Answers to Unsolved Rare Disease Mysteries May Be on the Horizon

The following article is an opinion piece written by Neil Ward. The views and opinions expressed in this article are those of the author and do not necessarily reflect the official position of Technology Networks.

Rare diseases remain shrouded in mystery. Although individually uncommon, collectively rare diseases impact millions. Over 7,000 exist, disproportionately affecting children. Yet, what causes many rare conditions remains unknown. Understanding the underlying causes of disease in order to develop treatment plans is a key priority in the UK – where 1 in 17 people are affected by a rare disease, and nearly half of these lack a diagnosis – with the Rare Diseases Action Plan launched in 2022. Many are currently facing a diagnostic odyssey, but new genetic technologies could bring hope, and provide clues to unlock these medical enigmas.

The hunt for answers

Over 70% of rare diseases have genetic origins. Pinpointing variations in a patient's DNA can elucidate underlying biological mechanisms to enable accurate diagnoses. As the adage goes, knowing is half the battle.

But conventional genetic testing methods often come up short. In England and Wales, the standard diagnosis pathway is via short-read genome sequencing. This involves DNA being broken into small fragments and aligned to a reference genome to identify variations. While short-read sequencing has useful applications in many other areas, for more than half of rare disease patients, short-read whole genome sequencing fails to identify causative mutations.

Another option, which is commonly used in Scotland and other countries globally, is exome sequencing. This technique looks for small genetic changes in protein-coding regions. These changes are typically associated with specific rare diseases, and the technique surveys around 50 million base pairs. The human genome consists of around three billion base pairs, meaning exome sequencing covers some 1.5% of DNA real estate. As such, this method can’t pick up the more complex variations linked to many rare diseases.

There are hundreds of genes known to be clinically important to rare diseases. However, many of these genes span multiple regions of the genome and evade these commonly used sequencing tests. More comprehensive approaches are clearly needed that offer an uninterrupted view of the genome.

Shining a light on the dark genome

Long-read sequencing delivers this with an end-to-end view of the genome, enabling detection of complex variants inaccessible to short-read approaches. Long reads also maintain molecular integrity to increase accuracy, since whole strands of DNA are sequenced in a single read rather than broken up and reassembled. This shines light into hard-to-sequence genomic dark regions and illuminates previously hidden links between genetics and rare diseases.

With other technologies, hard-to-sequence areas are too repetitive or convoluted for data to be appropriately extracted. One such example, called copy number variations, involves deleted or duplicated stretches of DNA. Research has associated certain large copy number variants with developmental delay, autism and congenital abnormalities. But short reads often miss copy number variants, while long reads readily highlight where copy number variants are high.

What’s more, long reads allow identification of single gene changes, which cannot be easily found using short-read sequencing. Single gene changes have been associated with rare diseases, including cystic fibrosis, Huntington’s disease and Polycystic kidney disease. Highly accurate long reads can even identify whether certain mutations originated from one parent, which is useful for tracing inheritance or spotting compound mutations in one patient. Even epigenetics, chemical changes that regulate gene activity, can be measured through long reads.

Both short- and long-read sequencing technologies have vastly improved in recent years. For example, improvements in the sensitivity and specificity of short reads hold huge promise for liquid biopsies, which have wide applicability in areas including cancer, heart disease and immune disorders. But for rare diseases, the area that is most exciting is long-read sequencing.

Scaling up

Since more than 70% of rare diseases have genetic origins, deploying long reads at scale will allow scientists to better understand the causal mechanisms of rare diseases. This is increasingly possible as long-read sequencing becomes more accessible, with the cost falling from over $100 million per genome in 2001 to under $1,000 today. The scale of samples that can be processed in a single experiment has also risen significantly, with a single machine now delivering more than 1,300 human genomes per year.

Understanding the genetic underpinnings of rare diseases is key to better diagnoses and treatments, but testing methods used today often fail to provide answers. As costs decrease and scale increases, long-read sequencing presents an exciting opportunity to finally solve many longstanding rare disease mysteries for patients and their families.

About the author: 

Neil Ward is the vice president and general manager for the PacBio’s Europe, Middle East, and Africa (EMEA) region.