An 11-year-old girl was diagnosed with Charcot-Marie-Tooth (CMT) disease only after the disease-causing mutation was detected by whole-genome sequencing, after being missed by other detection methods, according to a case report.
This case highlights how in-depth genetic sequencing technologies might be the most reliable for diagnosing genetic diseases such as CMT.
The report, “Whole genome sequencing reveals novel IGHMBP2 variant leading to unique cryptic splice‐site and Charcot‐Marie‐Tooth phenotype with early onset symptoms,” was published in the journal Molecular Genetics & Genomic Medicine.
The parents of the patient in the report had noticed abnormalities in the child’s development when she was as young as 3 months old. In the first few years of her life, she had atrophy (wasting) of the limbs and muscle weakness, as well as some seizure-like activity.
At 5 years old, she was seen at a genetics clinic, and after ruling out spinal muscular atrophy type 3, she was suspected of having “a variant of CMT.”
It wasn’t until she was 9 years old that she first underwent more thorough genetic testing, in this case, whole-exome sequencing. This technique is different from whole-genome sequencing because it only looks at a person’s exome — just the part of the genome that actually codes for proteins.
Since the exome only accounts for about 1% of a person’s total genome, and since most known disease-causing mutations are in these regions, doing whole-exome sequencing can be faster and more economical than whole-genome sequencing.
However, in this instance, whole-exome sequencing didn’t provide a definitive answer. One variant in the protein-coding region of the IGHMBP2 gene she had inherited from her mother was noted, but it wasn’t clear whether this mutation on its own would cause a functional change that would cause CMT.
She was later referred to the Undiagnosed Diseases Network, where her entire genome was sequenced.
This revealed an unnoticed mutation in her other copy of the IGHMBP2 gene (the one she inherited from her father). Because this mutation was in a part of the gene that didn’t code for the protein — called an intron — it hadn’t been picked up by whole-exome sequencing.
However, software analysis suggested that this mutation might actually have an effect on the protein, even though it wasn’t in the protein-coding part of the gene.
When RNA is made from a protein template, all the non-protein-coding parts need to be removed before the RNA is translated into protein. This process is called splicing, and it is dependent on certain sequences in both the coding and non-coding regions being present so that the proper parts can be recognized and removed or retained, as appropriate.
This non-coding mutation changed the way the IGHMBP2 RNA was being spliced. In addition to software predictions, this was confirmed by direct analysis of the patient’s RNA.
The changed splicing, in turn, led to the production of a shorter, non-functional version of the IGHMBP2 protein, which, in combination with the other mutation she inherited from her mother, likely explains the cause of CMT.
This case highlights how more in-depth whole-genome sequencing can catch mutations that other methods might miss — but this isn’t to say that whole-genome sequencing is always the best option.
“The choice between [whole-genome sequencing] or [whole-exome sequencing] is not easy,” the researchers wrote. “[Whole-exome sequencing] is less expensive and more readily available, but can miss disease‐causing mutations in noncoding regions as in this case.”
Thus, they argue that clinicians who choose to use whole-exome sequencing should be aware of its limitations, especially when it seems to fail to fully explain the clinical presentation of a patient.