How is genetic testing for 22q11.2 deletions done?

Array comparative genomic hybridization (aCGH)

For graphic illustration of this technique, please click here. What is compared is DNA from the individual to be tested and DNA from a healthy individual.

  • Aim: to identify substantially sized gains or losses of chromosomal regions in any part of the genome.

  • Process: Standard blood sample from the individual being tested is sent to a clinical lab

  • Advantages:

    • High resolution (can detect changes as small as 40kilobases, or 40kb). i.e. Detects typical and smaller or atypical 22q11.2 deletions
    • Screens the whole genome at the same time
    • Sensitive and specific
    • Fast and high throughput
  • Disadvantages:
    • Cannot detect chromosomal changes that do not result in changes in copy number, e.g. balanced translocations, inversions
    • Limited ability to detect mosaicism

For further information, please refer to the Microarray-based comparative genomic hybridisation (array CGH) brochure developed by the Rare Chromosome Disorder Support Group.

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Multiplex ligation-dependent probe amplification (MLPA)

For graphic illustration of this technique, please see Figure 2 of the article by Schouten et al.

  • Aim: to identify gains or losses of chromosomal regions in up to 45 areas within the genome

  • Process: Standard blood sample from the individual being tested is sent to a clinical lab

  • Advantages:

    • High resolution
    • Testing can be done for up to 45 genomic locations at the same time
      • Uses 7 probes within the typical 22q11.2 deletion region.
    • Sensitive and specific
    • Fast and high throughput
    • Cost-effective and robust
  • Disadvantages:
    • Cannot detect chromosomal changes that do not result in changes in copy number, e.g. balanced translocations, inversions
    • Only certain regions of the genome are assessed

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Fluorescence in situ hybridization (FISH): targetted testing

  • Aim: to check whether a specific section on one chromosome contains deletions, duplications, or translocations
  • Process: Standard blood sample from the individual being tested is sent to a clinical lab
  • Advantages:
    • Technically reasonably straightforward
    • Can identify a range of chromosomal aberrations including deletions, duplications, and translocations
  • Disadvantages:
    • Labour intensive so fastest turnaround time possible is 3 to 14 days
    • Cannot detect even large deletions if the binding site for the probe used is not in the actual deletion region
    • Cannot provide information on the length or exact position of a deletion
  • FISH test specific for typical 22q11.2 deletions:
    • Two probes are used to bind to chromosome 22:
      • TUPLE1 or N25 (here labelled with a red dye) binds to 22q11.2 (area of potential deletion)
      • ARSA (here labelled with a green dye) binds to 22q13.3 (area on the far end of chromosome 22; not deleted in 22q11.2DS
        • A normal chromosome 22 is not missing any parts, so both the red and the green probes can bind to their respective locations.
        • A chromosome 22 with a 22q11.2 deletion has the green probe bind to the 22q13.3 location, but has nowhere for the red 22q11.2 probe to bind.
      TUPLE or N25 (red) signal ARSA (green) signal
      Normal chromosome 22 Yes Yes
      Chromosome 22 with 22q11.2 deletion No Yes

      For graphic illustration of this technique, please click here.

      Note: A negative FISH result can mean:

      • The individual tested has no deletion at 22q11.2, but may have a genetic change somewhere else in the genome. e.g. 10p13-14
      • The individual tested has a deletion at 22q11.2, but it is not within binding site of the TUPLE or N25 probe and therefore not detectable using these probes. This is estimated to happen about 8% of the time.

      Because of FISH's inability detect deletions that are either proximal or distal to the probes used (as in the case described by Beaujard et al.), the preferred initial test for 22q11.2 DS is now aCGH or MLPA. There is strong evidence that chromosomal microarray (which includes aCGH) should be the first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. MLPA is also considered a rapid, reliable, economical, high-throughput method for the diagnosis of 22q11.2 deletion syndrome.

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