MLO: Solving rare paediatric disease mysteries

There is a loudly ticking clock looming over the process of diagnosing rare genetic diseases in children. It’s not just about finding the answer, but, even more importantly, about finding the answer in time to make a difference through early intervention.

A recent continuing education article published in MLO (short for Medical Laboratory Observer) tackles this critical topic. It comes from our own Nabihah Sachedina, Vice President, Health Programs here at Oxford Nanopore Technologies who is a trained paediatrician and has also worked in the healthcare policy field. She has seen the challenges of a diagnostic odyssey for her own patients and knows firsthand how much of a difference it can make to patients and their families to get an accurate diagnosis.

The whole article is worth a read, but if you don’t have time, here are a few highlights.

Key considerations

In the past, diagnosing rare paediatric diseases has generally entailed serial testing using a number of different assays and technologies. Now, the clear value of getting more comprehensive information from DNA sequencing is changing the approach for many clinical laboratories. But even within the world of sequencing tools, there are many factors to consider.

'For clinical laboratory teams, it can be instructive to consider the diagnostic outcomes of exome versus genome sequencing, proband versus trio sequencing, short-read versus long-read sequencing, the value of epigenetics, and more’, Nabihah wrote. Her article walks readers through the advantages and disadvantages of several of these concepts. Generally speaking, a single platform that generates high-quality genome assemblies along with methylation data in a simple workflow without needing parental DNA for trio sequencing will be the most useful, comprehensive, and cost-effective approach.

Long reads matter

In addition to the considerations above, clinical lab teams may want to avoid sequencing platforms that are limited to producing short-read data. ‘Sequencers that are able to produce long reads — often hundreds of kilobases in length — require far less assembly and are therefore less prone to errors in alignment and orientation’, Nabihah noted. Long reads make it possible to characterise regions of the genome that are inaccessible to short-read technologies.

Long-read data also makes it easier to detect large variants that cannot be fully captured in a single short read. While short-read data excels at identifying single-nucleotide variants and small insertions or deletions, it struggles to represent other variants accurately. ‘Structural variants such as copy number alterations, repeat expansions, inversions, and translocations, among many others, cannot be consistently and reliably identified with short-read data because these reads can collapse during assembly, misrepresenting the original DNA sequence’, Nabihah added.

Beyond DNA

Another major factor in solving more rare disease cases is going beyond the usual DNA variants. RNA-based transcriptome analyses can elucidate gene expression activity, providing a valuable layer of information that may not be obvious from the DNA sequence alone. Again, long reads provide an advantage because they can span full isoforms, eliminating the need for assembly and making it easier to represent the full diversity of splice variants.

Another key area is methylation, which is already useful for diagnosing some rare disorders. While conventional methylation arrays limit diagnoses to known motifs, generating genome-wide methylation data can open the door for discovery of novel methylation profiles that may be disease-related. Relying on the standard bisulfite sequencing process ‘adds a layer of complexity, time, and cost on top of the exome or genome sequencing process’, Nabihah wrote. ‘Some sequencing platforms can now directly detect methylation profiles as they sequence DNA, enabling valuable insights without additional cost or processing’.

The article concludes with several examples of rare disease research studies that have illustrated the diagnostic value of long-read sequencing for paediatric cases, including ones where methylation data and rapid sequencing made a real difference. ‘The ability to truly identify the genomic basis of disease is likely to result in growing implementation of long-read whole genome sequencing to support rare disease diagnosis in babies and children’, Nabihah concluded.