The Dalglish Family 22q Clinic

Whole genome sequencing (or simply genome sequencing) has been recommended as a diagnostic test in children with unexplained medical complexity. This method would be able to diagnose patients with uncommon variants (in 22q or other parts of the genome) which could otherwise be missed. It would also allow us to better understand the medical complexity of patients with 22q11.2 deletions.

• Aim: to detect any genetic changes in any part of the genome

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

  • An overview can be found in Figure 1 of the article by Costain et al., 2022

  • Additional information can be found in the Methods section of the article by Costain et al., 2020.

• Advantages:

  • Highest resolution compared to other methods of analysis

  • Improved coverage of exonic regions as well as comprehensive detection of all sequence and structural variation in the nuclear and mitochondrial DNA

  • Detects typical 22q11.2 deletions as well as the ones that other methods would miss

  • Screens the whole genome at the same time

  • Reduces the time and emotional burden of the diagnostic process

  • Detects both gains and losses in copy numbers resulted from a variety of causes (e.g. deletions, amplifications, loss of heterozygosity, uniparental disomy)

• Disadvantages:

  • Expensive (but the cost is becoming more manageable as time goes on)

  • Large amount of data to be processed

  • May be mistaken as a solution for all disease

  • The classification of some genetic variants may change over time as new information becomes available. Some ethnic groups are under-represented in reference databases, making it more difficult to interpret certain variants.

Further reading:

• Genome sequencing as a diagnostic test (Costain et al., 2022)
• Genome Sequencing as a Diagnostic Test in Children With Unexplained Medical Complexity (Costain et al., 2020) with Commentary in SickKids news

• This method is currently the preferred initial test for 22q11.2DS

  • Currently used at the Lab & Testing Services at the Hospital for Sick Children, Toronto

• Aim: to detect copy number variations in any part of the genome

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

  • Additional information can be found on technical documents such as the ones from Affymetrix.

• Advantages:

  • High resolution compared to older methods of analysis

  • Detects typical and smaller or atypical 22q11.2 deletions

  • Screens the whole genome at the same time

  • Fast and high throughput

  • Detects both gains and losses in copy numbers resulted from a variety of causes (e.g. deletions, amplifications, loss of heterozygosity, uniparental disomy)
• Disadvantages:
  • Cannot detect chromosomal changes that do not result in changes in copy number, e.g. balanced translocations, inversions

Further information:

• Affymetrix

• Genome-wide Mapping of Copy Number Variations Using SNP Arrays

• This is an older method for testing.

• 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 and for a schematic diagram, please refer to the Microarray-based Comparative Genomic Hybridization (aCGH) article by Nature Education.

• This is an older method for testing.

• 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

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

• 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.

For sample results of this technique, please see this set of images.

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, the preferred initial test for 22q11.2DS is genomic SNP array (described in the first section of this page).