How genome sequencing is revolutionizing healthcare

In recent years, medical science and technology have reached a point where it’s possible to map out the entire sequence of an individual's genetic material. While this phenomenon, known as whole genome sequencing (WGS), is still in its early days, it represents a major step forward for care providers, who can use it to improve our understanding of a range of diseases—including COVID-19.

The power of genome sequencing was illustrated in the findings of a study published in The New England Journal of Medicine in November, which probed the UK’s 100,000 Genomes Project. According to the study authors, roughly 6% of Western populations are affected by approximately 10,000 rare diseases, more than 80% of which have a genetic component.

These diseases are notoriously difficult to manage, often debilitating for the patient, and expensive to treat. One-third of children with a rare disease die before they reach 1 year. The project has been compiling a database of genomes with the intent of studying rare diseases, cancers, and infections since 2013.  

To assess the efficacy of whole genome sequencing in diagnosis, researchers used a cohort of 4,660 participants who presented with 161 rare disorders. They found that 25% of the diagnoses they made had “immediate ramifications for clinical decision making.” Overall, researchers concluded that whole-genome sequencing resulted in “a substantial increase in yield of genomic diagnoses.”

Here are four other areas where whole-genome sequencing is revolutionizing diagnosis and treatment.

COVID-19

SARS-CoV-2 and many similar viruses change over time. That’s why headlines everywhere are plastered with news of emerging variants of concern, like Delta and Omicron. But how do scientists monitor these changes? Increasingly, they’re using WGS to perform genomic surveillance, a tool used for monitoring changes in organisms over time and understanding how those changes might impact the characteristics of the diseases they cause.

During the pandemic, scientists have been using WGS and genomic surveillance to:

• Monitor the development of new variants

• Understand how changes in SARS-CoV-2 impact the severity of COVID-19, its transmissibility, its response to treatments like vaccines, and virus detection

• Identify potential outbreaks

As the CDC and its public health partners sequence more SARS-CoV-2 genomes, “we will improve our understanding of which variants are circulating in the US, how quickly variants emerge, and which variants are the most important to characterize and track in terms of health,” the CDC wrote.

Critically ill infants 

In 2019, a group of researchers decided to apply WGS to the clinical management of a population of 354 acutely ill infants. Half of the cohort received their clinical WGS results after 15 days (the early group) and half received results after 60 days (the delayed group). Their findings, which were published in JAMA Pediatrics in September, demonstrated that diagnosis with WGS was linked to “a significant increase in focused clinical management compared with usual care.”

Following the reception of clinical WGS results, twice as many infants in the early group received a change of management, compared with the delayed group. Patients with a pathogenic WGS finding were three times more likely to receive a change of management. The most common changes of management involved: subspecialty referrals (11%), surgery or other invasive procedures (4%), condition-specific medications (2%), or other supportive alterations in medication (3%). 

Authors noted that these changes of management had “notable clinical effect,” citing examples that included an infant who received a diagnosis of Wiskott-Aldrich syndrome by WGS and was successfully treated with a corrective bone marrow transplant. In some cases, WGS diagnosis led to an inappropriate treatment being halted. For example, one infant with epilepsy was  diagnosed by WGS with an unsuspected KCNQ2 variation. Subsequently, the ineffective administration of pyridoxine was stopped.

Researchers concluded that access to WGS should be made available to the general population and may “reduce healthcare disparities by enabling diagnostic equity.”

Schizophrenia 

WGS may also solve some of the mysteries surrounding schizophrenia, according to a study published in Nature Communications in 2020.

Researchers analyzed WGS data from 1,162 patients diagnosed with schizophrenia, along with 936 ancestry-matched population controls. They identified several incredibly rare genetic variations that led to increased risk for schizophrenia, possibly due to the resulting dysregulation of gene expression. Some of these mutations were previously undetectable, and have only been discovered because of WGS.

In a statement, one of the researchers said, “In the future, we could use this information…to help develop drugs or precision medicine treatments that could repair disrupted TADs or affected gene expressions which may improve patient outcomes.”

Alzheimer disease

Alzheimer disease (AD) is the single-most common neurodegenerative disorder, and it’s known to have genetic risk factors, including mutations in at least three genes: amyloid precursor protein (APP), presenilin 1 (PSEN1), and presenilin 2 (PSEN2). In a recent study published in Alzheimer’s & Dementia in April, researchers aimed to use WGS to examine rare mutations that contribute to AD risk. It was the first-ever WGS-based rare-variant association study in the history of AD research.

Researchers analyzed WGS data from a study of 2,247 participants from 605 multiplex AD families, along with a group of 1,669 unrelated individuals. They identified 13 new genetic areas where mutations appeared to increase AD risk, none of which had been previously associated with the disease.

Researchers concluded that their findings highlight several promising novel avenues for AD research and potential new targets for early treatment or even prevention of AD.