Skip to main content
Article thumbnail
Location of Repository

Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer

By Johan Staaf, Göran Jönsson, Markus Ringnér, Bo Baldetorp and Åke Borg
Topics: Research Article
Publisher: BioMed Central
OAI identifier:
Provided by: PubMed Central
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://www.pubmedcentral.nih.g... (external link)
  • Suggested articles


    1. (2010). A: ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays. Bioinformatics
    2. (2010). A: Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics. Breast Cancer Res
    3. (2007). A: Highresolution genomic profiles of breast cancer cell lines assessed by tiling BAC array comparative genomic hybridization. Genes Chromosomes Cancer
    4. (2010). A: Identification of subtypes in human epidermal growth factor receptor 2–positive breast cancer reveals a gene signature prognostic of outcome.
    5. (2010). al: Diverse somatic mutation patterns and pathway alterations in human cancers. Nature
    6. (2010). al: The landscape of somatic copy-number alteration across human cancers. Nature
    7. (2005). Allele-specific amplification in cancer revealed by SNP array analysis. PLoS Comput Biol
    8. (2011). AR: Tumor-infiltrating CD8+ lymphocytes predict clinical outcome in breast cancer.
    9. (2007). Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci USA
    10. (2001). Baldetorp B: Optimizing flow cytometric DNA ploidy and S-phase fraction as independent prognostic markers for node-negative breast cancer specimens. Cytometry
    11. (2004). Barillot E: Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics
    12. (2007). Bhanot G: High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates. Cancer Res
    13. (2010). Borresen-Dale AL: Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Sci Transl Med
    14. (2007). Breast tumor heterogeneity: cancer stem cells or clonal evolution? Cell Cycle
    15. (2009). Cavet G: Genetic alterations and oncogenic pathways associated with breast cancer subtypes. Mol Cancer Res
    16. Cell Line Genomic Profiling Data.
    17. (2004). Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics
    18. (1990). CJ: Nonrandom duplication of the chromosome bearing a mutated Ha-ras-1 allele in mouse skin tumors.
    19. (2007). DF: American Society of Clinical Oncology/College of American Pathologists guideline recommendations for human epidermal growth factor receptor 2 testing in breast cancer.
    20. Expression Omnibus.
    21. (2009). Foekens JA: Copy number alterations that predict metastatic capability of human breast cancer. Cancer Res
    22. (2011). Fu L: CD8(+) cytotoxic T cell and FOXP3(+) regulatory T cell infiltration in relation to breast cancer survival and molecular subtypes. Breast Cancer Res Treat
    23. (2010). Genome profiling of ERBB2-amplified breast cancers.
    24. (2008). Genome-wide functional synergy between amplified and mutated genes in human breast cancer. Cancer Res
    25. (2006). Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell
    26. (2011). GOBO: Gene Expression-Based Outcome for Breast Cancer Online. PLoS ONE
    27. (2008). High-resolution genomic and expression analyses of copy number alterations in breast tumors. Genes Chromosomes Cancer
    28. (2010). High-resolution genomic and expression analyses of copy number alterations in HER2-amplified breast cancer. Breast Cancer Res
    29. (1990). King CR: Pathologic findings from the National Surgical Adjuvant Breast and Bowel Project: prognostic significance of erbB-2 protein overexpression in primary breast cancer.
    30. (2004). Lengauer C: Aneuploidy and cancer. Nature
    31. (1987). McGuire WL: Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science
    32. (2009). MH: Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Genome Biol
    33. (2005). Pahlman S: Hypoxiainduced dedifferentiation of tumor cells–a mechanism behind heterogeneity and aggressiveness of solid tumors. Semin Cell Dev Biol
    34. (2009). Perou CM: Integrated study of copy number states and genotype calls using high-density SNP arrays. Nucleic Acids Res
    35. (2009). PS: Supervised risk predictor of breast cancer based on intrinsic subtypes.
    36. (2010). Reis-Filho JS: Breast cancer molecular profiling with single sample predictors: a retrospective analysis. Lancet Oncol
    37. (2008). Reis-Filho JS: Genomic analysis of the HER2/TOP2A amplicon in breast cancer and breast cancer cell lines. Lab Invest
    38. (2008). Ringner M: Normalization of Illumina Infinium wholegenome SNP data improves copy number estimates and allelic intensity ratios.
    39. (2008). Ringner M: Segmentationbased detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays. Genome Biol
    40. (2008). Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia-A comparative study of four differently designed, high resolution microarray platforms. Genes Chromosomes Cancer
    41. (1989). Statistical evaluation of cell kinetic data from DNA flow cytometry (FCM) by the EM algorithm. Cytometry
    42. (2008). The genomic profile of HER2-amplified breast cancers: the influence of ER status.
    43. (2009). TP: A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including
    44. (2011). Tumour evolution inferred by single-cell sequencing. Nature
    45. (2010). VN: Allele-specific copy number analysis of tumors. Proc Natl Acad Sci USA

    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.