Complexities of array CGH

Complexities associating with using array CGH.

These include:

• Accuracy of breakpoint coordinates

The reported array CGH breakpoint coordinates do not reflect the precise boundaries of deletions/duplications. Rather they represent the genomic coordinates of the first and last probe within the region of imbalance.

Some laboratories also report the first and last normal probes. In reality the breakpoints will fall between the last normal/first abnormal probe and the last abnormal/first normal probe.

So find out what your laboratory reports and beware of any genes that seem to lie adjacent to ‘breakpoints’. If you think they could be of relevance to the phenotype then be sure to check back with the lab as to whether they could be disrupted, given the information available.

• Apparent differences between deletions/duplications in the same family

Sometimes family members are reported as having similar, but not identical, deletions or duplications. In this case, check back with the lab.

It is most likely that they are in fact identical but that a slightly different platform has been used (including different software and different algorithms), or there is inconsistency in the way that the breakpoints have been called (as an artefact of the inherent noise of the calls).

• Genomic Build

The human reference genome is regularly updated, and a new ‘build’ (or version) brought out. At the time of writing, we are on the 38th build!

The breakpoint coordinates given by the lab will relate to a particular build, which should be referenced on the report.

If as a clinician you wish to enter the coordinates into a genome browser to see for yourself the extent of a deletion/duplication, make sure you use the same build as quoted on the report, or you could end up focused on the wrong genomic region.

• Partial duplications which may have a haploinsufficiency effect

Beware of any duplication, however small, that may contain a partial gene duplication.

A partial gene duplication inserted in tandem may cause functional disruption of the gene, with a resulting haploinsufficiency effect.

• Chromosome location of duplications - if not in tandem what are they interrupting?

Array CGH is a quantitative method that will tell you that there is a duplication, but not where it is inserted. Whilst a partial gene duplication in tandem may cause functional disruption of that particular gene, a duplication inserted elsewhere may interrupt and disrupt a completely different gene elsewhere in the genome.

If the phenotype doesn’t fit, or appears more severe than you expect, you would be wise to investigate further.

Source:-https://www.futurelearn.com/courses/molecular-techniques/6/steps/765706