Microarrays and Microdeletions: Key Concepts Summarized

WHAT IS IT?

A microarray describes a newer technology that can identify small duplications or deletions of genetic material that previously could not be identified using conventional karyotyping alone. It has become a critical tool to help identify submicroscopic chromosomal deletions/duplications that underlie clinically significant syndromes in the prenatal period and throughout the lifespan.

Key Concepts

What is a Deletion?

• A deletion describes a chromosomal break where genetic material is lost

Credit: US National Library of Medicine

• Deletions can be large or small, and can occur anywhere along a chromosome
  • Terminal deletion (end of a chromosome)
  • Interstitial (within the chromosome)
• Duplication describes when additional material is gained

What is a Microdeletion?

• Definition is based on size of missing DNA sequence
• 1Mb (megabase) = 1 million base pairs
• Conventional karyotype is based on light microscopy and can usually only detect deletions > 5 Mb
• Microdeletions refer to deletions smaller than those that can be seen on karyotype – i.e., < 5 Mb

What is a CNV (copy number variant)?

• Deletions or duplications are ≥ 1 kb (1000 base pairs) to many hundreds of Kb in size
• Small CNVs are common and found in 5 to 10% of individuals in the general population
  • Only 1 to 2% will have CNVs > 1Mb
• Most CNVs are simply a part of normal human variation
  • If CNVs delete or add sufficiently large number of genes or result in a breakpoint within a gene, they may have significant clinical consequences

Key Points:

CGH vs SNP arrays

CGH (Comparative genome hybridization)

• The array is constructed with single short DNA sequences from the regions of interest
• ‘Test’ and ‘control’ DNA are labelled with different fluorescent colors and then hybridized (annealed) to complementary sequences of interest on the array
• The relative amounts of test vs control DNA can be measured
  • Excess control DNA signal color signifies a deletion in the test sample
  • Excess test DNA signal color signifies duplication in the test sample

SNP array

• The array is constructed with short DNA sequences
  • Each region of interest will have two DNA sequences, representing the two possible alleles (versions) of known SNPs
• Only ‘test DNA’ is labelled and hybridized to the allele specific probes within the array
• Relative intensity of the hybridization signal is used to detect if DNA sequence is deleted or duplicated
  • Low/absent intensity signal signifies deletion
  • Excess signal signifies duplication

Additional capabilities of SNP array compared to CGH

• Can detect triploidy, maternal cell contamination and mosacism
• Can detect consanguinity and uniparental disomy (UPD) which can be associated with genetic syndromes
  • Rather than having one copy of each SNP allele, a region of identical SNPs, known as absence of heterozygosity (AOH), will be apparent
  • Labs may report AOH, raising concern for
    • Autosomal recessive disorders related to genes in that particular sequence or
    • UPD, depending on chromosome and region

Learn More – Primary Sources:

ACOG Committee Opinion 682: Microarrays and Next-Generation Sequencing Technology: The Use of Advanced Genetic Diagnostic Tools in Obstetrics and Gynecology

SMFM Consult Series 41: The use of chromosomal microarray for prenatal diagnosis

ACMG Standards and Guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: revision 2013

Yield of additional genetic testing after chromosomal microarray for diagnosis of neurodevelopmental disability and congenital anomalies: a clinical practice resource of the American College of Medical Genetics and Genomics (ACMG)