Rapid DNA sequencing promises rapid diagnosis of rare diseases

For children with rare diseases, it is usually it takes years to receive a diagnosis. This “diagnostic odysseyis filled with multiple references and a deluge of tests, seeking to uncover the root cause of the mysterious and debilitating symptoms.

A new DNA sequencing speed record could soon help families find answers to tough, life-changing questions faster.

In only 7 hours, 18 minutes, a team of Stanford Medicine researchers went from collecting a blood sample to offering a diagnosis of disease. This unprecedented turnaround is the result of ultra-fast DNA sequencing technology combined with massive cloud storage and computing. This improved method of disease diagnosis allows researchers to uncover previously undocumented sources of genetic diseases, shedding new light on the 6 billion letters in the human genome.

More … than 7,000 rare diseases affect 300 million people worldwide, 50% of whom are children. Among these diseases, 80% have a genetic component. The onset of some rare genetic diseases can be rapid and debilitating. Spotting the symptoms and identifying the root cause is a race against time for many families.

I am a biotechnology and policy researcher which works to improve access to innovative healthcare technologies. Whether simple and affordable tests or sophisticated and expensive gene therapies, medical breakthroughs need to reach people around the world. I believe ultra-fast DNA sequencing is key to expanding the network and accelerating the diagnosis of rare diseases.

A new Guinness World Record

the Human Genome Project, the first successful attempt to sequence a complete or “whole” human genome, took 13 years, from 1990 to 2003, and cost $2.7 billion. In 2014, the field of whole genome sequencing achieved another major milestone by reaching the $1,000 prize. Every year, the cost of sequencing continues to drop, driven by engineering and computational innovation.

In their quest for a world record, Stanford researchers turned to a DNA sequencing platform from the company Oxford Nanopore Technologieswho has developed a device that reads genomes by pulling large strands of DNA through pores comparable in size and composition to the openings of biological cell membranes. When a strand of DNA passes through the pore, the device reads the subtle electrical changes unique to each letter of DNA, thereby detecting the DNA sequence.

Thousands of these pores are distributed over a device called a flow cell. The researchers sequenced the genome of a single patient on 48 flow cells simultaneously, allowing them to read the entire genome in a record time of 5 hours and 2 minutes.

Ultra-fast DNA sequencing generated terabytes of data, which was transferred to a cloud-based storage system. In the cloud, algorithms scanned the genome, looking for tiny variations – mutations – in the DNA sequence that could help explain the origin of a genetic disease.

Rewrite the Diagnostic Odyssey

If the origin of a disease is thought to lie in the genome, the standard medical route is to prescribe a gene panel. This test sequences a list of predetermined genes for possible disease-causing mutations. Receipt of test results usually takes two to three weeks but can take up to eight weeksand may miss mutations in genes that are not on the list.

Shortening the sequencing and analysis process to seven hours and extending the sequencing of a few genes to the entire genome could fundamentally change the diagnostic odyssey. Ultra-rapid DNA sequencing has already made a difference in the lives of two children.

Matthew Junzman, a 13-year-old from Oregon, was rushed to Stanford Hospital and placed on life support. His heart was failing, and no one knew why. Doctors reduces the cause to two options: myocarditis, a reversible disease involving inflammation of the heart, or an incurable genetic disease.

In the Stanford study, doctors performed a super-fast DNA sequencing test, which quickly revealed that Matthew had a genetic condition. He was immediately placed on a transplant list and received a new heart three weeks later.

In the same study, a 3-month-old patient was admitted to pediatric hospital with seizures. Using the ultra-fast DNA sequencing process, doctors quickly spotted a mutation in a gene that explained the seizures. Standard tests would have initially missed this diagnosis.

Disease diagnosis is a global problem

Advances in healthcare technology usually come at a high price when they first become available. Business competition, cheaper materials and new generations of technology can help reduce costs. But infrastructure, policy and regulatory barriers all contribute to limiting global access.

Although the Oxford Nanopore technology is less expensive than several alternative sequencing devices, equipment and material costs are still prohibitive for laboratories in many countries. In the same way, less than 20% of low- and middle-income countries have modern data infrastructure. This removes the possibility of cloud computing in many places. https://www.youtube.com/embed/iHQQk2LUJVI?wmode=transparent&start=0 Researchers in Africa are working to ensure that African populations are represented and benefit from advances in genomics research.

Bringing ultra-fast DNA sequencing to these countries will mean investing in regional efforts to support genomics research. For example, the Human heredity and health in Africa The initiative invests in scientific infrastructure and workforce development to study the health and disease of African populations. Providing groups like these with the equipment and software needed for ultra-fast DNA sequencing will ensure that rare diseases that are more common in African populations do not go unexplored.

There is no approved treatment for 95% of rare diseases. The limited number of individuals affected by a given rare disease makes it difficult to study symptoms and design clinical trials. Create data sharing systems and develop regulations will be vital in enabling people to securely share their personal information between countries. the European joint program on rare diseases and the Global Alliance for Genomics and Health are making progress towards these goals, building bridges between rare disease communities around the world.

As ultra-rapid genome sequencing becomes a feature of hospitals in high-income countries, I believe it is important to consider how the wider rare disease community will gain access to these tools and benefit from the wave of new knowledge about diseases on the horizon.

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Kevin DoxzenPostdoctoral fellow in precision medicine and emerging biotechnologies, Arizona State University

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