Compendium of Cancer Genome Aberrations

Breast Cancer: Recurrent Genomic Alterations: Difference between revisions

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'''Table 1 - Clinically significant copy number alterations in breast cancer'''
{| class="wikitable"
{| class="wikitable"
|'''Alteration'''
|'''Alteration'''
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|-
|-
|1q gain
|1q gain
| unknown
|unknown
|2
|2
|Most common copy number alteration, often with 16q loss; all subtypes
|Most common copy number alteration, often with 16q loss; all subtypes
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|2
|2
|METABRIC IntClust1, ER Positive
|METABRIC IntClust1, ER Positive
|}
'''Table 2 - Major clinically significant genes associated with somatic sequence alterations in breast cancer'''
{| class="wikitable"
|'''Gene(s)'''
|'''CGC Evidence Level'''
|'''Clinical Significance and Subgroup Association(s)'''
|'''Therapy Implication(s)'''
|-
|''AKT1''
|2
|Metastatic BC
|AKT inhibitors
|-
|''ATM''
|1
|Possible hereditary risk; TNBC
|PARP inhibitors (germline)
|-
|''BRCA1, BRCA2''
|1
|Often hereditary risk; TNBC
|Platinum based therapy; PARP inhibitors (germline)
|-
|''CBFB''
|2
|ER-positive, Metastatic BC
|
|-
|''CCND1, CCNE1''*
|2
|HER2-enriched
|CDK4/6 inhibitors
|-
|''CDK4, CDK6''*
|2
|ER-positive, Metastatic BC
|CDK4/6 inhibitors
|-
|''CDH1''
|1
|Lobular histology; Possible hereditary risk
|
|-
|''CDKN2A''
|2
|Metastatic BC
|
|-
|''CHEK2''
|1
|Often hereditary risk
|PARP inhibitors (germline)
|-
|''ERBB2''*
|1
|Rare activating sequence alterations; kinase domain  resistance mutations; HER2-enriched
|HER2-targeted therapy
|-
|''ESR1''
|1
|Metastatic ER-positive
|Hormone therapy resistance
|-
|''FGFR1-4''
|2
|ER-positive
|FGFR inhibitors
|-
|''FOXA1''
|2
|ER-positive, Luminal subtype, lobular histology
|
|-
|''GATA3''
|2
|ER-positive, Luminal subtype
|
|-
|''JAK2''*
|2
|TNBC
|JAK2 inhibitors, immunotherapy
|-
|''MAP2K4''
|2
|Metastatic BC
|
|-
|''MAP3K1''
|2
|ER-positive, Metastatic BC
|
|-
|''MYC''*
|2
|
|
|-
|''NBN''
|1
|Possible hereditary risk
|PARP inhibitors (germline)
|-
|''NF1''
|1
|Possible hereditary risk
|mTOR/PI3K/AKT inhibitors (germline)
|-
|''NTRK1-3''
|1
|
|NTRK inhibitors
|-
|''PALB2''
|1
|Often hereditary risk
|PARP inhibitors (germline)
|-
|''PIK3CA''
|1
|ER-Positive, Luminal subtype
|PI3K inhibitors for selected hotspot mutations; acquired hormone resistance
|-
|''PTEN''
|2
|Loss in lobular BC
Possible hereditary risk
|mTOR/PI3K/AKT inhibitors; radiation contraindicated
|-
|''RB1''
|2
|Metastatic BC
|Acquired hormone resistance
|-
|''STK11''
|1
|Possible hereditary risk
|
|-
|''TBX3''
|2
|Lobular BC
|
|-
|''TOP2A''*
|2
|
|Anthracycline inhibitors
|-
|''TP53''
|1
|TNBC, HER2-enriched, Metastatic BC
Possible hereditary risk
|Radiation contraindicated
|}
<nowiki>*</nowiki> Indicates genes more commonly activated by amplification than by sequence variation
Abbreviations: BC, breast cancer. TNBC, triple negative breast cancer.
'''Cancer Genomics Consortium Levels of Evidence'''
{| class="wikitable"
|'''Tier'''
|'''Data Source(s)'''
|'''Interpretation'''
|-
|1
|FDA approved therapies, professional guidelines, multiple large clinical studies
|Strong evidence supporting clinical utility of variant(s) for diagnosis, selection of therapies, or predicting disease outcome
|-
|2
|One large study or multiple case reports
|Emerging evidence supporting clinical utility of variant(s)
|-
|3
|Case reports or expert opinion
|Unknown clinical significance
|-
|4
|Published evidence indicating lack of pathogenicity of variant(s)
|Benign or likely benign
|}
'''Table 3 - Genes with known hereditary risk associations in breast cancer'''
{| class="wikitable"
|'''Gene'''
|'''Associated Syndrome; Breast Cancer Subtype'''
|-
|''ATM''
|Ataxia telangiectasia syndrome
|-
|''BARD1''
|TNBC
|-
|''BRCA1''
|BRCA-Related Breast/ Ovarian Cancer Syndrome; TNBC
|-
|''BRCA2''
|BRCA-Related Breast/ Ovarian Cancer Syndrome; TNBC
|-
|''CDH1''
|Hereditary Diffuse Gastric Cancer and Lobular Breast Cancer
|-
|''CHEK2''
|Inherited breast cancer
|-
|''NBN''
|Nijmegen Breakage Syndrome
|-
|''NF1''
|Neurofibromatosis type 1
|-
|''PALB2''
|Fanconi anemia
|-
|''PTEN''
|Cowden syndrome
|-
|''RAD51C''
|TNBC
|-
|''RAD51D''
|TNBC
|-
|''STK11''
|Peutz-Jeghers syndrome
|-
|''TP53''
|Li-Fraumeni syndrome
|}
|}
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