How Pediatric Hospital's Rare Disease Sequencing System Unlocks the Entire Genome - MedCity News

The Children’s Mercy Kansas City This was reported by the research institute on Monday is being built what it calls “the world’s most advanced genome sequencing system.”

This statement refers to the work that Children’s Mercy does through its own Genomic Answers for Kids (GA4K) program.. The health system launched the program three years ago with the goal of collecting genomic data and health information on 30,000 children and their families — a database of at least 100,000 genomes is expected to be created over seven years. GA4K is now enjoying an important milestone: providing 1,000 children with rare disease diagnoses based on its genome sequence.

The program is unique because it uses 5-base genome sequencing. It’s a new technology that combines multiple genomic technologies that have been used before in one test, Dr. Tommy Pastinen, director of the Center for Genomic Medicine at Children’s Mercy in Kansas City, said in an interview.

“What 5-base genome sequencing allows us to do immediately in the clinical space is replace multiple, usually sequential, genetic tests that are performed on a patient into one combined test and accelerate the analysis of many different types of genetic diseases,” he said.

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

Genome sequencing tests currently interpret only the protein-coding portion of the genome, which Dr. Pastinen says makes up only about 2% of the human genome. Using 5-base genome sequencing revealed 98% of the genome currently not clinically analyzed. This is important because 60 percent of cases involving children in which doctors suspect a genetic disorder remain unresolved with current genetic testing methods, Dr. Pastinen said.

On average, about 30-40% of pediatric cases of rare diseases receive a diagnosis, according to Dr. Pastinen. He said 5-base sequencing could help bring that rate closer to half.

Dr. Pastinen claims that the database being built for GA4K is the first of its kind for several reasons. The first is its scale and the second is its comprehensiveness. Although there are pediatric rare disease studies that focus on specific indications, this program collects data from as many pediatric patients as possible who have been evaluated for an unsolved disease, Dr. Pastinen said.

That data comes from Children’s Mercy patients as well as patients at 17 partner institutions that participate in GA4K, two of which include NYU Langone Health and the University of Nebraska Medical Center, Dr. Pastinen said. These partners send their patients’ genomic samples for testing at Children’s Mercy.

“The program is unique because of the depth of patient data – and because it is dynamic,” said Dr. Pasinen. “And that means we’re actually querying the genome throughout the patient’s lifetime. The patient and his medical record 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 at GA4K expands on previous work done by pediatric hospitals to better understand rare diseases in children. For example, based in San Diego Children’s sake The Genomic Medicine Institute is also a pioneer in the space with a strong precision medicine program that uses rapid genome sequencing to quickly and accurately diagnose patients as early as possible. This program was supported by Dr Stephen Kingsmorewho served as director of the Center for Pediatric Genomic Medicine at Children’s Mercy from 2011-2015.

Photo: Andy, Getty Images

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