Compendium of Cancer Genome Aberrations

Breast Cancer: Recurrent Genomic Alterations: Difference between revisions

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|Gain of function
|Gain of function
|[https://omim.org/entry/164730 164730]
|[https://omim.org/entry/164730 164730]
|AKT1
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=AKT1 AKT1]
|AKT1 breast
|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=AKT1&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true AKT1 breast]
|sequence variants, amplification
|sequence variants, amplification
|Therapy: AKT inhibitors (FDA approved for E17K per CAPItello-291 trial); resistance to CDK4/6 inhibitors; Diseases: Metastatic BC, ER positive BC, lobular CA. Prognosis: risk of early relapse. Mutations occur early and are found in papillary lesions, proliferative lesions and cancer precusors. Absent in mucinous carcinoma (PMID: 22705004).
|Therapy: AKT inhibitors (FDA approved for E17K per CAPItello-291 trial); resistance to CDK4/6 inhibitors; Diseases: Metastatic BC, ER positive BC, lobular CA. Prognosis: risk of early relapse. Mutations occur early and are found in papillary lesions, proliferative lesions and cancer precusors. Absent in mucinous carcinoma (PMID: 22705004).
|19418217; 19898424; 22705004; 23352210; 24186142; 26926684; 37256976; 38811720
|[https://pubmed.ncbi.nlm.nih.gov/19418217/ 19418217]; [https://pubmed.ncbi.nlm.nih.gov/19898424/ 19898424]; [https://pubmed.ncbi.nlm.nih.gov/22705004/ 22705004]; [https://pubmed.ncbi.nlm.nih.gov/23352210/ 23352210]; [https://pubmed.ncbi.nlm.nih.gov/24186142/ 24186142]; [https://pubmed.ncbi.nlm.nih.gov/26926684/ 26926684]; [https://pubmed.ncbi.nlm.nih.gov/37256976/ 37256976]; [https://pubmed.ncbi.nlm.nih.gov/38811720/ 38811720]
|-
|-
|''ALK''
|''ALK''
|2
|2
|Gain of function
|Gain of function
|105590
|[https://omim.org/entry/105590 105590]
|ALK
|[https://cancer.sanger.ac.uk/cosmic/search?q=ALK ALK]
|ALK breast
|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=ALK&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true ALK breast]
|fusion
|fusion
|Therapy: ALK inhibitors. Very rare in breast cancer. More commonly associated with inflammatory myofibroblastic tumor (IMT), which can affect the breast. Can also be seen in ALK-positive histiocytosis in the breast.
|Therapy: ALK inhibitors. Very rare in breast cancer. More commonly associated with inflammatory myofibroblastic tumor (IMT), which can affect the breast. Can also be seen in ALK-positive histiocytosis in the breast.
|32348852; 34423228; 34650924; 35171116; 35171116; 34482333
|[https://pubmed.ncbi.nlm.nih.gov/32348852/ 32348852]; [https://pubmed.ncbi.nlm.nih.gov/34423228/ 34423228]; [https://pubmed.ncbi.nlm.nih.gov/34650924/ 34650924]; [https://pubmed.ncbi.nlm.nih.gov/35171116/ 35171116]; [https://pubmed.ncbi.nlm.nih.gov/34482333/ 34482333]
|-
|-
|''APC''
|''APC''
|2
|2
|Loss of function
|Loss of function
|611731
|[https://omim.org/entry/611731 611731]
|APC
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=APC APC]
|APC breast
|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=APC&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true APC breast]
|sequence variants, epigenetic modification
|sequence variants, epigenetic modification
|Diseases: fibromatosis, TNBC. Therapy: mutations and hypermethylation associated with therapy resistance; Prognosis: APC mutation associated with poor prognosis in TNBC
|Diseases: fibromatosis, TNBC. Therapy: mutations and hypermethylation associated with therapy resistance; Prognosis: APC mutation associated with poor prognosis in TNBC
|11823972; 34370741; 26049416; 35936696; 33369461; 35523804
|[https://pubmed.ncbi.nlm.nih.gov/11823972/ 11823972]; [https://pubmed.ncbi.nlm.nih.gov/34370741/ 34370741]; [https://pubmed.ncbi.nlm.nih.gov/26049416/ 26049416]; [https://pubmed.ncbi.nlm.nih.gov/35936696/ 35936696]; [https://pubmed.ncbi.nlm.nih.gov/33369461/ 33369461]; [https://pubmed.ncbi.nlm.nih.gov/35523804/ 35523804]
|-
|-
|''AR''
|''AR''
|2
|2
|Gain of function
|Gain of function
|313700
|[https://omim.org/entry/313700 313700]
|AR
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=AR AR]
|AR breast metastatic
|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=AR&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true AR breast metastatic]
|altered expression, sequence variants, amplification
|altered expression, sequence variants, amplification
|Therapy: androgen receptor inhibitor therapy for luminal AR-positive TNBC. AR splice variants lacking the ligand binding domain can occur pre or post treatment and may lead to constitutive activation of AR signaling and resistance to AR inhibition. Diseases: AR is expressed in 70-90% of breast cancers overall. AR positive is associated with apocrine features in TNBC and luminal AR subtype.
|Therapy: androgen receptor inhibitor therapy for luminal AR-positive TNBC. AR splice variants lacking the ligand binding domain can occur pre or post treatment and may lead to constitutive activation of AR signaling and resistance to AR inhibition. Diseases: AR is expressed in 70-90% of breast cancers overall. AR positive is associated with apocrine features in TNBC and luminal AR subtype.
|34593966; 31822498; 36097802; 35986801; 29453314; 23245877
|[https://pubmed.ncbi.nlm.nih.gov/34593966/ 34593966]; [https://pubmed.ncbi.nlm.nih.gov/31822498/ 31822498]; [https://pubmed.ncbi.nlm.nih.gov/36097802/ 36097802]; [https://pubmed.ncbi.nlm.nih.gov/35986801/ 35986801]; [https://pubmed.ncbi.nlm.nih.gov/29453314/ 29453314]; [https://pubmed.ncbi.nlm.nih.gov/23245877/ 23245877]
|-
|-
|''ARID1A''
|''ARID1A''
|2
|2
|Loss of function
|Loss of function
|603024
|[https://omim.org/entry/603024 603024]
|ARID1A
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=ARID1A ARID1A]
|ARID1A breast
|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=ARID1A&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true ARID1A breast]
|sequence variants, other structural rearrangement
|sequence variants, other structural rearrangement
|Diseases: endocrine-resistant ER+ BC. Enriched in special subtypes including neuroendocrine tumors, solid basaloid subtype of adenoid cystic carcinoma. Therapy: may be responsive to Ezh2 inhibitors; also may be responsive to Atr, PARP, and BET domain inhibitors
|Diseases: endocrine-resistant ER+ BC. Enriched in special subtypes including neuroendocrine tumors, solid basaloid subtype of adenoid cystic carcinoma. Therapy: may be responsive to Ezh2 inhibitors; also may be responsive to Atr, PARP, and BET domain inhibitors
|31932695; 33148628; 34804958; 26770240; 25686104; 27958275; 26069190; 29760405
|[https://pubmed.ncbi.nlm.nih.gov/31932695/ 31932695]; [https://pubmed.ncbi.nlm.nih.gov/33148628/ 33148628]; [https://pubmed.ncbi.nlm.nih.gov/34804958/ 34804958]; [https://pubmed.ncbi.nlm.nih.gov/26770240/ 26770240]; [https://pubmed.ncbi.nlm.nih.gov/25686104/ 25686104]; [https://pubmed.ncbi.nlm.nih.gov/27958275/ 27958275]; [https://pubmed.ncbi.nlm.nih.gov/26069190/ 26069190]; [https://pubmed.ncbi.nlm.nih.gov/29760405/ 29760405]
|-
|-
|''ATM''
|''ATM''
|1
|1
|Loss of function
|Loss of function
|607585
|[https://omim.org/entry/607585 607585]
|ATM
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=ATM ATM]
|ATM breast
|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=ATM&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true ATM breast]
|sequence variants, other structural rearrangement
|sequence variants, other structural rearrangement
|Diseases: hereditary BC (moderate penetrance, 21-24% risk according to NCCN, c.7271T>G higher penetrance) but most mutations detected in tumors are somatic not germline; (odds ratio 2.10, 95% CI 1.71–2.57 in 2022 NEJM study). ER positive BC. Therapy: PARP inhibitor (preclinical use - limited/conflicting evidence); no contra-indications for radiotherapy at this time
|Diseases: hereditary BC (moderate penetrance, 21-24% risk according to NCCN, c.7271T>G higher penetrance) but most mutations detected in tumors are somatic not germline; (odds ratio 2.10, 95% CI 1.71–2.57 in 2022 NEJM study). ER positive BC. Therapy: PARP inhibitor (preclinical use - limited/conflicting evidence); no contra-indications for radiotherapy at this time
|33471991; 21787400; 16832357; 30504931; 39636577; 29506079
|[https://pubmed.ncbi.nlm.nih.gov/33471991/ 33471991]; [https://pubmed.ncbi.nlm.nih.gov/21787400/ 21787400]; [https://pubmed.ncbi.nlm.nih.gov/16832357/ 16832357]; [https://pubmed.ncbi.nlm.nih.gov/30504931/ 30504931]; [https://pubmed.ncbi.nlm.nih.gov/39636577/ 39636577]; [https://pubmed.ncbi.nlm.nih.gov/29506079/ 29506079]
|-
|-
|''ATR''
|''ATR''
|2
|2
|Loss of function
|Loss of function
|601215
|[https://omim.org/entry/601215 601215]
|ATR
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=ATR ATR]
|ATR breast
|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=ATR&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true ATR breast]
|sequence variants, other structural rearrangement
|sequence variants, other structural rearrangement
|Diseases: TNBC. Therapy: Potentially targetable with PARP inhibitors and ATR inhibitors. ATR mutations can be germline or somatic. DNA damage response pathway gene.
|Diseases: TNBC. Therapy: Potentially targetable with PARP inhibitors and ATR inhibitors. ATR mutations can be germline or somatic. DNA damage response pathway gene.
|38539474
|[https://pubmed.ncbi.nlm.nih.gov/38539474/ 38539474]
|-
|-
|''AURKA''
|''AURKA''
|2
|2
|Gain of function
|Gain of function
|603072
|[https://omim.org/entry/603072 603072]
|AURKA
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=AURKA AURKA]
|AURKA breast
|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=AURKA&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true AURKA breast]
|amplification
|amplification
|Therapy: resistance to CDK4/6 inhibitors, assocaited with poor prognosis, in multiple clinical trials
|Therapy: resistance to CDK4/6 inhibitors, assocaited with poor prognosis, in multiple clinical trials
|29180466; 23186136; 36892847; 25362855; 20607239
|[https://pubmed.ncbi.nlm.nih.gov/29180466/ 29180466]; [https://pubmed.ncbi.nlm.nih.gov/23186136/ 23186136]; [https://pubmed.ncbi.nlm.nih.gov/36892847/ 36892847]; [https://pubmed.ncbi.nlm.nih.gov/25362855/ 25362855]; [https://pubmed.ncbi.nlm.nih.gov/20607239/ 20607239]
|-
|-
|''AXIN2''
|''AXIN2''
|2
|2
|Loss of function
|Loss of function
|604025
|[https://omim.org/entry/604025 604025]
|AXIN2
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=AXIN2 AXIN2]
|AXIN2 breast
|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=AXIN2&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true AXIN2 breast]
|sequence variants, other structural rearrangement
|sequence variants, other structural rearrangement
|Diseases: Inactivating alterations in a subset of ILC with retained CDH1 gene expression
|Diseases: Inactivating alterations in a subset of ILC with retained CDH1 gene expression
|38347189; 39941785
|[https://pubmed.ncbi.nlm.nih.gov/38347189/ 38347189]; [https://pubmed.ncbi.nlm.nih.gov/39941785/ 39941785]
|-
|-
|''BAP1''
|''BAP1''
|2
|2
|Loss of function
|Loss of function
|603089
|[https://omim.org/entry/603089 603089]
|BAP1
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=BAP1 BAP1]
|BAP1 breast
|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=BAP1&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true BAP1 breast]
|sequence variants, other structural rearrangement
|sequence variants, other structural rearrangement
|Diseases: hereditary cancer but breast cancer not an established association. Therapy: PARP inhibitor (preclinical and some clinical trials) for association with HRD.
|Diseases: hereditary cancer but breast cancer not an established association. Therapy: PARP inhibitor (preclinical and some clinical trials) for association with HRD.
|16341802; 32776290; 35905855; 33866194
|[https://pubmed.ncbi.nlm.nih.gov/16341802/ 16341802]; [https://pubmed.ncbi.nlm.nih.gov/32776290/ 32776290]; [https://pubmed.ncbi.nlm.nih.gov/35905855/ 35905855]; [https://pubmed.ncbi.nlm.nih.gov/33866194/ 33866194]
|-
|-
|''BARD1''
|''BARD1''
|1
|1
|Loss of function
|Loss of function
|601593
|[https://omim.org/entry/601593 601593]
|BARD1
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=BARD1 BARD1]
|BARD1 breast
|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=BARD1&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true BARD1 breast]
|sequence variants
|sequence variants
|Diseases: ER-negative BC. Constitutional pathogenic variants (truncating) associated with hereditary BC (moderate penetrance), HRD. Slight increased risk of breast cancer (odds ratio, 2.09; 95% CI, 1.35 to 3.23 in NEJM 2022 study).
|Diseases: ER-negative BC. Constitutional pathogenic variants (truncating) associated with hereditary BC (moderate penetrance), HRD. Slight increased risk of breast cancer (odds ratio, 2.09; 95% CI, 1.35 to 3.23 in NEJM 2022 study).
|20301425; 33471991; 31142030; 30504931
|[https://pubmed.ncbi.nlm.nih.gov/20301425/ 20301425]; [https://pubmed.ncbi.nlm.nih.gov/33471991/ 33471991]; [https://pubmed.ncbi.nlm.nih.gov/31142030/ 31142030]; [https://pubmed.ncbi.nlm.nih.gov/30504931/ 30504931]
|-
|-
|''BRAF''
|''BRAF''
Retrieved from "https://test.ccga.io/index.php/Breast_Cancer:_Recurrent_Genomic_Alterations"