Microarrays in Disease Diagnosis and Prognosis

Abstract

Progress in microarray technologies will soon lead to their application in clinical practice. These high‐throughput technologies are expected to have a major impact on molecular pathology, initially in tumour classification and tumour staging.

Keywords: microarrays; CLL; TMA; SNP

Figure 1.

Surveillance of disease progression and response to therapy using gene expression profiling. Expression profiles were conducted with peripheral blood lymphocyte samples taken from 13 patients at different times. (a) Analysis of filtered expression data for nine patients (arbitrary labels) using singular value decomposition revealed a generic shift in messenger ribonucleic acid expression associated with disease progression, thus defining a progression axis spanned by the first two singular vectors PCA 1 and PCA 2 of the principle component analysis. In order to follow the development of disease in a single patient (‘follow‐up patient’), all samples taken from this patient were projected on to the same plane spanned by vectors PCA 1 and PCA 2. Temporally consecutive samples are connected with arrow‐marked lines. Thick lines denote the time frame of therapy. (b) Patient (arbitrary labels) with an initial 13q deletion acquires an additional 11q deletion resulting in progression of the disease. Therapy is able to improve the patient's status. (c) A patient (arbitrary labels) with initially constant disease status receives therapy resulting in improvement. However, during that time he acquires a 17p deletion, which results in progression of therapy‐resistant disease.

close

References

Alizadeh AA, Eisen MB, Davis RE et al. (2000) Distinct types of diffuse large B‐cell lymphoma identified by gene expression profiling. Nature 403: 503–511.

Armstrong SA, Staunton JE, Silverman LB et al. (2001) MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nature Genetics 30: 41–47.

Belov L, de la Vega O, dos Remedios CG, Mulligan SP and Christopherson RI (2001) Immunophenotyping of leukemias using a cluster of differentiation antibody microarray. Cancer Research 61: 4483–4489.

Bichi R, Shinton SA, Martin ES et al. (2002) Human chronic lymphocytic leukemia modeled in mouse by targeted TCL1 expression. Proceedings of the National Academy of Sciences of the USA 99: 6955–6960.

Döhner H, Stilgenbauer S, Benner A et al. (2000) Genomic aberrations and survival in chronic lymphocytic leukemia. New England Journal of Medicine 343: 1910–1916.

Garraway LA, Widlund HR, Rubin MA et al. (2005) Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 436: 117–122.

Gentleman R, Carey V, Huber W, Irizarry R and Dudoit S (2005) Bioinformatics and Computational Biology Solutions Using R and Bioconductor. New York: Springer.

Glas AM, Floore A, Delahaye LJ et al. (2006) Converting a breast cancer microarray signature into a high‐throughput diagnostic test. BMC Genomics 7: 278 (Epub ahead of print).

Haslinger C, Schweifer N, Stilgenbauer S et al. (2004) Microarray gene expression profiling of B‐cell chronic lymphocytic leukemia subgroups defined by genomic aberrations and VH mutation status. Journal of Clinical Oncology 22: 3937–3949.

Hedenfalk I, Duggan D, Chen Y et al. (2001) Gene‐expression profiles in hereditary breast cancer. New England Journal of Medicine 344: 539–548.

Kallioniemi OP, Wagner U, Kononen J and Sauter G (2001) Tissue microarray technology for high‐throughput molecular profiling of cancer. Human Molecular Genetics 10: 657–662.

Kononen J, Bubendorf L, Kallioniemi A et al. (1998) Tissue microarrays for high‐throughput molecular profiling of tumor specimens. Nature Medicine 4: 844–847.

Lossos IS, Alizadeh AA, Eisen MB et al. (2000) Ongoing immunoglobulin somatic mutation in germinal center B cell‐like but not in activated B cell‐like diffuse large cell lymphomas. Proceedings of the National Academy of Sciences of the USA 97: 10209–10213.

Matutes E and Polliack A (2000) Morphological and immunophenotypic features of chronic lymphocytic leukemia. Review of Clinical and Experimental Hematology 4: 22–47.

Obermann EC, Went P, Tzankov A et al. (2006) Cell cycle phase distribution analysis in chronic lymphocytic leukaemia: a significant number of cells reside in early G1‐phase. Journal of Clinical Pathology doi: 10.1136/jcp.2006.040956.

Rosenwald A, Alizadeh AA, Widhopf G et al. (2001) Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia. Journal of Experimental Medicine 194: 1639–1647.

Rudd MF, Sellick GS, Webb EL et al. (2006) Variants in the ATM‐BRCA2‐CHEK2 axis predispose to chronic lymphocytic leukemia. Blood 108: 638–644.

Schwaenen C, Nessling M, Wessendorf S et al. (2004) Automated array‐based genomic profiling in chronic lymphocytic leukemia: development of a clinical tool and discovery of recurrent genomic alterations. Proceedings of the National Academy of Sciences of the USA 101: 1039–1044.

Solinas‐Toldo S, Lampel S, Stilgenbauer S et al. (1997) Matrix based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes, Chromosomes and Cancer 20: 399–407.

Stratowa C, Loffler G, Lichter P et al. (2001) cDNA microarray gene expression analysis of B‐cell chronic lymphocytic leukemia proposes potential new prognostic markers involved in lymphocyte trafficking. International Journal of Cancer 91: 474–480.

van't Veer LJ, Dai H, van de Vijver MJ et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415: 530–536.

Further Reading

Alizadeh A, Eisen M, Davis RE et al. (1999) The lymphochip: a specialized cDNA microarray for the genomic‐scale analysis of gene expression in normal and malignant lymphocytes. Cold Spring Harbor Symposia on Quantitative Biology 64: 71–78.

Alizadeh AA and Staudt LM (2000) Genomic‐scale gene expression profiling of normal and malignant immune cells. Current Opinion in Immunology 12: 219–225.

Allison DB, Cui X, Page GP and Sabripour M (2006) Microarray data analysis: from disarray to consolidation and consensus. Nature Review Genetics 7: 55–65.

Alter O, Brown PO and Botstein D (2000) Singular value decomposition for genome‐wide expression data processing and modeling. Proceedings of the National Academy of Sciences of the USA 97: 10101–10106.

Golub TR, Slonim DK, Tamayo P et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286: 531–537.

Hoheisel JD (2006) Microarray technology: beyond transcript profiling and genotype analysis. Nature Review Genetics 7: 200–210.

Lakhani SR and Ashworth A (2001) Microarray and histopathological analysis of tumours: the future and the past? Nature Review Cancer 1: 151–157.

Ludwig JA and Weinstein JN (2005) Biomarkers in cancer staging, prognosis and treatment selection. Nature Review Cancer 5: 845–856.

Matutes E and Polliack A (2000) Morphological and immunophenotypic features of chronic lymphocytic leukemia. Reviews of Clinical and Experimental Hematology 4: 22–47.

Stratowa C and Wilgenbus KK (1999) Gene expression profiling in drug discovery and development. Current Opinion in Molecular Therapeutics 1: 671–679.

Zhang H, Yu CY, Singer B and Xiong M (2001) Recursive partitioning for tumor classification with gene expression microarray data. Proceedings of the National Academy of Sciences of the USA 98: 6730–6735.

Web Links

v‐erb‐b2 erythroblastic leukaemia viral oncogene homologue 2, neuro/glioblastoma derived oncogene homologue (avian) (ERBB2); Entrez ID: 2064. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_udis=2064

Tumour protein p53 (Li–Fraumeni syndrome) (TP53); Entrez ID: 7157. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_udis=7157

v‐erb‐b2 erythroblastic leukaemia viral oncogene homologue 2, neuro/glioblastoma derived oncogene homologue (avian) (ERBB2); MIM number: 164870. OMIM: http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=164870

Tumour protein p53 (Li–Fraumeni syndrome) (TP53); MIM number: 191170. OMIM: http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=191170

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Stratowa, Christian(Jul 2007) Microarrays in Disease Diagnosis and Prognosis. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005946.pub2]