncogenic mutation MDM2/MDMX inhibitors Retinoblastoma Responsive D NO PMID:17080083;PMID:21515735 complete RB +input01 RB1 (R556*), RB1 (R579*), RB1 (C706F), RB1 (E748*) RB1 deletion MDM2/MDMX inhibitors Retinoblastoma Responsive D NO PMID:17080083;PMID:21515735 only gene RB +input01 RB1 (R556*), RB1 (R579*), RB1 (C706F), RB1 (E748*) RB1 oncogenic mutation Cisplatin (Chemotherapy) Bladder Responsive C NO PMID:26238431 complete BLCA +input01 RB1 (R556*), RB1 (R579*), RB1 (C706F), RB1 (E748*) RB1 deletion Cisplatin (Chemotherapy) Bladder Responsive C NO PMID:26238431 only gene BLCA +input01 RB1 (R556*), RB1 (R579*), RB1 (C706F), RB1 (E748*) RB1 overexpression Palbociclib (CDK4/6 inhibitor) Prostate adenocarcinoma Responsive D NO PMID:23708653 only gene PRAD +input01 RET MUT* (FPEEEKCFC612-620-) RET fusion RET inhibitors Lung adenocarcinoma Responsive D NO PMID:22327624;PMID:22327622 only gene LUAD +input01 RET MUT* (FPEEEKCFC612-620-) RET-TPCN1 fusion RET inhibitors Thyroid Responsive D NO PMID:23056499 only gene TH +input01 RET MUT* (FPEEEKCFC612-620-) RET (C634W,M918T) RET inhibitors Thyroid Responsive D NO PMID:23056499 only alteration type TH +input01 RET MUT* (FPEEEKCFC612-620-) RET fusion Cabozantinib (Pan-kinase inhibitor) Lung adenocarcinoma Responsive C NO PMID:28447912 only gene LUAD +input01 RET MUT* (FPEEEKCFC612-620-) RET-TPCN1 fusion Cabozantinib (Pan-kinase inhibitor) Thyroid carcinoma Responsive D NO PMID:21470995 only gene THCA +input01 RET MUT* (FPEEEKCFC612-620-) RET (C634W,M918T) Cabozantinib (Pan-kinase inhibitor) Thyroid Responsive D NO PMID:21470995 only alteration type TH +input01 RET MUT* (FPEEEKCFC612-620-) RET fusion Nintedanib (Pan-TK inhibitor) Lung adenocarcinoma Responsive C NO PMID:26787234 only gene LUAD +input01 RET MUT* (FPEEEKCFC612-620-) RET fusion Sunitinib (Pan-TK inhibitor) Lung adenocarcinoma Responsive C NO PMID:28447912 only gene LUAD +input01 RET MUT* (FPEEEKCFC612-620-) RET-TPCN1 fusion Sunitinib (Pan-TK inhibitor) Thyroid carcinoma Responsive D NO PMID:21470995 only gene THCA +input01 RET MUT* (FPEEEKCFC612-620-) RET (C634W,M918T) Sunitinib (Pan-TK inhibitor) Thyroid Responsive D NO PMID:21470995 only alteration type TH +input01 RET MUT* (FPEEEKCFC612-620-) RET fusion Vandetanib (Pan-TK inhibitor) Lung adenocarcinoma Responsive C NO PMID:28447912 only gene LUAD +input01 RET MUT* (FPEEEKCFC612-620-) RET-TPCN1 fusion Vandetanib (Pan-TK inhibitor) Thyroid carcinoma Responsive D NO PMID:21470995 only gene THCA +input01 RET MUT* (FPEEEKCFC612-620-) RET (618,620,634,768,791,891,918,C634W,M918T) Vandetanib (Pan-TK inhibitor) Thyroid carcinoma Responsive A NO PMID:20065189;PMID:22025146 only alteration type THCA +input01 STK11 (Q37*) STK11 oncogenic mutation MEK inhibitors Lung adenocarcinoma Responsive D NO PMID:19165201 complete LUAD +input01 STK11 (Q37*) STK11 deletion MEK inhibitors Lung adenocarcinoma Responsive D NO PMID:19165201 only gene LUAD +input01 STK11 (Q37*) STK11 oncogenic mutation MTOR inhibitors Any cancer type Responsive D YES PMID:19541609 complete CANCER +input01 STK11 (Q37*) STK11 deletion MTOR inhibitors Any cancer type Responsive D YES PMID:19541609 only gene CANCER +input01 STK11 (Q37*) STK11 oncogenic mutation SRC inhibitor + PI3K/MEK inhibitors Lung adenocarcinoma Responsive D NO PMID:20541700 complete LUAD +input01 STK11 (Q37*) STK11 deletion SRC inhibitor + PI3K/MEK inhibitors Lung adenocarcinoma Responsive D NO PMID:20541700 only gene LUAD +input01 STK11 (Q37*) STK11 (D194E) Everolimus (MTOR inhibitor) Pancreas Responsive C NO PMID:21189378 only alteration type PA +input01 STK11 (Q37*) STK11 oncogenic mutation Phenformin (Anti-diabetic) Lung adenocarcinoma Responsive D NO PMID:23352126 complete LUAD +input01 STK11 (Q37*) STK11 deletion Phenformin (Anti-diabetic) Lung adenocarcinoma Responsive D NO PMID:23352126 only gene LUAD +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 (R248Q,R175H) HSP90 inhibitors Any cancer type Responsive D YES PMID:26009011 only alteration type CANCER +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 (R248Q,R175H) HSP90 inhibitors Any cancer type Responsive D YES PMID:26009011 only alteration type CANCER +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 oncogenic mutation WEE1 inhibitors Head an neck Responsive D NO PMID:25125259 complete HNC +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 oncogenic mutation AZD6738 (ATR inhibitor) B cell lymphoma Responsive C NO NCT01955668;https://ash.confex.com/ash/2014/webprogram/Paper71027.html complete BCL +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 deletion AZD6738 (ATR inhibitor) B cell lymphoma Responsive C NO NCT01955668;https://ash.confex.com/ash/2014/webprogram/Paper71027.html only gene BCL +input01 NRAS (Q61H), NRAS (Q61H), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS oncogenic mutation Vemurafenib (BRAF inhibitor) Cutaneous melanoma Resistant D NO PMID:20179705 complete CM +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 oncogenic mutation Decitabine (Chemotherapy) Acute myeloid leukemia, Myelodisplasic proliferative syndrome Responsive C NO PMID:27959731 complete AML, MDPS +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 oncogenic mutation Doxorubicin (Anthracycline antitumor antibiotic) Bladder Responsive D NO PMID:27397505 complete BLCA +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 oncogenic mutation Gemcitabine (Chemotherapy) Bladder Responsive D NO PMID:27397505 complete BLCA +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 oncogenic mutation Mitomycin C (Chemotherapy) Bladder Responsive D NO PMID:27397505 complete BLCA +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 oncogenic mutation WEE1 inhibitors Ovary Responsive C NO PMID:27998224 complete OV +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 oncogenic mutation Pramlintide (Amylin analogue) Thymic Responsive D NO PMID:25409149 complete THYM +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 deletion Pramlintide (Amylin analogue) Thymic Responsive D NO PMID:25409149 only gene THYM +input01 EGFR (A289N), EGFR (A289D) EGFR (T790M) Afatinib + Erlotinib + Gefitinib Non-small cell lung Resistant A NO oncokb: oncokb=https://www.oncokb.org/gene/EGFR only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR (T790M,D761Y) Gefitinib Non-small cell lung Resistant B NO CIVIC,oncokb: CIVIC=https://civicdb.org/genes/19/summary|oncokb=https://www.oncokb.org/gene/EGFR only alteration type NSCLC +input01 MTOR (L1460P) MTOR (L2209V,L1460P,L2427Q) Temsirolimus Renal clear cell Responsive C NO oncokb: oncokb=https://www.oncokb.org/gene/MTOR complete RCCC +input01 MTOR (Q2223K) MTOR (Q2223K) Everolimus Renal clear cell Responsive C NO oncokb: oncokb=https://www.oncokb.org/gene/MTOR complete RCCC +input01 NRAS (Q61H), NRAS (Q61H), NRAS MUT* (Q61L), NRAS MUT* (Q61R), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS MUT* (Q61R), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS (Q61K,T50I,G13D,G60E,G12C,G12V,T58I,.,Q61H,G12R,G12D,Q61L,G13V,Q61R) Panitumumab + Cetuximab Colorectal adenocarcinoma Resistant A NO oncokb: oncokb=https://www.oncokb.org/gene/NRAS complete COREAD +input01 EGFR (A289N), EGFR (A289D) EGFR (R108K,T263P,A289V) Lapatinib Glioma Responsive D NO oncokb: oncokb=https://www.oncokb.org/gene/EGFR only alteration type G +input01 EGFR (A289N), EGFR (A289D) EGFR (C797G,C797S) Osimertinib Non-small cell lung Resistant B NO CIVIC,oncokb: CIVIC=https://civicdb.org/genes/19/summary|oncokb=https://www.oncokb.org/gene/EGFR only alteration type NSCLC +input01 MTOR (E2419K), MTOR (E2014K) MTOR (E2419K,E2014K) Everolimus Bladder Responsive C NO oncokb: oncokb=https://www.oncokb.org/gene/MTOR complete BLCA +input01 MTOR (R2505P), MTOR (I2500M), MTOR (I2500F), MTOR (E2419K), MTOR (Q2223K), MTOR (S2215F), MTOR (S2215Y), MTOR (S2215T), MTOR (P2213S), MTOR (F2108L), MTOR (E2014K), MTOR (H1968Y), MTOR (C1483W), MTOR (C1483F), MTOR (C1483Y), MTOR (C1483R), MTOR (L1460P) MTOR (E2419K,C1483F,L2172M,K1452N,L2230V,L2427Q,L2431P,F1888I,E1799K,L2216P,W1456R,C1483W,A1519T,L1460P,A2210P,T2232I,R2505P,M2327I,C1483R,V2006I,A1428T,Y1463S,I2500M,A1459P,F1888L,S2231W,T1977R,V2006F,T1977K,A2226S,I2500F,L2427R,T1977I,S2215F,.,Q2223K,I1973F,L1433S,F1888V,S2215T,D2512H,E2014K,S2215Y,R2217W,L2209V,V2006L,L2220F,L2427P,S2215P,P2273S,E2288K,C1483Y) Temsirolimus + Everolimus Any cancer type Responsive D YES oncokb: oncokb=https://www.oncokb.org/gene/MTOR complete CANCER +input01 NRAS (Q61H), NRAS (Q61H), NRAS MUT* (Q61L), NRAS MUT* (Q61R), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS MUT* (Q61R), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS (Q61K,T50I,G13D,G60E,G12C,G12V,T58I,.,Q61H,G12R,G12D,Q61L,G13V,Q61R) Binimetinib + Binimetinib + Ribociclib Cutaneous melanoma Responsive C NO oncokb: oncokb=https://www.oncokb.org/gene/NRAS complete CM +input01 HRAS (G12S) HRAS (Q61K,F28L,Q22K,A146T,Q61R,A146V,Q61H,G12A,G13R,K117R,G13D,G12C,T58I,.,K117N,A59G,G13V,A59T,G13C,G12V,G12D,Q61L,G12S,P34R) Tipifarnib Head an neck squamous Responsive C NO oncokb: oncokb=https://www.oncokb.org/gene/HRAS complete HNSC +input01 HRAS (G12S) HRAS amplification Tipifarnib Head an neck squamous Responsive C NO oncokb: oncokb=https://www.oncokb.org/gene/HRAS only gene HNSC +input01 AKT1 (E17K) AKT1 (E17K) Azd5363 Breast adenocarcinoma Responsive C YES CIVIC,oncokb: oncokb=https://www.oncokb.org/gene/AKT1|CIVIC=https://civicdb.org/genes/2/summary complete BRCA +input01 AKT1 (E17K) AKT1 (E17K) Azd5363 Endometrial adenocarcinoma Responsive C NO oncokb: oncokb=https://www.oncokb.org/gene/AKT1 complete EDA +input01 AKT1 (E17K) AKT1 (E17K) Azd5363 Ovary Responsive C NO oncokb: oncokb=https://www.oncokb.org/gene/AKT1 complete OV +input01 ATM (N2875H) ATM (R2832C,T1743I,R2642S,S2592C,.,R2032K,D2870A,V2424G,N2875K,L590R,R3008C) Olaparib Any cancer type Responsive D YES oncokb: oncokb=https://www.oncokb.org/gene/ATM complete CANCER +input01 ATM (N2875H) ATM deletion Olaparib Any cancer type Responsive D YES oncokb: oncokb=https://www.oncokb.org/gene/ATM only gene CANCER +input01 EGFR (A289N), EGFR (A289D) EGFR (T790M,D761Y) Osimertinib Non-small cell lung Responsive A NO CIVIC,oncokb: CIVIC=https://civicdb.org/genes/19/summary|oncokb=https://www.oncokb.org/gene/EGFR only alteration type NSCLC +input01 RET MUT* (FPEEEKCFC612-620-) RET fusion Cabozantinib + Vandetanib + Larotrectinib + 292 + 667 Non-small cell lung Responsive B NO oncokb: oncokb=https://www.oncokb.org/gene/RET only gene NSCLC +input01 RET MUT* (FPEEEKCFC612-620-) RET (C618R,C620R,C609Y,E768D,C630R,S904F,E511K,C634S,C634Y,V648I,I852M,S891A,A883T,A883F,C611Y,T338I,C634W,K603Q,D631Y,M918T,A919V,R833C,.,V804M,C634R,V804L,Y806C,M918V,L790F,M848T,R886W,Y791F) Larotrectinib + 292 + 667 Thyroid medullary Responsive C NO oncokb: oncokb=https://www.oncokb.org/gene/RET only alteration type THM +input01 RET MUT* (FPEEEKCFC612-620-) RET fusion Larotrectinib + 292 + 667 Thyroid medullary Responsive C NO oncokb: oncokb=https://www.oncokb.org/gene/RET only gene THM +input01 RET MUT* (FPEEEKCFC612-620-) RET-KIF5B fusion Larotrectinib + 292 + 667 Thyroid medullary Responsive C NO oncokb: oncokb=https://www.oncokb.org/gene/RET only gene THM +input01 RET MUT* (FPEEEKCFC612-620-) RET-CCDC6 fusion Larotrectinib + 292 + 667 Thyroid medullary Responsive C NO oncokb: oncokb=https://www.oncokb.org/gene/RET only gene THM +input01 NRAS (Q61H), NRAS (Q61H), NRAS MUT* (Q61L), NRAS MUT* (Q61R), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS MUT* (Q61R), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS (Q61K,T50I,G13D,G60E,G12C,G12V,T58I,.,Q61H,G12R,G12D,Q61L,G13V,Q61R) Selumetinib Thyroid carcinoma Responsive C NO oncokb: oncokb=https://www.oncokb.org/gene/NRAS complete THCA +input01 EGFR (A289N), EGFR (A289D) EGFR amplification Lapatinib Glioma Responsive D NO oncokb: oncokb=https://www.oncokb.org/gene/EGFR only gene G +input01 AKT1 (E17K) AKT1 E17K Vemurafenib Cutaneous melanoma Resistant D NO https://civicdb.org/links/molecular_profiles/4 complete CM +input01 AKT1 (E17K) AKT1 E17K Uprosertib Cutaneous melanoma Response D NO https://civicdb.org/links/molecular_profiles/4 complete CM +input01 AKT1 (Q79K) AKT1 Q79K Vemurafenib Cutaneous melanoma Resistant D NO https://civicdb.org/links/molecular_profiles/169 complete CM +input01 AKT1 (Q79K) AKT1 Q79K Dabrafenib Cutaneous melanoma Resistant C NO https://civicdb.org/links/molecular_profiles/169 complete CM +input01 ATM (N2875H) ATM Mutation Temozolomide Cutaneous melanoma Response D NO https://civicdb.org/links/molecular_profiles/178 complete CM +input01 BRAF wildtype BRAF WILD TYPE MEK Inhibitor RO4987655 Cutaneous melanoma Resistant B NO https://civicdb.org/links/molecular_profiles/422 complete CM +input01 EGFR (A289N), EGFR (A289D) EGFR A763_Y764insFQEA Erlotinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/1423 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR A763_Y764insFQEA Osimertinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1423 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR A767_V769dupASV Erlotinib Lung adenocarcinoma Resistant C NO https://civicdb.org/links/molecular_profiles/1487 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR A767_V769dupASV Osimertinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1487 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR A864T Erlotinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/1161 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR C797S Osimertinib Lung adenocarcinoma Resistant C NO https://civicdb.org/links/molecular_profiles/411 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR C797S Osimertinib Non-small cell lung Resistant B NO https://civicdb.org/links/molecular_profiles/411 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR D761Y Erlotinib,Gefitinib Non-small cell lung Resistant C NO https://civicdb.org/links/molecular_profiles/693 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR D770_N771insG Osimertinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1420 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR D770_N771insGL Erlotinib Lung adenocarcinoma Resistant C NO https://civicdb.org/links/molecular_profiles/1422 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR D770_N771insGT Erlotinib Lung adenocarcinoma Resistant C NO https://civicdb.org/links/molecular_profiles/1474 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR D770_N771insNPG Afatinib,Gefitinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/1477 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR D770delinsGY Erlotinib Lung adenocarcinoma Resistant C NO https://civicdb.org/links/molecular_profiles/2090 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR E746G Erlotinib Lung adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/705 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR E746_A750del Gefitinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/976 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR E746_A750del Gefitinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/976 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR EGFR::RAD51 Erlotinib Lung adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/2079 only gene LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR EGFR::RAD51 Icotinib Lung adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/2079 only gene LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR EGFR::RAD51 Osimertinib Lung adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/2079 only gene LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR G719 Erlotinib Lung adenocarcinoma Response B NO https://civicdb.org/links/molecular_profiles/699 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR G719 Gefitinib,Erlotinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/699 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR G719A Gefitinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/973 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR G719A Gefitinib,Erlotinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/973 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR G719D Gefitinib,Erlotinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1328 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR G719S Gefitinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/134 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR G719S Gefitinib,Erlotinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/134 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR G719S Erlotinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/134 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR H773_V774insNPH Erlotinib Lung adenocarcinoma Resistant C NO https://civicdb.org/links/molecular_profiles/1421 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR K757R Erlotinib Lung adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/704 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR K806E Gefitinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1771 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR KIF5B::EGFR Afatinib Lung adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/4169 only gene LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR L747P Gefitinib,Erlotinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1767 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L747_P753delinsS Erlotinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/986 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L747_P753delinsS Erlotinib Pancreas adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/986 only alteration type PAAD +input01 EGFR (A289N), EGFR (A289D) EGFR L747_S752delinsQ Erlotinib Lung adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/1488 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR L838P Gefitinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1365 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Afatinib Lung adenocarcinoma Response B NO https://civicdb.org/links/molecular_profiles/33 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Gefitinib Lung adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/33 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Gefitinib Lung adenocarcinoma Response B NO https://civicdb.org/links/molecular_profiles/33 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Erlotinib Lung adenocarcinoma Response B NO https://civicdb.org/links/molecular_profiles/33 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Erlotinib Lung adenocarcinoma Response D NO https://civicdb.org/links/molecular_profiles/33 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Cetuximab Lung adenocarcinoma Response D NO https://civicdb.org/links/molecular_profiles/33 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Crizotinib Non-small cell lung Resistant C NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Gefitinib,Erlotinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Gefitinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Erlotinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Afatinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Gefitinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Lapatinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Dacomitinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Neratinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Canertinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Erlotinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Erlotinib Non-small cell lung Response A NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Afatinib Non-small cell lung Response A NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Erlotinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Osimertinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Dacomitinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/33 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L858R Erlotinib Small cell lung Response D NO https://civicdb.org/links/molecular_profiles/33 only alteration type SCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L861 Erlotinib,Gefitinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/1742 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L861Q Gefitinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/994 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR L861R Gefitinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1385 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR M766_A767insAI Erlotinib Non-small cell lung Resistant D NO https://civicdb.org/links/molecular_profiles/1572 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR Mutation Afatinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/438 complete NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR Mutation Gefitinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/438 complete NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR Mutation Erlotinib,Gefitinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/438 complete NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR Mutation Erlotinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/438 complete NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR Mutation Erlotinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/438 complete NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR N826S Erlotinib Non-small cell lung Resistant D NO https://civicdb.org/links/molecular_profiles/1162 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR N826Y Gefitinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1772 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR N842S Gefitinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1775 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR P772_H773insYNP Erlotinib Non-small cell lung Resistant C NO https://civicdb.org/links/molecular_profiles/1575 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR R705K Erlotinib,Gefitinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/2206 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR R776C Erlotinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/1155 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR S720 Erlotinib Lung adenocarcinoma Resistant C NO https://civicdb.org/links/molecular_profiles/701 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR S768I Erlotinib Lung adenocarcinoma Resistant C NO https://civicdb.org/links/molecular_profiles/558 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR S768I Erlotinib Lung adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/558 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR S768I Gefitinib Lung adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/558 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR S768I Erlotinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/558 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Gefitinib,Erlotinib Lung adenocarcinoma Resistant B NO https://civicdb.org/links/molecular_profiles/34 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Osimertinib Lung adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/34 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Erlotinib Non-small cell lung Resistant A NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Gefitinib Non-small cell lung Resistant B NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Dacomitinib Non-small cell lung Resistant B NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Erlotinib,Gefitinib Non-small cell lung Resistant B NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Afatinib Non-small cell lung Resistant B NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Gefitinib,Erlotinib Non-small cell lung Resistant C NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Lapatinib Non-small cell lung Resistant D NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Pemetrexed,Erlotinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Rociletinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Rociletinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Osimertinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Osimertinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Osimertinib,Rociletinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Osimertinib Non-small cell lung Response A NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Dacomitinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Neratinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Afatinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Canertinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/34 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR T790M Osimertinib Pancreas adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/34 only alteration type PAAD +input01 EGFR (A289N), EGFR (A289D) EGFR T847I Gefitinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1371 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR V742A Erlotinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/975 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR V769_D770insASV Erlotinib Lung adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/717 only alteration type LUAD +input01 EGFR (A289N), EGFR (A289D) EGFR V774A Gefitinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1768 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR V774M Erlotinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1770 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR V834I Gefitinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1773 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR V851I Gefitinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1374 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR Y764_V765insHH Erlotinib Non-small cell lung Resistant D NO https://civicdb.org/links/molecular_profiles/1573 only alteration type NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR Amplification Platinum Compound,Cetuximab,Fluorouracil Head an neck squamous Response B NO https://civicdb.org/links/molecular_profiles/190 only gene HNSC +input01 EGFR (A289N), EGFR (A289D) EGFR Amplification Osimertinib,Rociletinib Non-small cell lung Resistant D NO https://civicdb.org/links/molecular_profiles/190 only gene NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR Amplification Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/190 only gene NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR Amplification Erlotinib,Gefitinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/190 only gene NSCLC +input01 EGFR (A289N), EGFR (A289D) EGFR Amplification Gefitinib,Erlotinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/190 only gene NSCLC +input01 GNAQ (Q209R) GNAQ Mutation JQ1 Uveal melanoma Response D NO https://civicdb.org/links/molecular_profiles/501 complete UVM +input01 GNAQ (Q209R) GNAQ Mutation Trametinib Uveal melanoma Response B NO https://civicdb.org/links/molecular_profiles/501 complete UVM +input01 GNAQ (Q209R) GNAQ Mutation Sotrastaurin Acetate,Mirdametinib Uveal melanoma Response D NO https://civicdb.org/links/molecular_profiles/501 complete UVM +input01 GNAQ (Q209R) GNAQ Mutation Cabozantinib Uveal melanoma Response B NO https://civicdb.org/links/molecular_profiles/501 complete UVM +input01 GNAQ (Q209R), GNAQ MUT* (Q209L) GNAQ Q209 Selumetinib Uveal melanoma Response B NO https://civicdb.org/links/molecular_profiles/503 complete UVM +input01 GNAQ (Q209R), GNAQ MUT* (Q209L) GNAQ Q209 Refametinib Uveal melanoma Response C NO https://civicdb.org/links/molecular_profiles/503 complete UVM +input01 HRAS (G12S) HRAS Mutation Tipifarnib Bladder Response B NO https://civicdb.org/links/molecular_profiles/271 complete BLCA +input01 HRAS (G12S) HRAS Mutation Tipifarnib Head an neck squamous Response B NO https://civicdb.org/links/molecular_profiles/271 complete HNSC +input01 JAK1 (V658F), JAK1 (S646F), JAK1 (A634D) JAK1 S703I Ruxolitinib Hepatic carcinoma Response D NO https://civicdb.org/links/molecular_profiles/800 only alteration type HC +input01 KIT wildtype KIT WILDTYPE Regorafenib Gastrointestinal stromal Response B NO https://civicdb.org/links/molecular_profiles/2520 complete GIST +input01 MTOR (R2505P), MTOR (I2500M), MTOR (I2500F), MTOR (E2419K), MTOR (Q2223K), MTOR (S2215F), MTOR (S2215Y), MTOR (S2215T), MTOR (P2213S), MTOR (F2108L), MTOR (E2014K), MTOR (H1968Y), MTOR (C1483W), MTOR (C1483F), MTOR (C1483Y), MTOR (C1483R), MTOR (L1460P) MTOR E1799K Sirolimus Renal clear cell Response D NO https://civicdb.org/links/molecular_profiles/540 only alteration type RCCC +input01 MTOR (H1968Y) MTOR H1968Y PI3K/BET Inhibitor LY294002,Capivasertib Cutaneous melanoma Response D NO https://civicdb.org/links/molecular_profiles/279 complete CM +input01 MTOR (P2213S) MTOR P2213S PI3K/BET Inhibitor LY294002,Capivasertib Cutaneous melanoma Response D NO https://civicdb.org/links/molecular_profiles/280 complete CM +input01 NRAS (G13D) NRAS G13D Tanespimycin Cutaneous melanoma Response C NO https://civicdb.org/links/molecular_profiles/93 complete CM +input01 NRAS (Q61H), NRAS (Q61H), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS Mutation MEK Inhibitor RO4987655 Cutaneous melanoma Resistant C NO https://civicdb.org/links/molecular_profiles/208 complete CM +input01 NRAS (Q61H), NRAS (Q61H), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS Mutation Dabrafenib,Vemurafenib Cutaneous melanoma Resistant B NO https://civicdb.org/links/molecular_profiles/208 complete CM +input01 NRAS (Q61H), NRAS (Q61H), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS Mutation Trametinib Cutaneous melanoma Response B NO https://civicdb.org/links/molecular_profiles/208 complete CM +input01 NRAS (Q61H), NRAS (Q61H), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS Mutation Trametinib,Omipalisib Cutaneous melanoma Response D NO https://civicdb.org/links/molecular_profiles/208 complete CM +input01 NRAS (Q61H), NRAS (Q61H), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K), NRAS (A18T), NRAS (G13V), NRAS (G13A), NRAS (G13D), NRAS (G13C), NRAS (G13R), NRAS (G13S), NRAS (G12V), NRAS (G12A), NRAS (G12D) NRAS Mutation Binimetinib Cutaneous melanoma Response D NO https://civicdb.org/links/molecular_profiles/208 complete CM +input01 NRAS (Q61H), NRAS (Q61H), NRAS MUT* (Q61L), NRAS MUT* (Q61R), NRAS (Q61L), NRAS (Q61R), NRAS (Q61P), NRAS MUT* (Q61R), NRAS (Q61*), NRAS (Q61E), NRAS (Q61K) NRAS Q61 Vemurafenib Cutaneous melanoma Resistant B NO https://civicdb.org/links/molecular_profiles/94 complete CM +input01 NRAS (Q61K) NRAS Q61K Binimetinib,Everolimus Neuroblastoma Response D NO https://civicdb.org/links/molecular_profiles/423 complete NB +input01 NRAS (Q61K) NRAS Q61K Trametinib,Selumetinib Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/423 complete NSCLC +input01 NRAS (Q61L) NRAS Q61L Temozolomide Cutaneous melanoma Response C NO https://civicdb.org/links/molecular_profiles/95 complete CM +input01 NRAS (Q61R) NRAS Q61R Temozolomide Cutaneous melanoma Response C NO https://civicdb.org/links/molecular_profiles/96 complete CM +input01 RB1 (R556*), RB1 (R579*), RB1 (C706F), RB1 (E748*) RB1 Mutation Chemotherapy Small cell lung Response B NO https://civicdb.org/links/molecular_profiles/777 complete SCLC +input01 RET MUT* (FPEEEKCFC612-620-) RET CCDC6::RET Nintedanib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/622 only gene NSCLC +input01 RET MUT* (FPEEEKCFC612-620-) RET Fusion Cabozantinib Lung adenocarcinoma Response B NO https://civicdb.org/links/molecular_profiles/1595 only gene LUAD +input01 RET MUT* (FPEEEKCFC612-620-) RET Fusion Vandetanib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/1595 only gene NSCLC +input01 RET MUT* (FPEEEKCFC612-620-) RET Fusion Alectinib Non-small cell lung Response C NO https://civicdb.org/links/molecular_profiles/1595 only gene NSCLC +input01 RET MUT* (FPEEEKCFC612-620-) RET Fusion Selpercatinib Non-small cell lung Response B NO https://civicdb.org/links/molecular_profiles/1595 only gene NSCLC +input01 RET MUT* (FPEEEKCFC612-620-) RET Fusion Pralsetinib Non-small cell lung Response A NO https://civicdb.org/links/molecular_profiles/1595 only gene NSCLC +input01 RET MUT* (FPEEEKCFC612-620-) RET KIF5B::RET Vandetanib Lung adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/269 only gene LUAD +input01 RET MUT* (FPEEEKCFC612-620-) RET KIF5B::RET Vandetanib,Everolimus Lung adenocarcinoma Response C NO https://civicdb.org/links/molecular_profiles/269 only gene LUAD +input01 RUNX1 (R201*) RUNX1 Mutation Cytarabine Acute myeloid leukemia Resistant B NO https://civicdb.org/links/molecular_profiles/155 complete AML +input01 STK11 (Q37*) STK11 Mutation Atezolizumab,Pembrolizumab,Nivolumab Lung adenocarcinoma Resistant B NO https://civicdb.org/links/molecular_profiles/696 complete LUAD +input01 STK11 (Q37*) STK11 Loss Docetaxel,Selumetinib Non-small cell lung Resistant D NO https://civicdb.org/links/molecular_profiles/481 only gene NSCLC +input01 STK11 (Q37*) STK11 Loss Everolimus,Sirolimus Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/481 only gene NSCLC +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 Mutation Selumetinib,Docetaxel Non-small cell lung Response D NO https://civicdb.org/links/molecular_profiles/222 complete NSCLC +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 Mutation Chemotherapy Stomach Response B NO https://civicdb.org/links/molecular_profiles/222 complete ST +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 R273H Doxorubicin,Methotrexate Osteosarcoma Resistant D NO https://civicdb.org/links/molecular_profiles/122 only alteration type OS +input01 TP53 (R306*), TP53 (E286V), TP53 (E286G), TP53 (E286A), TP53 (E286Q) TP53 Loss Docetaxel Non-small cell lung Resistant D NO https://civicdb.org/links/molecular_profiles/4407 only gene NSCLC diff --git a/example_files/cgi_test_out/cgi_test_out.cgi_results/cna_analysis.tsv b/example_files/cgi_test_out/cgi_test_out.cgi_results/cna_analysis.tsv new file mode 100644 index 0000000..778c483 --- /dev/null +++ b/example_files/cgi_test_out/cgi_test_out.cgi_results/cna_analysis.tsv @@ -0,0 +1,4 @@ +internal_id sample gene cna cancer predicted_in_tumors gene_role known_in_tumors driver driver_statement predicted_match known_match +input01_1 test_1 ERBB2 AMP CANCER CESC;ESCA;HNSC;LUAD;PAAD;STAD;UCEC Act BRCA;OV;CANCER;NSCLC;ST;BT;COREAD;BLCA;GEJA;HNC;ED known known in: BRCA;OV;CANCER;NSCLC;ST;BT;COREAD;BLCA;GEJA;HNC;ED known_match known_match +input01_2 test_1 TP53 DEL CANCER S LoF THYM;BCL known known in: THYM;BCL known_match known_match +input01_3 test_1 EGFR AMP CANCER BLCA;CESC;ESCA;LGG;LUAD;LUSC;STAD Act G;NSCLC;ED;HNSC;COREAD known known in: G;NSCLC;ED;HNSC;COREAD known_match known_match diff --git a/querynator/__main__.py b/querynator/__main__.py index 919f5c4..f4da0c6 100644 --- a/querynator/__main__.py +++ b/querynator/__main__.py @@ -419,6 +419,13 @@ def query_api_cgi(mutations, cnas, translocations, cancer, genome, token, email, required=True, default="GRCh38", ) +@click.option( + "-c", + "--cancer", + help="the cancer DOID (id or name) to be searched.", + default=None, + type=click.STRING, +) @click.option( "-f", "--filter_vep", @@ -427,14 +434,7 @@ def query_api_cgi(mutations, cnas, translocations, cancer, genome, token, email, show_default=True, default=False, ) -@click.option( - "-c", - "--cancer", - help="the cancer DOID (id or name) to be searched.", - default=None, - type=click.STRING, -) -def query_api_civic(vcf, outdir, genome, cancer_doid, filter_vep): +def query_api_civic(vcf, outdir, genome, cancer, filter_vep): try: result_dir = get_unique_querynator_dir(f"{outdir}") dirname, basename = os.path.split(result_dir) @@ -447,7 +447,7 @@ def query_api_civic(vcf, outdir, genome, cancer_doid, filter_vep): logger.info("Query the Clinical Interpretations of Variants In Cancer (CIViC)") # run analysis - query_civic(candidate_variants, result_dir, logger, vcf, genome, cancer_doid, filter_vep) + query_civic(candidate_variants, result_dir, logger, vcf, genome, cancer, filter_vep) else: logger.info("Query the Clinical Interpretations of Variants In Cancer (CIViC)") diff --git a/tests/test_querynator.py b/tests/test_querynator.py index 28cfd4c..4cdcc9f 100644 --- a/tests/test_querynator.py +++ b/tests/test_querynator.py @@ -2,50 +2,220 @@ """Tests for `querynator` package.""" +import os +import shutil import unittest from click.testing import CliRunner -import querynator.__main__ +from querynator.__main__ import querynator_cli -class testCLI(unittest.TestCase): +class testCliHelp(unittest.TestCase): + + def setUp(self): + self.runner = CliRunner() def test_commandLineInterface(self): """Test the CLI.""" - runner = CliRunner() - result = runner.invoke(querynator.__main__.querynator_cli) - assert result.exit_code == 0 + result = self.runner.invoke(querynator_cli) + self.assertEqual(result.exit_code, 0) + def test_helpMessage(self): """Test help message""" - help_result = runner.invoke(querynator.__main__.querynator_cli, ["--help"]) - assert help_result.exit_code == 0 - assert "--help Show this message and exit." in help_result.output + help_result = self.runner.invoke(querynator_cli, ["--help"]) + self.assertEqual(help_result.exit_code, 0) + self.assertIn("--help Show this message and exit.", help_result.output) + self.assertNotIn("+++lalelu+++this is not part of the help message+++", help_result.output) + def test_CgiHelp(self): """Test CGI help message""" - cgi_help_result = runner.invoke(querynator.__main__.querynator_cli, ["query-api-cgi", "--help"]) - assert cgi_help_result.exit_code == 0 - assert "--help Show this message and exit." in cgi_help_result.output + cgi_help_result = self.runner.invoke(querynator_cli, ["query-api-cgi", "--help"]) + self.assertEqual(cgi_help_result.exit_code, 0) + self.assertIn("--help Show this message and exit.", cgi_help_result.output) + def test_CivicHelp(self): """Test CIVIC help message""" - civic_help_result = runner.invoke(querynator.__main__.querynator_cli, ["query-api-civic", "--help"]) - assert civic_help_result.exit_code == 0 - assert "--help Show this message and exit." in civic_help_result.output + civic_help_result = self.runner.invoke(querynator_cli, ["query-api-civic", "--help"]) + self.assertEqual(civic_help_result.exit_code, 0) + self.assertIn("--help Show this message and exit.", civic_help_result.output) + def test_CreatereportHelp(self): """Test CREATE-REPORT help message""" - civic_help_result = runner.invoke(querynator.__main__.querynator_cli, ["create-report", "--help"]) - assert civic_help_result.exit_code == 0 - assert "--help Show this message and exit." in civic_help_result.output + report_help_result = self.runner.invoke(querynator_cli, ["create-report", "--help"]) + self.assertEqual(report_help_result.exit_code, 0) + self.assertIn("--help Show this message and exit.", report_help_result.output) + def test_nonExistingSubcommand(self): """Test non-existing subcommand""" - result = runner.invoke(querynator.__main__.querynator_cli, ["query-api-clinvar"]) - assert result.exit_code == 2 - assert "No such command" in result.output + result = self.runner.invoke(querynator_cli, ["query-api-clinvar"]) + self.assertEqual(result.exit_code, 2) + self.assertIn("No such command", result.output) + def test_nonExistingOption(self): """Test non-existing option""" - result = runner.invoke(querynator.__main__.querynator_cli, ["query-api-cgi", "--baz"]) - assert result.exit_code == 2 - assert "No such option" in result.output + result = self.runner.invoke(querynator_cli, ["query-api-cgi", "--baz"]) + self.assertEqual(result.exit_code, 2) + self.assertIn("No such option", result.output) + + +class testCliRun(unittest.TestCase): + unittest_dir = f"{os.getcwd()}/example_files/unittest_out" + + # helper functions + def assertIsFile(self, path, msg=None): + msg = f"{path} is not a file" if msg is None else msg + self.assertTrue(os.path.isfile(path), msg) + + def get_testdir(self): + """Get the test directory for the current test method.""" + method_name = str(self).split()[0] + return f"{self.unittest_dir}/{method_name}" + + def clean_testdir(self): + try: + shutil.rmtree(self.get_testdir()) + except FileNotFoundError: + pass + + # tests + def setUp(self): + self.runner = CliRunner() + self.clean_testdir() + + def test_queryApiCivic(self): + """Test query-api-civic""" + outdir = self.get_testdir() + result = self.runner.invoke( + querynator_cli, + [ + "query-api-civic", + "--vcf", + f"{os.getcwd()}/example_files/example.vcf", + "--genome", + "GRCh37", + "--outdir", + outdir, + "--filter_vep", + ], + ) + self.assertEqual(result.exit_code, 0, "non-zero exit code") + self.assertIsFile(f"{outdir}/{outdir.split('/')[-1]}.civic_results.tsv", "civic_results.tsv not created") + + def test_queryApiCivic_Cancer(self): + """Test query-api-civic""" + outdir = self.get_testdir() + + result = self.runner.invoke( + querynator_cli, + [ + "query-api-civic", + "--vcf", + "example_files/example.vcf", + "--genome", + "GRCh37", + "--outdir", + outdir, + "--cancer", + "Cholangiocarcinoma", + "--filter_vep", + ], + ) + self.assertEqual(result.exit_code, 0, "non-zero exit code") + self.assertIsFile(f"{outdir}/{outdir.split('/')[-1]}.civic_results.tsv", "civic_results.tsv not created") + + def test_queryApiCgi(self): + """test querynator query-api-cgi with dummy credentials""" + outdir = self.get_testdir() + result = self.runner.invoke( + querynator_cli, + [ + "query-api-cgi", + "--mutations", + f"{os.getcwd()}/example_files/example.vcf", + "--genome", + "GRCh37", + "--outdir", + outdir, + "--email", + "dummy@internet.by", + "--token", + "thisisadummytoken", + "--filter_vep", + ], + ) + self.assertEqual(result.exit_code, 1) + + def test_queryApiCgi_Cancer(self): + """test querynator query-api-cgi with dummy credentials""" + outdir = self.get_testdir() + result = self.runner.invoke( + querynator_cli, + [ + "query-api-cgi", + "--mutations", + f"{os.getcwd()}/example_files/example.vcf", + "--genome", + "GRCh37", + "--outdir", + outdir, + "--cancer", + "Breast adenocarcinoma", + "--email", + "dummy@internet.by", + "--token", + "thisisadummytoken", + "--filter_vep", + ], + ) + self.assertEqual(result.exit_code, 1) + + def test_queryApiCgi_invalidCancer(self): + """test querynator query-api-cgi with dummy credentials""" + outdir = self.get_testdir() + result = self.runner.invoke( + querynator_cli, + [ + "query-api-cgi", + "--mutations", + f"{os.getcwd()}/example_files/example.vcf", + "--genome", + "GRCh37", + "--outdir", + outdir, + "--cancer", + "this is not cancer, 'tis but a flesh wound", + "--email", + "dummy@internet.by", + "--token", + "thisisadummytoken", + "--filter_vep", + ], + ) + self.assertEqual(result.exit_code, 2) + + def test_createReport(self): + """test querynator create-report on example files""" + outdir = self.get_testdir() + result = self.runner.invoke( + querynator_cli, + [ + "create-report", + "--cgi_path", + f"{os.getcwd()}/example_files/cgi_test_out", + "--civic_path", + f"{os.getcwd()}/example_files/civic_test_out", + "--outdir", + outdir, + ], + ) + self.assertEqual(result.exit_code, 0, "non-zero exit code") + self.assertIsFile(f"{outdir}/combined_files/civic_cgi_vep.tsv", "combined file not created") + self.assertIsFile(f"{outdir}/report/{outdir.split('/')[-1]}_overall_report.html", "report not created") + + def tearDown(self): + """Clean up output directories after tests are run.""" + self.clean_testdir() if __name__ == "__main__":