|
1
|
Elsheikh S, Green AR, Aleskandarany MA,
Grainge M, Paish CE, Lambros MB, Reis-Filho JS and Ellis IO: CCND1
amplification and cyclin D1 expression in breast cancer and their
relation with proteomic subgroups and patient outcome. Breast
Cancer Res Treat. 109:325–335. 2008. View Article : Google Scholar : PubMed/NCBI
|
|
2
|
Cancer Genome Atlas Network, .
Comprehensive molecular portraits of human breast tumours. Nature.
490:61–70. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
3
|
Fallah Y, Brundage J, Allegakoen P and
Shajahan-Haq AN: MYC-driven pathways in breast cancer subtypes.
Biomolecules. 7:532017. View Article : Google Scholar : PubMed/NCBI
|
|
4
|
Haupt S, Vijayakumaran R, Miranda PJ,
Burgess A, Lim E and Haupt Y: The role of MDM2 and MDM4 in breast
cancer development and prevention. J Mol Cell Biol. 9:53–61. 2017.
View Article : Google Scholar : PubMed/NCBI
|
|
5
|
Perez-Garcia J, Munoz-Couselo E, Soberino
J, Racca F and Cortes J: Targeting FGFR pathway in breast cancer.
Breast. 37:126–133. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
6
|
Wolff AC, Hammond MEH, Allison KH, Harvey
BE, Mangu PB, Bartlett JMS, Bilous M, Ellis IO, Fitzgibbons P,
Hanna W, et al: Human epidermal growth factor receptor 2 testing in
breast cancer: American society of clinical oncology/college of
American pathologists clinical practice guideline focused update. J
Clin Oncol. 36:2105–2122. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
7
|
Braso-Maristany F, Filosto S, Catchpole S,
Marlow R, Quist J, Francesch-Domenech E, Plumb DA, Zakka L,
Gazinska P, Liccardi G, et al: PIM1 kinase regulates cell death,
tumor growth and chemotherapy response in triple-negative breast
cancer. Nat Med. 22:1303–1313. 2016. View
Article : Google Scholar : PubMed/NCBI
|
|
8
|
Musolino A, Campone M, Neven P, Denduluri
N, Barrios CH, Cortes J, Blackwell K, Soliman H, Kahan Z, Bonnefoi
H, et al: Phase II, randomized, placebo-controlled study of
dovitinib in combination with fulvestrant in postmenopausal
patients with HR+, HER2− breast cancer that
had progressed during or after prior endocrine therapy. Breast
Cancer Res. 19:182017. View Article : Google Scholar : PubMed/NCBI
|
|
9
|
Andre F, Bachelot T, Campone M, Dalenc F,
Perez-Garcia JM, Hurvitz SA, Turner N, Rugo H, Smith JW, Deudon S,
et al: Targeting FGFR with dovitinib (TKI258): Preclinical and
clinical data in breast cancer. Clin Cancer Res. 19:3693–3702.
2013. View Article : Google Scholar : PubMed/NCBI
|
|
10
|
de Lint K, Poell JB, Soueidan H,
Jastrzebski K, Vidal Rodriguez J, Lieftink C, Wessels LF and
Beijersbergen RL: Sensitizing triple-negative breast cancer to PI3K
inhibition by cotargeting IGF1R. Mol Cancer Ther. 15:1545–1556.
2016. View Article : Google Scholar : PubMed/NCBI
|
|
11
|
Dembla V, Somaiah N, Barata P, Hess K, Fu
S, Janku F, Karp DD, Naing A, Piha-Paul SA, Subbiah V, et al:
Prevalence of MDM2 amplification and coalterations in 523 advanced
cancer patients in the MD Anderson phase 1 clinic. Oncotarget.
9:33232–33243. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
12
|
Al-Kuraya K, Schraml P, Torhorst J, Tapia
C, Zaharieva B, Novotny H, Spichtin H, Maurer R, Mirlacher M,
Köchli O, et al: Prognostic relevance of gene amplifications and
coamplifications in breast cancer. Cancer Res. 64:8534–8540. 2004.
View Article : Google Scholar : PubMed/NCBI
|
|
13
|
Lundberg A, Lindstrom LS, Li J, Harrell
JC, Darai-Ramqvist E, Sifakis EG, Foukakis T, Perou CM, Czene K,
Bergh J and Tobin NP: The long-term prognostic and predictive
capacity of cyclin D1 gene amplification in 2305 breast tumours.
Breast Cancer Res. 21:342019. View Article : Google Scholar : PubMed/NCBI
|
|
14
|
Elbauomy Elsheikh S, Green AR, Lambros MB,
Turner NC, Grainge MJ, Powe D, Ellis IO and Reis-Filho JS: FGFR1
amplification in breast carcinomas: A chromogenic in situ
hybridisation analysis. Breast Cancer Res. 9:R232007. View Article : Google Scholar : PubMed/NCBI
|
|
15
|
Pereira CBL, Leal MF, Abdelhay ESFW,
Demachki S, Assumpção PP, de Souza MC, Moreira-Nunes CA, Tanaka
AMDS, Smith MC and Burbano RR: MYC amplification as a predictive
factor of complete pathologic response to docetaxel-based
neoadjuvant chemotherapy for breast cancer. Clin Breast Cancer.
17:188–194. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
16
|
Lundgren K, Brown M, Pineda S, Cuzick J,
Salter J, Zabaglo L, Howell A, Dowsett M and Landberg G; TransATAC
investigators, : Effects of cyclin D1 gene amplification and
protein expression on time to recurrence in postmenopausal breast
cancer patients treated with anastrozole or tamoxifen: A TransATAC
study. Breast Cancer Res. 14:R572012. View Article : Google Scholar : PubMed/NCBI
|
|
17
|
Pinkel D and Albertson DG: Array
comparative genomic hybridization and its applications in cancer.
Nat Genet. 37 (Suppl 1):S11–S17. 2005. View
Article : Google Scholar : PubMed/NCBI
|
|
18
|
Carter NP: Methods and strategies for
analyzing copy number variation using DNA microarrays. Nat Genet.
39 (Suppl 7):S16–S21. 2007. View
Article : Google Scholar : PubMed/NCBI
|
|
19
|
Van Loo P, Nordgard SH, Lingjaerde OC,
Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A,
Naume B, et al: Allele-specific copy number analysis of tumors.
Proc Natl Acad Sci USA. 107:16910–16915. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
20
|
Cancer Genome Atlas Research Network, .
Comprehensive genomic characterization defines human glioblastoma
genes and core pathways. Nature. 455:1061–1068. 2008. View Article : Google Scholar : PubMed/NCBI
|
|
21
|
Cancer Genome Atlas Research Network, .
Integrated genomic analyses of ovarian carcinoma. Nature.
474:609–615. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
22
|
Cancer Genome Atlas Network, .
Comprehensive molecular characterization of human colon and rectal
cancer. Nature. 487:330–337. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
23
|
Rajan R, Poniecka A, Smith TL, Yang Y,
Frye D, Pusztai L, Fiterman DJ, Gal-Gombos E, Whitman G, Rouzier R,
et al: Change in tumor cellularity of breast carcinoma after
neoadjuvant chemotherapy as a variable in the pathologic assessment
of response. Cancer. 100:1365–1373. 2004. View Article : Google Scholar : PubMed/NCBI
|
|
24
|
Reisenbichler ES, Dupont W, Plummer WD and
Hameed O: Is tumor cellularity in primary invasive breast carcinoma
of prognostic significance? Virchows Arch. 470:611–617. 2017.
View Article : Google Scholar : PubMed/NCBI
|
|
25
|
Tsuda H; General Rule Committee of the
Japanese Breast Cancer Society, : Histological classification of
breast tumors in the General rules for clinical and pathological
recording of breast cancer (18th edition). Breast Cancer.
27:309–321. 2020. View Article : Google Scholar : PubMed/NCBI
|
|
26
|
Meyerson M, Gabriel S and Getz G: Advances
in understanding cancer genomes through second-generation
sequencing. Nat Rev Genet. 11:685–696. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
27
|
Favero F, Joshi T, Marquard AM, Birkbak
NJ, Krzystanek M, Li Q, Szallasi Z and Eklund AC: Sequenza:
Allele-specific copy number and mutation profiles from tumor
sequencing data. Ann Oncol. 26:64–70. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
28
|
Condorelli R, Mosele F, Verret B, Bachelot
T, Bedard PL, Cortes J, Hyman DM, Juric D, Krop I, Bieche I, et al:
Genomic alterations in breast cancer: Level of evidence for
actionability according to ESMO scale for clinical actionability of
molecular targets (ESCAT). Ann Oncol. 30:365–373. 2019. View Article : Google Scholar : PubMed/NCBI
|
|
29
|
Tsuchida J, Rothman J, McDonald KA,
Nagahashi M, Takabe K and Wakai T: Clinical target sequencing for
precision medicine of breast cancer. Int J Clin Oncol. 24:131–140.
2019. View Article : Google Scholar : PubMed/NCBI
|
|
30
|
Riester M, Singh AP, Brannon AR, Yu K,
Campbell CD, Chiang DY and Morrissey MP: PureCN: Copy number
calling and SNV classification using targeted short read
sequencing. Source Code Biol Med. 11:132016. View Article : Google Scholar : PubMed/NCBI
|
|
31
|
Talevich E, Shain AH, Botton T and Bastian
BC: CNVkit: Genome-wide copy number detection and visualization
from targeted DNA Sequencing. PLoS Comput Biol. 12:e10048732016.
View Article : Google Scholar : PubMed/NCBI
|
|
32
|
Takeda M, Takahama T, Sakai K, Shimizu S,
Watanabe S, Kawakami H, Tanaka K, Sato C, Hayashi H, Nonagase Y, et
al: Clinical application of the foundationOne CDx assay to
therapeutic decision-making for patients with advanced solid
tumors. Oncologist. 26:e588–e596. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
33
|
Segal CV and Dowsett M: Estrogen receptor
mutations in breast cancer-new focus on an old target. Clin Cancer
Res. 20:1724–1726. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
34
|
Jung HS, Lefferts JA and Tsongalis GJ:
Utilization of the oncoscan microarray assay in cancer diagnostics.
Appl Cancer Res. 37:2017. View Article : Google Scholar : PubMed/NCBI
|
|
35
|
von Minckwitz G, Darb-Esfahani S, Loibl S,
Huober J, Tesch H, Solbach C, Holms F, Eidtmann H, Dietrich K, Just
M, et al: Responsiveness of adjacent ductal carcinoma in situ and
changes in HER2 status after neoadjuvant chemotherapy/trastuzumab
treatment in early breast cancer-results from the GeparQuattro
study (GBG 40). Breast Cancer Res Treat. 132:863–870. 2012.
View Article : Google Scholar : PubMed/NCBI
|
|
36
|
Brunelli M, Manfrin E, Martignoni G,
Miller K, Remo A, Reghellin D, Bersani S, Gobbo S, Eccher A,
Chilosi M and Bonetti F: Genotypic intratumoral heterogeneity in
breast carcinoma with HER2/neu amplification: Evaluation according
to ASCO/CAP criteria. Am J Clin Pathol. 131:678–682. 2009.
View Article : Google Scholar : PubMed/NCBI
|
|
37
|
Seol H, Lee HJ, Choi Y, Lee HE, Kim YJ,
Kim JH, Kang E, Kim SW and Park SY: Intratumoral heterogeneity of
HER2 gene amplification in breast cancer: Its clinicopathological
significance. Mod Pathol. 25:938–948. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
38
|
Frampton GM, Fichtenholtz A, Otto GA, Wang
K, Downing SR, He J, Schnall-Levin M, White J, Sanford EM, An P, et
al: Development and validation of a clinical cancer genomic
profiling test based on massively parallel DNA sequencing. Nat
Biotechnol. 31:1023–1031. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
39
|
Sunami K, Ichikawa H, Kubo T, Kato M,
Fujiwara Y, Shimomura A, Koyama T, Kakishima H, Kitami M,
Matsushita H, et al: Feasibility and utility of a panel testing for
114 cancer-associated genes in a clinical setting: A hospital-based
study. Cancer Sci. 110:1480–1490. 2019. View Article : Google Scholar : PubMed/NCBI
|
|
40
|
Singh RR, Mehrotra M, Chen H,
Almohammedsalim AA, Sahin A, Bosamra A, Patel KP, Routbort MJ, Lu
X, Ronald A, et al: Comprehensive screening of gene copy number
aberrations in formalin-fixed, paraffin-embedded solid tumors using
molecular inversion probe-based single-nucleotide polymorphism
array. J Mol Diagn. 18:676–687. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
41
|
Singh RR, Patel KP, Routbort MJ, Aldape K,
Lu X, Manekia J, Abraham R, Reddy NG, Barkoh BA, Veliyathu J, et
al: Clinical massively parallel next-generation sequencing analysis
of 409 cancer-related genes for mutations and copy number
variations in solid tumours. Br J Cancer. 111:2014–2023. 2014.
View Article : Google Scholar : PubMed/NCBI
|
|
42
|
Hamblin A, Wordsworth S, Fermont JM, Page
S, Kaur K, Camps C, Kaisaki P, Gupta A, Talbot D, Middleton M, et
al: Clinical applicability and cost of a 46-gene panel for genomic
analysis of solid tumours: Retrospective validation and prospective
audit in the UK National health service. PLoS Med. 14:e10022302017.
View Article : Google Scholar : PubMed/NCBI
|
