Comparing whole genomes using DNA microarrays

Key Points

• Hybridization between complementary strands of DNA enables the interrogation of unknown DNA by comparison with DNA of known sequence or genomic context.

• DNA microarrays containing hundreds of thousands or millions of probes can be used to interrogate genomic sequence. Advances in array-based approaches have enabled detection of the main forms of genomic variation: amplifications, deletions, insertions, rearrangements and base-pair changes.

• Structural variation in the genome — deletions and duplications, copy number variation, insertions, inversions and chromosomal translocations — can be detected using array comparative genome hybridization. For this application it is often sufficient to have large probes (such as PCR products, cDNA clones or long oligonucleotides) that allow for hybridization despite some sequence differences.

• When DNA probes are short, hybridization efficiency is acutely sensitive to mismatches; such probes therefore facilitate comparison of genomes at the nucleotide level.

• Global mapping of insertion sites is performed by isolating the insertion element and its immediately neighbouring DNA. The DNA is then hybridized to a whole-genome array to identify its genomic location.

• Comprehensive detection of mutations in a complex genome is carried out using whole-genome overlapping tiling arrays, which provide multiple measurements of the effect of an SNP on hybridization.

• Resequencing arrays use at least four probes per interrogated base and have been used to resequence small genomes.

• Microarrays offer a relatively inexpensive and efficient means of comparing all known classes of genomic diversity between closely related genomes. However, they are not appropriate for some applications, such as detecting unknown sequences or interrogating highly repetitive or low-complexity sequences.

Abstract

Microarray-based approaches are a fast, flexible and inexpensive alternative to genome sequencing for characterizing the genomes of many individuals within a species. This article reviews the advances that are making microarrays a viable choice for detecting all forms of genetic diversity.

Abstract

The rapid accumulation of complete genomic sequences offers the opportunity to carry out an analysis of inter- and intra-individual genome variation within a species on a routine basis. Sequencing whole genomes requires resources that are currently beyond those of a single laboratory and therefore it is not a practical approach for resequencing hundreds of individual genomes. DNA microarrays present an alternative way to study differences between closely related genomes. Advances in microarray-based approaches have enabled the main forms of genomic variation (amplifications, deletions, insertions, rearrangements and base-pair changes) to be detected using techniques that are readily performed in individual laboratories using simple experimental approaches.