Studying Genomic and Epigenetic Aberrations by Microarray Profiling

Abstract

Genomic (genetic and epigenetic) changes are important for interindividual variation and can cause or influence a person's predisposition for a wide range of human diseases, including cancer. An important tool for the study of these genetic and epigenetic changes is the microarray. For example, high‐density single nucleotide polymorphism (SNP) arrays have been used extensively to study inherited traits using genome‐wide association studies (GWASs). SNP arrays have also been commonly used to profile copy number changes which occur in and are specific to cancer cells. The same microarray technology can be used to assay deoxyribonucleic acid (DNA) methylation status across the genome. Despite the emergence of next‐generation sequencing, microarrays are a relatively low cost and high‐throughput platform that will continue to play a role in unravelling the complexity of human diseases.

Key Concepts

  • Genomic variation exists between individuals.
  • Microarrays can assay SNPs, copy number and methylation changes.
  • Microarrays have been used to study human diseases, inherited genetic traits and cancer.
  • Compared to single nucleotide polymorphisms, the contribution of inherited copy number variants to human development and disease remains relatively understudied.
  • Microarray analysis remains simpler and cheaper than next-generation sequencing, but lack the resolution of next‐generation sequencing.

Keywords: SNP arrays; microarrays; single nucleotide variation (SNV); copy number variation (CNV); genomics; methylation; inherited genetic traits; cancer

Figure 1. A schematic of the design of a whole‐genome SNP (single nucleotide polymorphism)‐ or CNV (copy number variation)‐trait association analysis.
Figure 2. Illumina SNP array B‐allele frequency (BAF) and Log R Ratio plots for a range of tumour sample purities. A patient‐derived cancer cell line and matched normal DNA were mixed in different proportions to represent 100%, 80%, 60%, 40%, 20% and 0% tumour content. Samples were then assayed using Illumina SNP arrays. The schematic of chromosome 4 indicates that part of one of the chromosome 4 pairs has been deleted in the tumour sample, retaining approximately 12 Mb of the distal p arm. The plots indicate the SNP array data from Illumina Infinium Omni2.5‐8 v1.0 for samples ranging from 100% to 0% tumour DNA (left to right). The BAF plots indicate the diploid section of the chromosome with a three‐band pattern and the region of loss as a two‐ or four‐band pattern, depending on the purity of the sample. As the tumour cellularity decreases, the separation of the BAF also decreases. The LogR ratio is the total microarray intensity signal.
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Walker, Logan C, Nones, Katia, Patch, Ann‐Marie, and Waddell, Nicola(Nov 2016) Studying Genomic and Epigenetic Aberrations by Microarray Profiling. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0022417.pub2]