Saving Children’s Lives with Big Genomics Data

It’s estimated than one in 30 children is afflicted by one of 8,000 or so genetic diseases that we have discovered. Thanks to progress in the world of genomic testing—including faster genomic sequencers and better algorithms for making more accurate diagnoses—doctors are making progress in identifying genetic diseases and getting children the treatment they need.
While the medical community has been studying genetic diseases for decades, its ability to correctly diagnose genetic diseases and prescribe a suitable course of treatment has been limited. That puts stress not only on the patient, but on the patients’ families too.
One group that’s pushing the envelope in genomics is Children’s Mercy Hospital of Kansas City. Shane Corder, a senior HPC system engineer at Children’s Mercy, shared his experiences with pediatric genomics during a keynote address at the recent Leverage Big Data conference in Florida.
“We know the causes of less than 5,000 of these genetic diseases,” Corder says in the keynote, which you can view on YouTube. “Diagnoses often take years. That’s unacceptable for families and ultimately it should be unacceptable to society as a whole.”

Stephen Kingsmore, executive director of Medical Panomics at Children’s Mercy Hospital of Kansas City, uses an Illumina sequencer.

Children’s Mercy is a leader in the adoption of genomics in a clinical setting, and has treated thousands of children and babies over the past few years. It has two primary types of patients, include newborns who display characteristics of a genetic disease—where time is critical–and children who have been unable to get an accurate diagnose elsewhere.
The hospital brings two main genomics tests to bear on these patients, including full-genome tests and partial genome tests. Genetic sequencing is a very data- and compute-intensive business. With more than 6.4 billion letters in a person’s DNA–which involves 22,000 genes that code for 100,000 proteins–there’s a lot of data to analyze.
It took 10 years and $3 billion to completely map the first human genome, which you will remember as the Human Genome Project. But thanks to technological advances over the years—including next-gen sequencers from Illumina and the Dragen Bio-IT processor from Edico Genome—geneticists, doctors, and technologists have whittled down the amount of time it takes to sequence a given person’s genome, which comes out to about 250GB per person.
“There are some fairly exciting new technological advances that we’re hoping to implement here in the center that will eventually let us go sub-24 hours on a full genome,” Corder says. “Currently our fastest sequence technology is pushing 50 hours for a full genome, from sample-taking to diagnoses.”
When Corder joined the team, the hospital was able to diagnose and begin treatment (using standard medical approaches mostly—gene therapy is something else entirely) of genetic diseases on about 47 percent of its patients. Now it’s up to 52 percent of its patients.
“Genomic sequencing is wonderful, but it’s not infallible,” he says. “When a child is waiting for a diagnoses, a lot of times the disease lays waste to their body or their mind. With quicker diagnoses and treatment, that can ultimately change the child’s life forever.”
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