HomeScienceGeneticsHow a pediatric hospital's rare disease sequencing system unlocks the entire genome

How a pediatric hospital’s rare disease sequencing system unlocks the entire genome

The Children’s Mercy Kansas City Research institute announced on Monday that it’s building what it calls the “most advanced genomic sequencing system in the world.”

This claim refers to the work Children’s Mercy does through its Program Genomic Answers for Kids (GA4K). The health system rolled out the program three years ago with the goal of collecting genomic data and health information for 30,000 children and their families — it expects to create a database of at least 100,000 genomes over seven years. GA4K is already enjoying an important milestone: providing 1,000 children with rare disease diagnoses based on genome sequencing.

The program is unique because it uses 5-base genomic sequencing. This is a new technology that combines multiple genomic technologies previously used in a single test, said Dr. Tomi Pastinen, the director of the Center for Genomic Medicine at Children’s Mercy Kansas City, in an interview.

“What we can do with 5-base genomic sequencing immediately in the clinical space is to replace multiple, usually sequential, genetic tests performed on a patient in a single combined test and accelerate the analysis of multiple different types of genetic diseases,” he said.

In addition to the ability to diagnose all types of genetic diseases, 5-base genomic sequencing opens up our ability to “read the genome beyond the currently interpreted clinical genome,” added Dr. Pastin to it.

Genomic sequencing tests currently only interpret the protein-coding portion of the genome, which Dr. Pastinen claimed it makes up only about 2% of the human genome. The use of 5-base genomic sequencing reveals the 98% of the genome that is not currently being analyzed clinically. This is important because 60% of cases involving children, where doctors suspect a genetic disease, remain unresolved with current genetic testing methods, said Dr. Pastins.

According to Dr. Pastinen is diagnosed with an average of about 30-40% of rare disease cases in children. He said 5-base sequencing can bring that percentage of centimeters closer to half.

dr. Pastinen claimed that the database being built for GA4K will be the first of its kind for a number of reasons. The first is its scope and the second is its comprehensiveness. While there have been studies of rare diseases in children that focus on specific indications, this program collects data from as many pediatric patients as possible who have been evaluated for unresolved disease, said Dr. Pastins.

This data comes from Children’s Mercy patients, as well as patients from the 17 partner institutions participating in GA4K, including two NYU Langone Health and the University of Nebraska Medical Center, said Dr. Pastins. These partners send their patients’ genomic samples for testing at Children’s Mercy.

“The program is unique because of the in-depth data per patient — and because it’s dynamic,” said Dr. pasins. “And what that means is that we actually query the genome throughout the patient’s life. The patient and his medical file live with us. If there are changes in the medical record or changes in our understanding of the genome, we update the analysis in real time and actually share the data in real time with the scientific community and physician scientists.”

The 5-base sequencing used in GA4K is an extension of previous work done by pediatric hospitals to better understand rare diseases in children. For example, based in San Diego Rady Children’s Institute for Genomic Medicine is also a pioneer in the space, with a strong precision medicine program that leverages rapid genomic sequencing to diagnose patients as quickly and accurately as possible. This program was championed by dr. Stephen Kingsmorewho was director of Children’s Mercy’s Center for Pediatric Genomic Medicine from 2011-2015.

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