Genomic Architecture Characterizes Tumor Progression Paths and Fate in Breast Cancer Patients

Overview

Journal Sci Transl Med

Specialties General Medicine
Science

Date 2010 Jul 2

PMID 20592421

Citations 84

Authors

Hege G Russnes

Hans Kristian Moen Vollan

Ole Christian Lingjaerde

Alexander Krasnitz

Par Lundin

Bjorn Naume

Therese Sorlie

Elin Borgen

Inga H Rye

Anita Langerod

Suet-Feung Chin

Andrew E Teschendorff

Philip J Stephens

Susanne Maner

Ellen Schlichting

Lars O Baumbusch

Rolf Karesen

Michael P Stratton

Michael Wigler

Carlos Caldas

Anders Zetterberg

James Hicks

Anne-Lise Borresen-Dale

Affiliations

Soon will be listed here.

Abstract

Distinct molecular subtypes of breast carcinomas have been identified, but translation into clinical use has been limited. We have developed two platform-independent algorithms to explore genomic architectural distortion using array comparative genomic hybridization data to measure (i) whole-arm gains and losses [whole-arm aberration index (WAAI)] and (ii) complex rearrangements [complex arm aberration index (CAAI)]. By applying CAAI and WAAI to data from 595 breast cancer patients, we were able to separate the cases into eight subgroups with different distributions of genomic distortion. Within each subgroup data from expression analyses, sequencing and ploidy indicated that progression occurs along separate paths into more complex genotypes. Histological grade had prognostic impact only in the luminal-related groups, whereas the complexity identified by CAAI had an overall independent prognostic power. This study emphasizes the relation among structural genomic alterations, molecular subtype, and clinical behavior and shows that objective score of genomic complexity (CAAI) is an independent prognostic marker in breast cancer.

Citing Articles

Luminal breast epithelial cells of BRCA1 or BRCA2 mutation carriers and noncarriers harbor common breast cancer copy number alterations.

Williams M, Oliphant M, Au V, Liu C, Baril C, OFlanagan C Nat Genet. 2024; 56(12):2753-2762.

PMID: 39567747 PMC: 11631757. DOI: 10.1038/s41588-024-01988-0.

Pan-cancer mutational signature surveys correlated mutational signature with geospatial environmental exposures and viral infections.

Bai J, Ma K, Xia S, Geng R, Shen C, Jiang L Comput Struct Biotechnol J. 2023; 21:5413-5422.

PMID: 38022689 PMC: 10652135. DOI: 10.1016/j.csbj.2023.10.041.

A semiparametric Bayesian model for comparing DNA copy numbers.

Nieto-Barajas L, Ji Y, Baladandayuthapani V Braz J Probab Stat. 2023; 30(3):345-365.

PMID: 37799327 PMC: 10552905. DOI: 10.1214/15-bjps283.

Molecular classification and biomarkers of clinical outcome in breast ductal carcinoma in situ: Analysis of TBCRC 038 and RAHBT cohorts.

Strand S, Rivero-Gutierrez B, Houlahan K, Seoane J, King L, Risom T Cancer Cell. 2022; 40(12):1521-1536.e7.

PMID: 36400020 PMC: 9772081. DOI: 10.1016/j.ccell.2022.10.021.

Genetic alterations associated with multiple primary malignancies.

Nyqvist J, Kovacs A, Einbeigi Z, Karlsson P, Forssell-Aronsson E, Helou K Cancer Med. 2021; 10(13):4465-4477.

PMID: 34057285 PMC: 8267160. DOI: 10.1002/cam4.3975.

References

Barrett M, Scheffer A, Ben-Dor A, Sampas N, Lipson D, Kincaid R . Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci U S A. 2004; 101(51):17765-70. PMC: 535426. DOI: 10.1073/pnas.0407979101. View

Teixeira M, Pandis N, Heim S . Cytogenetic clues to breast carcinogenesis. Genes Chromosomes Cancer. 2001; 33(1):1-16. DOI: 10.1002/gcc.1206. View

Courjal F, Cuny M, Simony-Lafontaine J, Louason G, SPEISER P, Zeillinger R . Mapping of DNA amplifications at 15 chromosomal localizations in 1875 breast tumors: definition of phenotypic groups. Cancer Res. 1997; 57(19):4360-7. View

Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, Dudoit S . Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5(10):R80. PMC: 545600. DOI: 10.1186/gb-2004-5-10-r80. View

Sieuwerts A, Kraan J, Bolt J, van der Spoel P, Elstrodt F, Schutte M . Anti-epithelial cell adhesion molecule antibodies and the detection of circulating normal-like breast tumor cells. J Natl Cancer Inst. 2009; 101(1):61-6. PMC: 2639293. DOI: 10.1093/jnci/djn419. View

Curtis C, Lynch A, Dunning M, Spiteri I, Marioni J, Hadfield J . The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics. 2009; 10:588. PMC: 2797821. DOI: 10.1186/1471-2164-10-588. View

Tsarouha H, Pandis N, Bardi G, Teixeira M, Andersen J, Heim S . Karyotypic evolution in breast carcinomas with i(1)(q10) and der(1;16)(q10;p10) as the primary chromosome abnormality. Cancer Genet Cytogenet. 1999; 113(2):156-61. DOI: 10.1016/s0165-4608(99)00016-3. View

Buerger H, Mommers E, Littmann R, Simon R, Diallo R, Poremba C . Ductal invasive G2 and G3 carcinomas of the breast are the end stages of at least two different lines of genetic evolution. J Pathol. 2001; 194(2):165-70. DOI: 10.1002/path.875. View

McCLINTOCK B . The Stability of Broken Ends of Chromosomes in Zea Mays. Genetics. 1941; 26(2):234-82. PMC: 1209127. DOI: 10.1093/genetics/26.2.234. View

10.

Peppercorn J, Perou C, Carey L . Molecular subtypes in breast cancer evaluation and management: divide and conquer. Cancer Invest. 2008; 26(1):1-10. DOI: 10.1080/07357900701784238. View

11.

Baudis M . Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data. BMC Cancer. 2007; 7:226. PMC: 2225423. DOI: 10.1186/1471-2407-7-226. View

12.

Paterson A, Pole J, Blood K, Garcia M, Cooke S, Teschendorff A . Co-amplification of 8p12 and 11q13 in breast cancers is not the result of a single genomic event. Genes Chromosomes Cancer. 2007; 46(5):427-39. DOI: 10.1002/gcc.20424. View

13.

van den Ijssel P, Tijssen M, Chin S, Eijk P, Carvalho B, Hopmans E . Human and mouse oligonucleotide-based array CGH. Nucleic Acids Res. 2005; 33(22):e192. PMC: 1316119. DOI: 10.1093/nar/gni191. View

14.

Lusa L, McShane L, Reid J, De Cecco L, Ambrogi F, Biganzoli E . Challenges in projecting clustering results across gene expression-profiling datasets. J Natl Cancer Inst. 2007; 99(22):1715-23. DOI: 10.1093/jnci/djm216. View

15.

Sims A, Howell A, Howell S, Clarke R . Origins of breast cancer subtypes and therapeutic implications. Nat Clin Pract Oncol. 2007; 4(9):516-25. DOI: 10.1038/ncponc0908. View

16.

Stefansson O, Jonasson J, Johannsson O, Olafsdottir K, Steinarsdottir M, Valgeirsdottir S . Genomic profiling of breast tumours in relation to BRCA abnormalities and phenotypes. Breast Cancer Res. 2009; 11(4):R47. PMC: 2750106. DOI: 10.1186/bcr2334. View

17.

FORSSLUND G, Nilsson B, Zetterberg A . Near tetraploid prostate carcinoma. Methodologic and prognostic aspects. Cancer. 1996; 78(8):1748-55. View

18.

Campbell P, Stephens P, Pleasance E, OMeara S, Li H, Santarius T . Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet. 2008; 40(6):722-9. PMC: 2705838. DOI: 10.1038/ng.128. View

19.

Coe B, Ylstra B, Carvalho B, Meijer G, MacAulay C, Lam W . Resolving the resolution of array CGH. Genomics. 2007; 89(5):647-53. DOI: 10.1016/j.ygeno.2006.12.012. View

20.

Wiedswang G, Borgen E, Karesen R, Kvalheim G, Nesland J, Qvist H . Detection of isolated tumor cells in bone marrow is an independent prognostic factor in breast cancer. J Clin Oncol. 2003; 21(18):3469-78. DOI: 10.1200/JCO.2003.02.009. View