Studying Genomic Aberrations by Microarray Profiling

Logan C Walker, Queensland Institute of Medical Research, Brisbane, Australia
Nic Waddell, Institute for Molecular Bioscience, Brisbane, Australia

Published online: April 2010

DOI: 10.1002/9780470015902.a0022417

Inherited genetic variation between individuals is the main reason why we are different from one another. Genomic aberrations also play an important in the development of human diseases. An important tool for the study of these genetic changes is the microarray. Array technology has evolved over the years from traditional comparative genomic hybridization arrays to high-resolution single nucleotide polymorphism (SNP) arrays, which can be used for SNP genotyping and the determination of copy number and loss of heterozygosity. These platforms will continue to play an important role in unravelling the complexity of diseases.

Key concepts:

  • Microarrays are a useful tool to assay changes in copy number, single nucleotide polymorphisms and loss of heterozygosity.
  • There is inherited genetic diversity between individuals.
  • Genomic aberrations play a key role in the development of many diseases.

Keywords: microarray; genetic variation; copy number; single nucleotide polymorphism; genotyping; genome-wide association studies

Figure 1. Schematic diagram of comparative genomic hybridization (CGH), array-CGH and Illumina's Infinium HD SNP chip assay. For CGH and aCGH, DNA samples extracted from samples and reference tissue are individually labelled with distinguishable fluorescent dyes. After denaturation, a 1:1 mixture of both labelled DNAs supplemented with human Cot1 DNA to block repetitive sequences cohybridize onto metaphase spreads (CGH) or spotted DNA sequences (aCGH). Post-hybridization washes are carried out to remove unbound probes. DNA copy number changes in the tumour genome are estimated by measuring the fluorescence intensity corresponding to sample and reference fluorochromes. Genomic DNA analysed by the Infinium HD assay (Illumina) is amplified and fragmented before hybridizing to a high-density SNP array. Using the hybridized DNA as a template, a single base extension of the oligonucleotide probes is performed that incorporates fluorochrome-labelled nucleotides to indicate the SNP genotype.
Figure 2. Copy number variations detected in a human tumour sample using the Illumina SNP array platform. The genomic profile of chromosome 20 is shown. The upper two plots show the B allele frequency and log R (a). The B allele frequency highlights regions of LOH and the log R ratio is an indication of copy number and is calculated from the observed divided by the reference or expected value. Tools such as cnvPartition can be used to infer copy number (b). The chromosome and some of the genes within the regions of gain and loss are shown (c).
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 References
    Albertson DG and Pinkel D (2003) Genomic microarrays in human genetic disease and cancer. Human Molecular Genetics 12(Spec No 2): R145–R152.
    Albertson DG, Ylstra B, Segraves R et al. (2000) Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nature Genetics 25: 144–146.
    Assie G, LaFramboise T, Platzer P et al. (2008) SNP arrays in heterogeneous tissue: highly accurate collection of both germline and somatic genetic information from unpaired single tumor samples. American Journal of Human Genetics 82: 903–915.
    Backx L, Van Esch H, Melotte C et al. (2007) Array painting using microdissected chromosomes to map chromosomal breakpoints. Cytogenetic and Genome Research 116: 158–166.
    Baptista J, Mercer C, Prigmore E et al. (2008) Breakpoint mapping and array CGH in translocations: comparison of a phenotypically normal and an abnormal cohort. American Journal of Human Genetics 82: 927–936.
    Bignell GR, Huang J, Greshock J et al. (2004) High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Research 14: 287–295.
    Colella S, Yau C, Taylor JM et al. (2007) QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Research 35: 2013–2025.
    other Conrad DF, Pinto D, Redon R et al. (2009) Origins and functional impact of copy number variation in the human genome. Nature doi: 10.1038/nature08516.
    Diskin SJ, Hou C, Glessner JT et al. (2009) Copy number variation at 1q21.1 associated with neuroblastoma. Nature 459: 987–991.
    Feuk L, Carson AR and Scherer SW (2006) Structural variation in the human genome. Nature Reviews Genetics 7: 85–97.
    Fiegler H, Redon R, Andrews D et al. (2006) Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Research 16: 1566–1574.
    Gribble SM, Ng BL, Prigmore E, Fitzgerald T and Carter NP (2009) Array painting: a protocol for the rapid analysis of aberrant chromosomes using DNA microarrays. Nature Protocol 4: 1722–1736.
    HapMap (2003) The International HapMap Project. Nature 426: 789–796.
    Hindorff LA, Sethupathy P, Junkins HA et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences of the USA 106: 9362–9367.
    Howarth KD, Blood KA, Ng BL et al. (2008) Array painting reveals a high frequency of balanced translocations in breast cancer cell lines that break in cancer-relevant genes. Oncogene 27: 3345–3359.
    Hyman E, Kauraniemi P, Hautaniemi S et al. (2002) Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Research 62: 6240–6245.
    Ishkanian AS, Malloff CA, Watson SK et al. (2004) A tiling resolution DNA microarray with complete coverage of the human genome. Nature Genetics 36: 299–303.
    Kallioniemi A, Kallioniemi OP, Sudar D et al. (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258: 818–821.
    Kauraniemi P, Barlund M, Monni O and Kallioniemi A (2001) New amplified and highly expressed genes discovered in the ERBB2 amplicon in breast cancer by cDNA microarrays. Cancer Research 61: 8235–8240.
    Kennedy GC, Matsuzaki H, Dong S et al. (2003) Large-scale genotyping of complex DNA. Nature Biotechnology 21: 1233–1237.
    Lee C, Iafrate AJ and Brothman AR (2007) Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nature Genetics 39: S48–54.
    Liu W, Sun J, Li G et al. (2009) Association of a germ-line copy number variation at 2p24.3 and risk for aggressive prostate cancer. Cancer Research 69: 2176–2179.
    Okou DT, Steinberg KM, Middle C et al. (2007) Microarray-based genomic selection for high-throughput resequencing. Nature Methods 4: 907–909.
    Pinkel D, Segraves R, Sudar D et al. (1998) High-resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genetics 20: 207–211.
    Pollack JR, Perou CM, Alizadeh AA et al. (1999) Genome-wide analysis of DNA copy number changes using cDNA microarrays. Nature Genetics 23: 41–46.
    Pollack JR, Sorlie T, Perou CM et al. (2002) Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proceedings of the National Academy of Sciences of the USA 99: 12963–12968.
    Porkka K, Saramaki O, Tanner M and Visakorpi T (2002) Amplification and overexpression of Elongin C gene discovered in prostate cancer by cDNA microarrays. Laboratory Investigation 82: 629–637.
    Rauch A, Ruschendorf F, Huang J et al. (2004) Molecular karyotyping using an SNP array for genome-wide genotyping. Journal of Medical Genetics 41: 916–922.
    Rodriguez-Perales S, Melendez B, Gribble SM et al. (2004) Cloning of a new familial t(3;8) translocation associated with conventional renal cell carcinoma reveals a 5 kb microdeletion and no gene involved in the rearrangement. Human Molecualr Genetics 13: 983–990.
    Schena M, Shalon D, Davis RW and Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467–470.
    Sebat J, Lakshmi B, Malhotra D et al. (2007) Strong association of de novo copy number mutations with autism. Science 316: 445–449.
    Shlien A and Malkin D (2009) Copy number variations and cancer. Genome Medicine 1: 62.
    Shlien A, Tabori U, Marshall CR et al. (2008) Excessive genomic DNA copy number variation in the Li–Fraumeni cancer predisposition syndrome. Proceedings of the National Academy of Sciences of the USA 105: 11264–11269.
    Snijders AM, Nowak N, Segraves R et al. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nature Genetics 29: 263–264.
    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.
    Squire JA, Pei J, Marrano P et al. (2003) High-resolution mapping of amplifications and deletions in pediatric osteosarcoma by use of CGH analysis of cDNA microarrays. Genes, Chromosomes and Cancer 38: 215–225.
    Vissers LE, van Ravenswaaij CM, Admiraal R et al. (2004) Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. Nature Genetics 36: 955–957.
    Vissers LE, Veltman JA, van Kessel AG and Brunner HG (2005) Identification of disease genes by whole genome CGH arrays. Human Molecular Genetics 14(Spec No. 2): R215–R223.
    Walsh T, McClellan JM, McCarthy SE et al. (2008) Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science 320: 539–543.
    Wang K, Li M, Hadley D et al. (2007) PennCNV: an integrated Hidden Markov Model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Research 17: 1665–1674.
 Further Reading
    book Bowtell D and Sambrook J (2003) Part 1: Microarray-based Detection of DNA Copy Number. DNA Microarrays: A Molecular Cloning Manual. Cold Spring Harbor, New York: CSHL Press.
    book Knight JC (2009) Human Genetic Diversity: Functional Consequences for Health and Disease. Oxford, USA: Oxford University Press.
    Manolio TA, Collins FS, Cox NJ et al. (2009) Finding the missing heritability of complex diseases. Nature 461: 747–753.
    book Patrinos GP and Ansorge W (2005) Molecular Diagnostics. Burlingtom, MA: Academic Press.

Related Sub-Topics:

Techniques and Tools in Clinical Genetics | Linkage Analysis | Chromosomal Disorders | Gene Mapping by Disease Association | Genomic Disorders | Chromosomes and Chromatin Modifications | Techniques and Tools in Molecular Biology
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Article Title: Studying Genomic Aberrations by Microarray Profiling
 
How to Cite close
Walker, Logan C, and Waddell, Nic(Apr 2010) Studying Genomic Aberrations by Microarray Profiling. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0022417]