View source for Breast Cancer Table: Recurrent Genomic Alterations Detected by Chromosomal Microarray

'''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>
{| class="wikitable"
|'''Alteration'''
|'''Relevant Gene(s)'''
|'''CGC Evidence Level'''†
|'''Subgroup Association(s)'''
|-
|1q gain
|unknown
|2
|Most common copy number alteration, often with 16q loss; all subtypes
|-
|8p11.2 amplification
|''[[FGFR1]]'', ''[[ZNF703]]''
|2
|METABRIC IntClust6, ER positive
|-
|8q24 amplification
|''[[MYC]]''
|2
|METABRIC IntClust9, ER positive
|-
|9p24 amplification
|''[[JAK2]], [[CD274]], [[PDCD1LG2]]''
|2
|Enriched in TNBC
|-
|10q23.3 loss or LOH
|''[[PTEN]]''
|2
|Enriched in TNBC and in lobular carcinoma
|-
|11q13-q14 gain / amplification
|''[[CCND1]]'', ''[[EMS1]]'', and others
|2
|METABRIC IntClust2
|-
|16q loss / LOH
|''[[CDH1]]''
|2
|METABRIC IntClust2, ER positive
|-
|17p loss / LOH
|''[[TP53]]''
|2
|TNBC, basal-like intrinsic subtype
|-
|17q12 amplification
|''[[ERBB2]]'' (''HER2'')
|1
|METABRIC IntClust5, HER2-enriched
|-
|17q21 amplification
|''[[TOP2A]]''
|2
|METABRIC IntClust5, HER2-enriched
|-
|17q23 amplification (“17q distal amplicon”)
|''[[RPS6KB]]'', others
|2
|METABRIC IntClust1
|-
|19q12
|''[[CCNE1]]''
|2
|METABRIC IntClust5; HER2-enriched
|-
|20q gain; 20q13 amp
|''[[AURKA]]'', ''[[GNAS]]'', ''[[ZNF217]]''
|2
|METABRIC IntClust1, ER Positive
|}
† See table below Table 2 for CGC Evidence levels

Abbreviations: TNBC, triple negative breast cancer; LOH, loss of heterozygosity.


'''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.
{| 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]], [[FGFR2]], [[FGFR3]], [[FGFR4]]''
|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]], [[NTRK2]], [[NTRK3]]''
|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.''' Table derived from Geiersbach et al., 2018 [[https://pubmed.ncbi.nlm.nih.gov/32087595/ PMID 32087595]] with permission from Cancer Genetics.
{| class="wikitable"
|'''Gene'''
|'''Associated Syndrome; Breast Cancer Subtype'''
|-
|''[[ATM]]''
|Ataxia telangiectasia syndrome
|-
|''[[BARD1]]''
|TNBC
|-
|''[[BRCA1]]''
|[[BRCA1 syndrome|BRCA-Related Breast/ Ovarian Cancer Syndrome]]; TNBC
|-
|''[[BRCA2]]''
|[[BRCA2 syndrome|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
|}
Abbreviations: TNBC, triple negative breast cancer.