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Breast Cancer Table: Recurrent Genomic Alterations Detected by Chromosomal Microarray (view source)
Revision as of 17:42, 22 April 2021
, 17:42, 22 April 2021no edit summary
'''Table 1 - Clinically significant copy number alterations in breast cancer'''
'''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"
{| class="wikitable"
|'''Alteration'''
|'''Alteration'''
|'''Relevant Gene(s)'''
|'''Relevant Gene(s)'''
|'''CGC Evidence Level'''
|'''CGC Evidence Level'''†
|'''Subgroup Association(s)'''
|'''Subgroup Association(s)'''
|-
|-
|-
|-
|8p11.2 amplification
|8p11.2 amplification
|''FGFR1'', ''ZNF703''
|''[[FGFR1]]'', ''[[ZNF703]]''
|2
|2
|METABRIC IntClust6, ER positive
|METABRIC IntClust6, ER positive
|-
|-
|8q24 amplification
|8q24 amplification
|''MYC''
|''[[MYC]]''
|2
|2
|METABRIC IntClust9, ER positive
|METABRIC IntClust9, ER positive
|-
|-
|9p24 amplification
|9p24 amplification
|''JAK2, CD274, PDCD1LG2''
|''[[JAK2]], [[CD274]], [[PDCD1LG2]]''
|2
|2
|Enriched in TNBC
|Enriched in TNBC
|-
|-
|10q23.3 loss or LOH
|10q23.3 loss or LOH
|''PTEN''
|''[[PTEN]]''
|2
|2
|Enriched in TNBC and in lobular carcinoma
|Enriched in TNBC and in lobular carcinoma
|-
|-
|11q13-q14 gain / amplification
|11q13-q14 gain / amplification
|''CCND1'', ''EMS1'', and others
|''[[CCND1]]'', ''[[EMS1]]'', and others
|2
|2
|METABRIC IntClust2
|METABRIC IntClust2
|-
|-
|16q loss / LOH
|16q loss / LOH
|''CDH1''
|''[[CDH1]]''
|2
|2
|METABRIC IntClust2, ER positive
|METABRIC IntClust2, ER positive
|-
|-
|17p loss / LOH
|17p loss / LOH
|''TP53''
|''[[TP53]]''
|2
|2
|TNBC, basal-like intrinsic subtype
|TNBC, basal-like intrinsic subtype
|-
|-
|17q12 amplification
|17q12 amplification
|''ERBB2'' (''HER2'')
|''[[ERBB2]]'' (''HER2'')
|1
|1
|METABRIC IntClust5, HER2-enriched
|METABRIC IntClust5, HER2-enriched
|-
|-
|17q21 amplification
|17q21 amplification
|''TOP2A''
|''[[TOP2A]]''
|2
|2
|METABRIC IntClust5, HER2-enriched
|METABRIC IntClust5, HER2-enriched
|-
|-
|17q23 amplification (“17q distal amplicon”)
|17q23 amplification (“17q distal amplicon”)
|''RPS6KB'', others
|''[[RPS6KB]]'', others
|2
|2
|METABRIC IntClust1
|METABRIC IntClust1
|-
|-
|19q12
|19q12
|''CCNE1''
|''[[CCNE1]]''
|2
|2
|METABRIC IntClust5; HER2-enriched
|METABRIC IntClust5; HER2-enriched
|-
|-
|20q gain; 20q13 amp
|20q gain; 20q13 amp
|''AURKA'', ''GNAS'', ''ZNF217''
|''[[AURKA]]'', ''[[GNAS]]'', ''[[ZNF217]]''
|2
|2
|METABRIC IntClust1, ER Positive
|METABRIC IntClust1, ER Positive
|}
|}
'''Table 2 - Major clinically significant genes associated with somatic sequence alterations in breast cancer'''
† 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"
{| class="wikitable"
|'''Gene(s)'''
|'''Gene(s)'''
|'''CGC Evidence Level'''
|'''CGC Evidence Level'''†
|'''Clinical Significance and Subgroup Association(s)'''
|'''Clinical Significance and Subgroup Association(s)'''
|'''Therapy Implication(s)'''
|'''Therapy Implication(s)'''
|-
|-
|''AKT1''
|''[[AKT1]]''
|2
|2
|Metastatic BC
|Metastatic BC
|AKT inhibitors
|AKT inhibitors
|-
|-
|''ATM''
|''[[ATM]]''
|1
|1
|Possible hereditary risk; TNBC
|Possible hereditary risk; TNBC
|PARP inhibitors (germline)
|PARP inhibitors (germline)
|-
|-
|''BRCA1, BRCA2''
|''[[BRCA1]], [[BRCA2]]''
|1
|1
|Often hereditary risk; TNBC
|Often hereditary risk; TNBC
|Platinum based therapy; PARP inhibitors (germline)
|Platinum based therapy; PARP inhibitors (germline)
|-
|-
|''CBFB''
|''[[CBFB]]''
|2
|2
|ER-positive, Metastatic BC
|ER-positive, Metastatic BC
|
|
|-
|-
|''CCND1, CCNE1''*
|''[[CCND1]], [[CCNE1]]''*
|2
|2
|HER2-enriched
|HER2-enriched
|CDK4/6 inhibitors
|CDK4/6 inhibitors
|-
|-
|''CDK4, CDK6''*
|''[[CDK4]], [[CDK6]]''*
|2
|2
|ER-positive, Metastatic BC
|ER-positive, Metastatic BC
|CDK4/6 inhibitors
|CDK4/6 inhibitors
|-
|-
|''CDH1''
|''[[CDH1]]''
|1
|1
|Lobular histology; Possible hereditary risk
|Lobular histology; Possible hereditary risk
|
|
|-
|-
|''CDKN2A''
|''[[CDKN2A]]''
|2
|2
|Metastatic BC
|Metastatic BC
|
|
|-
|-
|''CHEK2''
|''[[CHEK2]]''
|1
|1
|Often hereditary risk
|Often hereditary risk
|PARP inhibitors (germline)
|PARP inhibitors (germline)
|-
|-
|''ERBB2''*
|''[[ERBB2]]''*
|1
|1
|Rare activating sequence alterations; kinase domain resistance mutations; HER2-enriched
|Rare activating sequence alterations; kinase domain resistance mutations; HER2-enriched
|HER2-targeted therapy
|HER2-targeted therapy
|-
|-
|''ESR1''
|''[[ESR1]]''
|1
|1
|Metastatic ER-positive
|Metastatic ER-positive
|Hormone therapy resistance
|Hormone therapy resistance
|-
|-
|''FGFR1-4''
|''[[FGFR1]], [[FGFR2]], [[FGFR3]], [[FGFR4]]''
|2
|2
|ER-positive
|ER-positive
|FGFR inhibitors
|FGFR inhibitors
|-
|-
|''FOXA1''
|''[[FOXA1]]''
|2
|2
|ER-positive, Luminal subtype, lobular histology
|ER-positive, Luminal subtype, lobular histology
|
|
|-
|-
|''GATA3''
|''[[GATA3]]''
|2
|2
|ER-positive, Luminal subtype
|ER-positive, Luminal subtype
|
|
|-
|-
|''JAK2''*
|''[[JAK2]]''*
|2
|2
|TNBC
|TNBC
|JAK2 inhibitors, immunotherapy
|JAK2 inhibitors, immunotherapy
|-
|-
|''MAP2K4''
|''[[MAP2K4]]''
|2
|2
|Metastatic BC
|Metastatic BC
|
|
|-
|-
|''MAP3K1''
|''[[MAP3K1]]''
|2
|2
|ER-positive, Metastatic BC
|ER-positive, Metastatic BC
|
|
|-
|-
|''MYC''*
|''[[MYC]]''*
|2
|2
|
|
|
|
|-
|-
|''NBN''
|''[[NBN]]''
|1
|1
|Possible hereditary risk
|Possible hereditary risk
|PARP inhibitors (germline)
|PARP inhibitors (germline)
|-
|-
|''NF1''
|''[[NF1]]''
|1
|1
|Possible hereditary risk
|Possible hereditary risk
|mTOR/PI3K/AKT inhibitors (germline)
|mTOR/PI3K/AKT inhibitors (germline)
|-
|-
|''NTRK1-3''
|''[[NTRK1]], [[NTRK2]], [[NTRK3]]''
|1
|1
|
|
|NTRK inhibitors
|NTRK inhibitors
|-
|-
|''PALB2''
|''[[PALB2]]''
|1
|1
|Often hereditary risk
|Often hereditary risk
|PARP inhibitors (germline)
|PARP inhibitors (germline)
|-
|-
|''PIK3CA''
|''[[PIK3CA]]''
|1
|1
|ER-Positive, Luminal subtype
|ER-Positive, Luminal subtype
|PI3K inhibitors for selected hotspot mutations; acquired hormone resistance
|PI3K inhibitors for selected hotspot mutations; acquired hormone resistance
|-
|-
|''PTEN''
|''[[PTEN]]''
|2
|2
|Loss in lobular BC
|Loss in lobular BC
|mTOR/PI3K/AKT inhibitors; radiation contraindicated
|mTOR/PI3K/AKT inhibitors; radiation contraindicated
|-
|-
|''RB1''
|''[[RB1]]''
|2
|2
|Metastatic BC
|Metastatic BC
|Acquired hormone resistance
|Acquired hormone resistance
|-
|-
|''STK11''
|''[[STK11]]''
|1
|1
|Possible hereditary risk
|Possible hereditary risk
|
|
|-
|-
|''TBX3''
|''[[TBX3]]''
|2
|2
|Lobular BC
|Lobular BC
|
|
|-
|-
|''TOP2A''*
|''[[TOP2A]]''*
|2
|2
|
|
|Anthracycline inhibitors
|Anthracycline inhibitors
|-
|-
|''TP53''
|''[[TP53]]''
|1
|1
|TNBC, HER2-enriched, Metastatic BC
|TNBC, HER2-enriched, Metastatic BC
Abbreviations: BC, breast cancer. TNBC, triple negative breast cancer.
Abbreviations: BC, breast cancer. TNBC, triple negative breast cancer.
'''Cancer Genomics Consortium Levels of Evidence'''
†'''Cancer Genomics Consortium Levels of Evidence'''
{| class="wikitable"
{| class="wikitable"
|'''Tier'''
|'''Tier'''
|Benign or likely benign
|Benign or likely benign
|}
|}
'''Table 3 - Genes with known hereditary risk associations in breast cancer'''
'''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"
{| class="wikitable"
|'''Gene'''
|'''Gene'''
|'''Associated Syndrome; Breast Cancer Subtype'''
|'''Associated Syndrome; Breast Cancer Subtype'''
|-
|-
|''ATM''
|''[[ATM]]''
|Ataxia telangiectasia syndrome
|Ataxia telangiectasia syndrome
|-
|-
|''BARD1''
|''[[BARD1]]''
|TNBC
|TNBC
|-
|-
|''BRCA1''
|''[[BRCA1]]''
|BRCA-Related Breast/ Ovarian Cancer Syndrome; TNBC
|[[BRCA1 syndrome|BRCA-Related Breast/ Ovarian Cancer Syndrome]]; TNBC
|-
|-
|''BRCA2''
|''[[BRCA2]]''
|BRCA-Related Breast/ Ovarian Cancer Syndrome; TNBC
|[[BRCA2 syndrome|BRCA-Related Breast/ Ovarian Cancer Syndrome]]; TNBC
|-
|-
|''CDH1''
|''[[CDH1]]''
|Hereditary Diffuse Gastric Cancer and Lobular Breast Cancer
|Hereditary Diffuse Gastric Cancer and Lobular Breast Cancer
|-
|-
|''CHEK2''
|''[[CHEK2]]''
|Inherited breast cancer
|Inherited breast cancer
|-
|-
|''NBN''
|''[[NBN]]''
|Nijmegen Breakage Syndrome
|Nijmegen Breakage Syndrome
|-
|-
|''NF1''
|''[[NF1]]''
|Neurofibromatosis type 1
|Neurofibromatosis type 1
|-
|-
|''PALB2''
|''[[PALB2]]''
|Fanconi anemia
|Fanconi anemia
|-
|-
|''PTEN''
|''[[PTEN]]''
|Cowden syndrome
|Cowden syndrome
|-
|-
|''RAD51C''
|''[[RAD51C]]''
|TNBC
|TNBC
|-
|-
|''RAD51D''
|''[[RAD51D]]''
|TNBC
|TNBC
|-
|-
|''STK11''
|''[[STK11]]''
|Peutz-Jeghers syndrome
|Peutz-Jeghers syndrome
|-
|-
|''TP53''
|''[[TP53]]''
|Li-Fraumeni syndrome
|Li-Fraumeni syndrome
|}
|}
Abbreviations: TNBC, triple negative breast cancer.
==Reference==
<references />