How genomic techniques can pin down rare genetic diseases more quickly

Rare disorders are very challenging to diagnose. With about 7000 diagnosed disorders across the world, doctors are often unfamiliar with all the distinguishing features of a particular condition or confuse the condition with similar genetic or acquired disorders.

As a result, for most patients diagnosis is lengthy and costly. It involves a myriad of consultations with medical specialists and many laboratory tests or invasive interventions. And, in the end, there may be no definitive answers.

Up to 50% of people suffering from a rare genetic disease never receive a diagnosis. In a middle income country like South Africa, this likelihood is increased by the relatively limited suite of highly specialised tests.

Developments in genomics have helped. Technologies such as whole exome sequencing – where only the small coding part of the genome is analysed – have transformed diagnostic testing for genetic diseases by simplifying and speeding up the process.

The challenge, however, is that this technology is only relied on as the fourth – and in many cases the final tier – of tests after a battery of others have been unable to produce a diagnosis.

Our study shows that whole exome sequencing can also be used as a first resort to produce a diagnosis in developing countries. It short circuits the process and is less invasive. We were able to identify the first cases in South Africa of a rare genetic condition known as trichohepatoenteric syndrome (THES).

Our research highlights why whole exome sequencing should become a first tier diagnostic test for patients with suspected rare diseases, even in developing countries. This is becoming increasingly feasible as costs continue to fall.

Understanding whole exome sequencing

The complement of DNA in the cell is known as the genome. This is made up of exons and introns. Exons are the part of the DNA in a cell that plans how the proteins are created. Exons only make up about 1.2% of the genome, yet most of the mutations that cause rare genetic conditions are found here.

Introns (DNA sequences between exons) and intragenic regions (DNA sequences between genes) make up the rest of the genome. For a long time it was known as junk DNA, but we know now that it contains regulatory sequences that dictate when, where and how much of a gene will be switched on.

Before whole exome sequencing was developed, geneticists had to rely on linkage analysis, a method which identifies regions of DNA that are common to people in a family who have the disease. This is followed by the sequencing of candidate genes to find the disease-causing mutations. But this method was very time consuming. It could take decades to locate the mutation. In contrast, whole exome sequencing sequences all exons in the genome (known as the exome) within a few days at a fraction of the cost.

Exome sequencing cuts out the need to identify candidate genes for analyses as well as the need to rely on DNA samples from other family members to make a diagnosis.

To date, the use of this technology has resulted in about 40% of the previously unexplained cases being diagnosed.

Since 2014 we have been using whole exome sequencing to provide genetic diagnoses for patients with primary immunodeficiency disorders who are at the end of their diagnostic odysseys. Primary immunodeficiency disorders are genetic disorders individuals are born with that make them more susceptible to fungal, viral and bacterial infections.

Primary immunodeficiency disorders are difficult to diagnose because their symptoms can vary widely. In many cases, patients will not present with all the symptoms of a particular syndrome.

A rare case

We were able to provide a detailed case study using this technique in the case of a Somalian baby boy.

He was born weighing less than two kilograms and spent his first three weeks in hospital for jaundice and poor weight gain. He was re-admitted to hospital for pneumonia when he was three months old.

At the time he had patchy areas of darker skin and somewhat unusual facial features. He also had mild diarrhoea. After three weeks of intensive care treatment, he died of pneumonia. At the time, doctors suspected he suffered from combined immunodeficiency.

With the use of exome sequencing, however, we found that one of his genes had a mutation which he inherited from both his mother and father. Mutations in this gene have been shown to cause an extremely rare genetic condition known as THES.

This syndrome affects about one in every 500,000 live births. Since its first description in 1982, less than 70 cases have been reported worldwide. Before the case we studied, none had been diagnosed in South Africa.

Babies who have the condition have explosive and ongoing diarrhoea, skin abnormalities, growth retardation both in-utero and after birth, liver disease, immunodeficiency and woolly hair. Although some survive, most die in infancy.

The challenge with the Somalian boy’s case was that the diagnosis of THES was not considered, because he lacked two classical features: he did not have significant diarrhoea, and his hair could not be assessed because it had been shaven.

It was only when we found the same mutation in DNA extracted from a well-preserved tissue sample of his deceased sibling – who, in addition to having similar complications to him, also had severe diarrhoea and hair which his parents described as “sticking out” – that we were able to diagnose this syndrome.

Using the technology more regularly

Without whole exome sequencing we would not have been able to diagnose THES in the Somali boy. The case highlights the potential impact of whole exome sequencing on patient care and why it should be used more systematically as a first tier test.

While whole exome sequencing is a great advance, it’s not yet a panacea for rare disease identification. There are still practical and ethical challenges that come with generating vast quantities of genetic information. These include the need to ensure the confidentiality of large quantities of data that are stored and regularly reviewed.