Compendium of Cancer Genome Aberrations

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Breast Cancer Table: Recurrent Genomic Alterations Detected by Chromosomal Microarray (view source)

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'''Table 1 - Clinically significant copy number alterations and regions of loss of heterozygosity in breast cancer.''' Table derived from Geiersbach et al., 2018 [[https://pubmed.ncbi.nlm.nih.gov/32087595/ PMID 32087595]] with permission from Cancer Genetics.<ref>{{Cite journal|last=Geiersbach|first=Katherine B.|last2=Chen|first2=Hui|last3=Emmadi|first3=Rajyasree|last4=Haskell|first4=Gloria T.|last5=Lu|first5=Xinyan|last6=Liu|first6=Yajuan J.|last7=Swisshelm|first7=Karen|date=2020-06|title=Current concepts in breast cancer genomics: An evidence based review by the CGC breast cancer working group|url=https://pubmed.ncbi.nlm.nih.gov/32087595|journal=Cancer Genetics|volume=244|pages=11–20|doi=10.1016/j.cancergen.2020.02.002|issn=2210-7762|pmid=32087595}}</ref>
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{| class="wikitable"
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|'''Alteration'''
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|'''Relevant Gene(s)'''
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|'''CGC Evidence Level'''†
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|'''Subgroup Association(s)'''
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|-
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|1q gain
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|unknown
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|2
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|Most common copy number alteration, often with 16q loss; all subtypes
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|-
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|8p11.2 amplification
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|''[[FGFR1]]'', ''[[ZNF703]]''
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|2
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|METABRIC IntClust6, ER positive
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|-
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|8q24 amplification
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|''[[MYC]]''
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|2
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|METABRIC IntClust9, ER positive
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|-
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|9p24 amplification
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|''[[JAK2]], [[CD274]], [[PDCD1LG2]]''
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|2
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|Enriched in TNBC
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|-
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|10q23.3 loss or LOH
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|''[[PTEN]]''
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|2
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|Enriched in TNBC and in lobular carcinoma
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|-
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|11q13-q14 gain / amplification
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|''[[CCND1]]'', ''[[EMS1]]'', and others
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|2
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|METABRIC IntClust2
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|-
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|16q loss / LOH
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|''[[CDH1]]''
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|2
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|METABRIC IntClust2, ER positive
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|-
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|17p loss / LOH
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|''[[TP53]]''
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|2
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|TNBC, basal-like intrinsic subtype
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|-
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|17q12 amplification
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|''[[ERBB2]]'' (''HER2'')
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|1
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|METABRIC IntClust5, HER2-enriched
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|-
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|17q21 amplification
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|''[[TOP2A]]''
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|2
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|METABRIC IntClust5, HER2-enriched
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|-
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|17q23 amplification (“17q distal amplicon”)
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|''[[RPS6KB]]'', others
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|2
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|METABRIC IntClust1
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|-
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|19q12
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|''[[CCNE1]]''
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|2
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|METABRIC IntClust5; HER2-enriched
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|-
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|20q gain; 20q13 amp
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|''[[AURKA]]'', ''[[GNAS]]'', ''[[ZNF217]]''
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|2
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|METABRIC IntClust1, ER Positive
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|}
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† See table below Table 2 for CGC Evidence levels
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Abbreviations: TNBC, triple negative breast cancer; LOH, loss of heterozygosity.
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 +
 
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'''Table 2 - Major clinically significant genes associated with somatic sequence alterations in breast cancer.''' Table derived from Geiersbach et al., 2018 [[https://pubmed.ncbi.nlm.nih.gov/32087595/ PMID 32087595]] with permission from Cancer Genetics.
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{| class="wikitable"
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|'''Gene(s)'''
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|'''CGC Evidence Level'''†
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|'''Clinical Significance and Subgroup Association(s)'''
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|'''Therapy Implication(s)'''
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|-
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|''[[AKT1]]''
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|2
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|Metastatic BC
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|AKT inhibitors
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|-
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|''[[ATM]]''
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|1
 +
|Possible hereditary risk; TNBC
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|PARP inhibitors (germline)
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|-
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|''[[BRCA1]], [[BRCA2]]''
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|1
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|Often hereditary risk; TNBC
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|Platinum based therapy; PARP inhibitors (germline)
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|-
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|''[[CBFB]]''
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|2
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|ER-positive, Metastatic BC
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|
 +
|-
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|''[[CCND1]], [[CCNE1]]''*
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|2
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|HER2-enriched
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|CDK4/6 inhibitors
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|-
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|''[[CDK4]], [[CDK6]]''*
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|2
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|ER-positive, Metastatic BC
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|CDK4/6 inhibitors
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|-
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|''[[CDH1]]''
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|1
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|Lobular histology; Possible hereditary risk
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|
 +
|-
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|''[[CDKN2A]]''
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|2
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|Metastatic BC
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|
 +
|-
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|''[[CHEK2]]''
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|1
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|Often hereditary risk
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|PARP inhibitors (germline)
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|-
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|''[[ERBB2]]''*
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|1
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|Rare activating sequence alterations; kinase domain  resistance mutations; HER2-enriched
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|HER2-targeted therapy
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|-
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|''[[ESR1]]''
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|1
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|Metastatic ER-positive
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|Hormone therapy resistance
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|-
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|''[[FGFR1]], [[FGFR2]], [[FGFR3]], [[FGFR4]]''
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|2
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|ER-positive
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|FGFR inhibitors
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|-
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|''[[FOXA1]]''
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|2
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|ER-positive, Luminal subtype, lobular histology
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|
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|-
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|''[[GATA3]]''
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|2
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|ER-positive, Luminal subtype
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|
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|-
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|''[[JAK2]]''*
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|2
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|TNBC
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|JAK2 inhibitors, immunotherapy
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|-
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|''[[MAP2K4]]''
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|2
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|Metastatic BC
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|
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|-
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|''[[MAP3K1]]''
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|2
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|ER-positive, Metastatic BC
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|
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|-
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|''[[MYC]]''*
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|2
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|
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|
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|-
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|''[[NBN]]''
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|1
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|Possible hereditary risk
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|PARP inhibitors (germline)
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|-
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|''[[NF1]]''
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|1
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|Possible hereditary risk
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|mTOR/PI3K/AKT inhibitors (germline)
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|-
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|''[[NTRK1]], [[NTRK2]], [[NTRK3]]''
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|1
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|
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|NTRK inhibitors
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|-
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|''[[PALB2]]''
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|1
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|Often hereditary risk
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|PARP inhibitors (germline)
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|-
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|''[[PIK3CA]]''
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|1
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|ER-Positive, Luminal subtype
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|PI3K inhibitors for selected hotspot mutations; acquired hormone resistance
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|-
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|''[[PTEN]]''
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|2
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|Loss in lobular BC
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Possible hereditary risk
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|mTOR/PI3K/AKT inhibitors; radiation contraindicated
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|-
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|''[[RB1]]''
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|2
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|Metastatic BC
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|Acquired hormone resistance
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|-
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|''[[STK11]]''
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|1
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|Possible hereditary risk
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|
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|-
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|''[[TBX3]]''
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|2
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|Lobular BC
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|
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|-
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|''[[TOP2A]]''*
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|2
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|
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|Anthracycline inhibitors
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|-
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|''[[TP53]]''
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|1
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|TNBC, HER2-enriched, Metastatic BC
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Possible hereditary risk
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|Radiation contraindicated
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|}
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<nowiki>*</nowiki> Indicates genes more commonly activated by amplification than by sequence variation
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Abbreviations: BC, breast cancer. TNBC, triple negative breast cancer.
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†'''Cancer Genomics Consortium Levels of Evidence'''
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{| class="wikitable"
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|'''Tier'''
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|'''Data Source(s)'''
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|'''Interpretation'''
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|-
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|1
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|FDA approved therapies, professional guidelines, multiple large clinical studies
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|Strong evidence supporting clinical utility of variant(s) for diagnosis, selection of therapies, or predicting disease outcome
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|-
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|2
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|One large study or multiple case reports
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|Emerging evidence supporting clinical utility of variant(s)
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|-
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|3
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|Case reports or expert opinion
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|Unknown clinical significance
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|-
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|4
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|Published evidence indicating lack of pathogenicity of variant(s)
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|Benign or likely benign
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|}
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'''Table 3 - Genes with known hereditary risk associations in breast cancer.''' Table derived from Geiersbach et al., 2018 [[https://pubmed.ncbi.nlm.nih.gov/32087595/ PMID 32087595]] with permission from Cancer Genetics.
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{| class="wikitable"
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|'''Gene'''
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|'''Associated Syndrome; Breast Cancer Subtype'''
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|-
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|''[[ATM]]''
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|Ataxia telangiectasia syndrome
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|-
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|''[[BARD1]]''
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|TNBC
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|-
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|''[[BRCA1]]''
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|[[BRCA1 syndrome|BRCA-Related Breast/ Ovarian Cancer Syndrome]]; TNBC
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|-
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|''[[BRCA2]]''
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|[[BRCA2 syndrome|BRCA-Related Breast/ Ovarian Cancer Syndrome]]; TNBC
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|-
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|''[[CDH1]]''
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|Hereditary Diffuse Gastric Cancer and Lobular Breast Cancer
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|-
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|''[[CHEK2]]''
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|Inherited breast cancer
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|-
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|''[[NBN]]''
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|Nijmegen Breakage Syndrome
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|-
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|''[[NF1]]''
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|Neurofibromatosis type 1
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|-
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|''[[PALB2]]''
 +
|Fanconi anemia
 +
|-
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|''[[PTEN]]''
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|Cowden syndrome
 +
|-
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|''[[RAD51C]]''
 +
|TNBC
 +
|-
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|''[[RAD51D]]''
 +
|TNBC
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|-
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|''[[STK11]]''
 +
|Peutz-Jeghers syndrome
 +
|-
 +
|''[[TP53]]''
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|Li-Fraumeni syndrome
 +
|}
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Abbreviations: TNBC, triple negative breast cancer.
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==Reference==
 +
<references />
Retrieved from "https://ccga.io/index.php/Special:MobileDiff/10130...10155"