Compendium of Cancer Genome Aberrations

Breast Cancer: Recurrent Genomic Alterations: Difference between revisions

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|Loss of function
|Loss of function
|613484
|[https://omim.org/entry/613484?search=613484&highlight=613484 613484]
|SPEN
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=SPEN SPEN]
|SPEN 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=SPEN&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true SPEN breast]
|sequence variants, altered expression
|sequence variants, altered expression
|Diseases: altered in 1-2% of invasisive breast carcinoma (CBioPortal); recent evidence suggests SPEN acts as a tumor suppressor in ER-positive breast cancer and overexpressed SPEN sensitizes HR-positive breast cancer cells to the effects of tamoxifen; more mutations detected in patients with ER+/PR- breast cancer or detectable MRD
|Diseases: altered in 1-2% of invasisive breast carcinoma (CBioPortal); recent evidence suggests SPEN acts as a tumor suppressor in ER-positive breast cancer and overexpressed SPEN sensitizes HR-positive breast cancer cells to the effects of tamoxifen; more mutations detected in patients with ER+/PR- breast cancer or detectable MRD
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|2
|2
|Loss of function
|Loss of function
|[https://omim.org/entry/613484?search=613484&highlight=613484 602216]
|[https://omim.org/entry/602216?search=602216&highlight=602216 602216]
|STK11
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=STK11 STK11]
|STK11 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=STK11&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true STK11 breast]
|sequence variants
|sequence variants
|Diseases: syndromic risk for hereditary BC and other cancers (Peutz-Jeghers syndrome) (high penetrance, but most mutations detected in tumors are somatic not germline). Lkb1 activates AMPK and negatively regulates the mTOR pathway in response to cellular energy levels. Therapy: may be responsive to mTOR inhibitors.
|Diseases: syndromic risk for hereditary BC and other cancers (Peutz-Jeghers syndrome) (high penetrance, but most mutations detected in tumors are somatic not germline). Lkb1 activates AMPK and negatively regulates the mTOR pathway in response to cellular energy levels. Therapy: may be responsive to mTOR inhibitors.
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|2
|2
|Gain of function
|Gain of function
|137290
|[https://omim.org/entry/137290?search=137290&highlight=137290 137290]
|TACSTD2
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=TACSTD2 TACSTD2]
|TACSTD2 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=TACSTD2&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true TACSTD2 breast]
|altered expression
|altered expression
|Diseases: mBC. Trop-2 is protein product of TACSTD2, and is expressed in the majority of breast cancers. Therapy: Trop-2 expression is targeted by antibody-drug conjugate (ADC) sacituzumab govitecan in TNBC and HR+, HER2- mBC previously treated with endocrine therapy, a CDK4/6 inhibitor, and a multiple lines of chemotherapy.
|Diseases: mBC. Trop-2 is protein product of TACSTD2, and is expressed in the majority of breast cancers. Therapy: Trop-2 expression is targeted by antibody-drug conjugate (ADC) sacituzumab govitecan in TNBC and HR+, HER2- mBC previously treated with endocrine therapy, a CDK4/6 inhibitor, and a multiple lines of chemotherapy.
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|2
|2
|Gain of function
|Gain of function
|601621
|[https://omim.org/entry/601621?search=601621&highlight=601621 601621]
|TBX3
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=TBX3 TBX3]
|TBX3 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=TBX3&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true TBX3 breast]
|sequence variants, amplification, altered expression
|sequence variants, amplification, altered expression
|Diseases: ER positive BC, Enriched in special subtypes including neuroendocrine tumors, lobular BC; metastatic breast cancer. Therapy: hormone resistance. TBX3 is one of several estrogen receptor transcriptional regulators also including MYC, CTCF, FOXA1.
|Diseases: ER positive BC, Enriched in special subtypes including neuroendocrine tumors, lobular BC; metastatic breast cancer. Therapy: hormone resistance. TBX3 is one of several estrogen receptor transcriptional regulators also including MYC, CTCF, FOXA1.
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|2
|2
|Gain of function
|Gain of function
|187270
|[https://omim.org/entry/187270?search=187270&highlight=187270 187270]
|TERT
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=TERT TERT]
|TERT 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=TERT&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true TERT breast]
|amplification, sequence variants
|amplification, sequence variants
|Diseases: phyllodes tumor, more frequent in borderline and malignant tumors (promoter mut); carcinoma (TERT amplification), metaplastic carcinoma (promoter mutation)
|Diseases: phyllodes tumor, more frequent in borderline and malignant tumors (promoter mut); carcinoma (TERT amplification), metaplastic carcinoma (promoter mutation)
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|2
|2
|Gain of function
|Gain of function
|126430
|[https://omim.org/entry/126430?search=126430&highlight=126430 126430]
|TOP2A
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=TOP2A TOP2A]
|TOP2A 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=TOP2A&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true TOP2A breast]
|amplification, sequence variants
|amplification, sequence variants
|Therapy: responsiveness to anthracycline inhibitors. Prognosis: increased TOP2A expression is an adverse prognostic indicator.
|Therapy: responsiveness to anthracycline inhibitors. Prognosis: increased TOP2A expression is an adverse prognostic indicator.
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|2
|2
|Loss of function
|Loss of function
|191170
|[https://omim.org/entry/191170?search=191170&highlight=191170 191170]
|TP53
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=TP53 TP53]
|TP53 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=TP53&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true TP53 breast]
|sequence variants, other structural rearrangement, altered expression
|sequence variants, other structural rearrangement, altered expression
|Diseases: HER2 positive BC, ER positive BC; metastatic BC; syndromic risk for hereditary BC and other cancers (Li-Fraumeni syndrome; odds ratio, 3.06; 95% CI, 0.63 to 14.91; in 2022 NEJM study). Prognosis: unfavorable. Therapy: mutations in TP53 may increase resistance to ionizing radiation therapy; therapies for TP53mut BC in development.
|Diseases: All subtypes; enriched in TNBC. Constitutional variants associated with syndromic risk for hereditary BC and other cancers (Li-Fraumeni syndrome). Prognosis: unfavorable. Therapy: mutations in TP53 may increase resistance to ionizing radiation therapy; therapies for TP53mut BC in development.
|20301425; 33471991; 28027327; 32636452; 24803582; 14576853; 30504931
|20301425; 33471991; 28027327; 32636452; 24803582; 14576853; 30504931
|-
|-
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|2
|2
|Other/Complex
|Other/Complex
|604386
|[https://omim.org/entry/604386?search=604386&highlight=604386 604386]
|TRPS1
|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=TRPS1 TRPS1]
|TRPS1 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=TRPS1&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true TRPS1 breast]
|altered expression
|altered expression
|Diseases: BC all types, diagnostic utility in identifying breast origin (IHC marker), including TNBC where it is useful as GATA3 expression is usually absent. TRPS1 is a GATA gene family member and paralog of GATA3. Overexpression is observed in breast cancer and is of uncertain prognostic significance. Therapy: overexpression is linked to multidrug resistance in BC.
|Diseases: BC all types, diagnostic utility in identifying breast origin (IHC marker), including TNBC where it is useful as GATA3 expression is usually absent. TRPS1 is a GATA gene family member and paralog of GATA3. Overexpression is observed in breast cancer and is of uncertain prognostic significance. Therapy: overexpression is linked to multidrug resistance in BC.
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