INTEGRATED GENOMIC ANALYSIS OF BREAST CANCERS
Addou-Klouche L1,2, Adélaïde1 J, Cornen S1, Bekhouche I1, Finetti P1, Guille A1,
Sircoulomb F1, Raynaud S1, Bertucci F1,3,4, Birnbaum D1, Chaffanet M1,*
*Corresponding Author: Max Chaffanet, Ph.D., HDR, Department of Molecular Oncology, Institut Paoli
Calmettes, 232 Boulevard Sainte Marguerite, 13009 Marseille, France; Tel.: +33-(0)4-91-22-34-77; Fax: +33-
(0)4-91-22-35-44; E-mail: CHAFFANETM@ipc.unicancer.fr
page: 71
|
|
REFERENCES
1. Solinas-Toldo S, Lampel S, Stilgenbauer S, et al.
Matrix-based comparative genomic hybridization:
biochips to screen for genomic imbalances.Genes
Chromosomes Cancer. 1997; 20(4): 399-407.
2. Pinkel D, Segraves R, Sudar D, et al. High resolution
analysis of DNA copy number variation using
comparative genomic hybridization to microarrays.
Nat Genet. 1998; 20(2): 207-211.
3. van Beers EH, Nederlof PM. Array-CGH and breast
cancer. Breast Cancer Res. 2006; 8(3): 210-219.
4. Curtis C, Lynch AG, Dunning MJ, et al. The pitfalls
of platform comparison: DNA copy number array
technologies assessed. BMC Genomics. 2009; 10:
588-610.
5. Bertucci F, Houlgatte R, Nguyen C, Viens P, Jordan
BR, Birnbaum D. Gene expression profiling of cancer
by use of DNA arrays: how far from the clinic?
Lancet Oncol. 2001; 2(11): 674-682.
6. Perou CM, Sørlie T, Eisen MB, et al. Molecular portraits
of human breast tumours. Nature. 2000; 406
(6797): 747-752. 7. Sørlie T, Perou CM, Tibshirani R, et al. Gene expression
patterns of breast carcinomas distinguish tumor
subclasses with clinical implications. Proc Natl Acad
Sci USA. 2001; 98(19): 10869-10874.
8. Sotiriou C, Pusztai L. Gene-expression signatures in
breast cancer. N Engl J Med. 2009; 360(8): 790-800.
9. Chang JC, Wooten EC, Tsimelzon A, et al. Gene expression
profiling for the prediction of therapeutic
response to docetaxel in patients with breast cancer.
Lancet. 2003; 362(9381):362-369.
10. Ayers M, Symmans WF, Stec J, et al. Gene expression
profiles predict complete pathologic response to
neoadjuvant paclitaxel and fluorouracil, doxorubicin,
and cyclophosphamide chemotherapy in breast cancer.
J Clin Oncol. 2004; 22(12): 2284-2293.
11. Bonnefoi H, Potti A, Delorenzi M, et al. Validation
of gene signatures that predict the response of breast
cancer to neoadjuvant chemotherapy: a substudy of
the EORTC 10994/BIG 00-01 clinical trial. Lancet
Oncol. 2007; 8(12): 1071-1078.
12. Farmer P, Bonnefoi H, Anderle P, et al. A stromarelated
gene signature predicts resistance to neoadjuvant
chemotherapy in breast cancer. Nat Med. 2009;
5(1): 68-74.
13. Dunn L, Demichele A. Genomic predictors of outcome
and treatment response in breast cancer. Diagn
Mol Ther. 2009; 13(2): 73-90.
14. Gelsi-Boyer V, Trouplin V, Adélaïde J, et al. Genome
profiling of chronic myelomonocytic leukemia: frequent
alterations of RAS and RUNX1 genes. BMC
Cancer. 2008; 8: 299-313.
15. Bergamaschi A, Kim YH, Wang P, et al. Distinct
patterns of DNA copy number alteration are associated
with different clinicopathological features and
gene-expression subtypes of breast cancer. Genes
Chromosomes Cancer. 2006; 45(11): 1033-1040.
16. Chin K, de Vries S, Fridlyand J, et al. Genomic and
transcriptional aberrations linked to breast cancer
pathophysiologies. Cancer Cell. 2006; 10(6): 529-
541.
17. Stransky N, Vallot C, Reyal F, et al. Regional copy
number-independent deregulation of transcription in
cancer. Nat Genet. 2006; 38(12): 1386-1396.
18. Neve RM, Chin K, Fridlyand J, et al. A collection of
breast cancer cell lines for the study of functionally
distinct cancer subtypes. Cancer Cell. 2006; 10(6):
515-527.
19. Adélaïde J, Finetti P, Bekhouche I, et al. Integrated
profiling of basal and luminal breast cancers. Cancer
Res. 2007; 67(24): 11565-11575.
20. Chin SF, Teschendorff AE, Marioni JC, et al. Highresolution
aCGH and expression profiling identifies
a novel genomic subtype of ER negative breast cancer.
Genome Biol. 2007; 8(10): R215-R231. 21. Bernard-Pierrot I, Gruel N, Stransky N, et al.
Characterization of the recurrent 8p11-12 amplicon
identifies PPAPDC1B, a phosphatase protein, as a
new therapeutic target in breast cancer. Cancer Res.
2008; 68(17): 7165-7175.
22. Vincent-Salomon A, Lucchesi C, Gruel N, et al.
Integrated genomic and transcriptomic analysis of
ductal carcinoma in situ of the breast. Clin Cancer
Res. 2008; 14(7): 1956-1965.
23. André F, Job B, Dessen P, et al. Molecular characterization
of breast cancer with high-resolution oligonucleotide
comparative genomic hybridization array.
Clin Cancer Res. 2009; 15(2): 441-451.
24. Horlings HM, Lai C, Nuyten DS, et al. Integration of
DNA copy number alterations and prognostic gene
expression signatures in breast cancer patients. Clin
Cancer Res. 2010; 16(2): 651-663.
25. Popovici C, Basset C, Bertucci F, et al. Reciprocal
translocations in breast tumor cell lines: cloning
of a t(3;20) that targets the FHIT gene. Genes
Chromosomes Cancer. 2002; 35(3): 204-218.
26. Adélaïde J, Huang HE, Murati A, et al. A recurrent
chromosome translocation breakpoint in breast and
pancreatic cancer targets the heregulin/NRG1 gene
at 8p12. Genes Chromosomes Cancer. 2003; 37(4):
333-345.
27. Huang HE, Chin S-F, Ginestier C, et al. A recurrent
chromosome breakpoint in breast cancer at the
NRG1/ neuregulin 1/heregulin gene. Cancer Res.
2004; 64(19): 6840-6844.
28. Letessier A, Ginestier C, Charafe-Jauffret E, et al.
ETV6 gene rearrangements in invasive breast carcinoma.
Genes Chromosomes Cancer. 2005; 44(1):
103-108.
29. Letessier A, Garrido-Urbani S, Ginestier C, et al.
Correlated break at PARK2/FRA6E and loss of AF-
6/ Afadin protein expression are associated with poor
outcome in breast cancer. Oncogene. 2007; 26(2):
298-307.
30. Ginestier C, Bardou V-J, Popovici C, et al. Absence
of FHIT protein expression correlates with adverse
evolution in good prognosis localized breast cancer.
Int J Cancer. 2003; 107(5): 854-862.
31. Letessier A, Sircoulomb F, Ginestier C, et al.
Frequency, prognostic impact, and subtype association
of 8p12, 8q24, 11q13, 12p13, 17q12, and 20q13
amplifications in breast cancers. BMC Cancer. 2006;
6(1): 245-257.
32. Bekhouche I, Finetti P, Adélaïde J, et al. Genome
profiling of inflammatory breast cancer. PLoS One.
2011; 6(2): e16950-16962.
33. Sircoulomb F, Bekhouche I, Finetti P, et al. Genome
profiling of ERBB2-amplified breast cancers. BMC
Cancer. 2010; 10: 539-556. 34. Addou-Klouche L, Adélaïde J, Finetti P, et al. Loss,
mutation and deregulation of L3MBTL4 in breast
cancers. Mol Cancer. 2010; 9(1): 213-225.
35. Sircoulomb F, Nicolas N, Ferrari A, et al. ZNF703
gene amplification at 8p12 specifies luminal B breast
cancer. EMBO Mol Med. 2011; 3(3): 153-166.
36. Jones PA, Baylin SB. The fundamental role of epigenetic
events in cancer. Nat Rev Genet. 2002; 3(6):
415-428.
37. Lund AH, van Lohuizen M. Epigenetics and cancer.
Genes Dev. 2004; 18(19): 2315-2335.
38. Rice KL, Hormaeche I, Licht JD. Epigenetic regulation
of normal and malignant hematopoiesis.
Oncogene. 2007; 26(47): 6697-6714.
39. Goll MG, Bestor TH. Histone modification and replacement
in chromatin activation. Genes Dev. 2002;
16(14): 1739-1742.
40. Klose RJ, Bird AP. Genomic DNA methylation: the
mark and its mediators. Trends Biochem Sci. 2006;
31(2): 89-97.
41. Esteller M. Epigenetic gene silencing in cancer:
the DNA hypermethylome. Hum Mol Genet. 2007;
16(Spec 1): R50-R59.
42. Wildschwendter M, Jones PA. DNA methylation
and breast carcinogenesis. Oncogene. 2002; 21(35):
5462-5482.
43. Mulero-Navarro S, Esteller M. Epigenetic biomarkers
for human cancer: The time is now. Crit Rev
Oncol Hematol. 2008; 68(1): 1-11.
44. Ordway JM, Budiman MA, Korshunova Y, et al.
Identification of novel high-frequency DNA methylation
changes in breast cancer. PLoS One. 2007;
2(12): e1314-1325.
45. Bediaga NG, Acha-Sagredo A, Guerra I, et al. DNA
methylation epigenotypes in breast cancer molecular
subtypes. Breast Cancer Res. 2010; 12(5): R77-R78.
46. Holm K, Hegardt C, Staaf J, et al. Molecular subtypes
of breast cancer are associated with characteristic
DNA methylation patterns. Breast Cancer Res.
2010; 12 (3): R36-R51.
47. van der Auwera I, Yu W, Suo L, et al. Array-based
DNA methylation profiling for breast cancer subtype
discrimination. PLoS One. 2010; 5(9): e12616-
12625.
48. Fackler MJ, Umbricht CB, Williams D, et al.
Genome-wide methylation analysis identifies genes
specific to breast cancer hormone receptor status and
risk of recurrence. Cancer Res. 2011; 71(19): 6195-
6207.
49. Hill VK, Ricketts C, Bieche I, et al. Genome-wide DNA
methylation profiling of CpG islands in breast cancer
identifies novel genes associated with tumorigenicity.
Cancer Res. 2011; 71(8): 2988-2999.
|
|
|
|
 |
Number 27
VOL. 27 (2), 2024 |
Number 27
VOL. 27 (1), 2024 |
Number 26
Number 26 VOL. 26(2), 2023 All in one |
Number 26
VOL. 26(2), 2023 |
Number 26
VOL. 26, 2023 Supplement |
Number 26
VOL. 26(1), 2023 |
Number 25
VOL. 25(2), 2022 |
Number 25
VOL. 25 (1), 2022 |
Number 24
VOL. 24(2), 2021 |
Number 24
VOL. 24(1), 2021 |
Number 23
VOL. 23(2), 2020 |
Number 22
VOL. 22(2), 2019 |
Number 22
VOL. 22(1), 2019 |
Number 22
VOL. 22, 2019 Supplement |
Number 21
VOL. 21(2), 2018 |
Number 21
VOL. 21 (1), 2018 |
Number 21
VOL. 21, 2018 Supplement |
Number 20
VOL. 20 (2), 2017 |
Number 20
VOL. 20 (1), 2017 |
Number 19
VOL. 19 (2), 2016 |
Number 19
VOL. 19 (1), 2016 |
Number 18
VOL. 18 (2), 2015 |
Number 18
VOL. 18 (1), 2015 |
Number 17
VOL. 17 (2), 2014 |
Number 17
VOL. 17 (1), 2014 |
Number 16
VOL. 16 (2), 2013 |
Number 16
VOL. 16 (1), 2013 |
Number 15
VOL. 15 (2), 2012 |
Number 15
VOL. 15, 2012 Supplement |
Number 15
Vol. 15 (1), 2012 |
Number 14
14 - Vol. 14 (2), 2011 |
Number 14
The 9th Balkan Congress of Medical Genetics |
Number 14
14 - Vol. 14 (1), 2011 |
Number 13
Vol. 13 (2), 2010 |
Number 13
Vol.13 (1), 2010 |
Number 12
Vol.12 (2), 2009 |
Number 12
Vol.12 (1), 2009 |
Number 11
Vol.11 (2),2008 |
Number 11
Vol.11 (1),2008 |
Number 10
Vol.10 (2), 2007 |
Number 10
10 (1),2007 |
Number 9
1&2, 2006 |
Number 9
3&4, 2006 |
Number 8
1&2, 2005 |
Number 8
3&4, 2004 |
Number 7
1&2, 2004 |
Number 6
3&4, 2003 |
Number 6
1&2, 2003 |
Number 5
3&4, 2002 |
Number 5
1&2, 2002 |
Number 4
Vol.3 (4), 2000 |
Number 4
Vol.2 (4), 1999 |
Number 4
Vol.1 (4), 1998 |
Number 4
3&4, 2001 |
Number 4
1&2, 2001 |
Number 3
Vol.3 (3), 2000 |
Number 3
Vol.2 (3), 1999 |
Number 3
Vol.1 (3), 1998 |
Number 2
Vol.3(2), 2000 |
Number 2
Vol.1 (2), 1998 |
Number 2
Vol.2 (2), 1999 |
Number 1
Vol.3 (1), 2000 |
Number 1
Vol.2 (1), 1999 |
Number 1
Vol.1 (1), 1998 |
|
|
