On a sunny day near Perth, Australia, two-year-old Scarlett Whitmore stares intently at her left shoulder. With absolute concentration, she raises her head to look at her physical therapist, who is holding onto Scarlett’s arm to keep her steady. “I’m so proud of you,” her mother, Kate Whitmore, cheers as she films the session with her camera phone. Looking proud herself, Scarlett rolls onto her back, stretches out her arms and legs, and smiles broadly. Her smile is infectious. Her green eyes grow wide whenever she flashes her toothy grin—the inspiration for “Scarlett’s Smile,” the name of the foundation her parents started to raise money for Scarlett’s medical expenses.
Scarlett has poor hearing and vision and hasn’t learned to sit up on her own, stand, walk, or speak. And for the first year of her life, her parents had no idea why. Just after Scarlett was born, “I remember my husband saying in the hospital, ‘She doesn’t cry,’ and I just said, ‘She’s a good baby,’” says Kate. After five months, however, Scarlett failed to meet typical milestones, such as making eye contact with her parents. And then the tests began. Full workups on her blood and spinal fluid didn’t suggest anything amiss. Neither did a test for large-scale chromosomal abnormalities. A viral screen revealed that Scarlett had been exposed to cytomegalovirus, a known cause of brain damage when contracted during development. But a blood sample from Scarlett’s newborn screens showed she was clear of the virus at birth. “So, we were back to the drawing board,” says Kate.
Months passed, and more tests came back negative. The Whitmores focused on early intervention therapies for Scarlett, trying to stay positive and enjoy spending time with their daughter. But whenever Scarlett cried, Kate agonized, not knowing if her daughter’s pain resulted from expected things, such as teething, or from her mysterious illness. “It was just eating me up not knowing what was wrong with her,” she says. While Scarlett slept, Kate researched her symptoms, which ranged from visual impairment to hypotonia (muscle weakness), trying desperately to figure out what was causing them in her child.
Finally, Kate came across information about an organization in Seattle, Washington, called MyGene2 that was offering to sequence and analyze the genomes of patients with undiagnosed diseases for about $700 per sample. Kate had heard of this type of sequencing before, but it was nearly impossible for the family to access it in Australia, and Scarlett’s geneticist had recommended against it—the approach is not routine in Australian hospitals, making it more expensive and the data more difficult to interpret. Nevertheless, just after Scarlett’s first birthday, the Whitmores sent saliva samples to MyGene2, where scientists sequenced each family member’s exome—the 1.5 percent of the genome that encodes proteins. Researchers at Washington University in Seattle then compared Scarlett’s exome sequence to databases containing thousands of sequences in search of a mutation that could explain her symptoms.
In January 2017, a verdict emerged: Scarlett had a rare mutation in the gene encoding G protein subunit beta 1 (GNB1), a component of a molecular switch protein complex known to regulate some neuronal functions. The Whitmores learned that Scarlett had not inherited the mutation from them, and that the disease will most likely spare her heart and lungs, giving them huge peace of mind. “This was worth its weight in gold,” says Kate. Along with just 30 other patients with GNB1 mutations worldwide, the Whitmores enrolled in a research study describing the mutation’s effects, and a paper reporting the findings is now being prepared for publication.
Just ten years ago, the Whitmores’ story would have been very different. Back then, sequencing and analyzing a single exome cost between $70,000 and $80,000 and took months to complete. These days, clinicians can easily order an exome sequence and analysis, and at a commercial cost of around $700-$5,000 the test has become widely available and is often covered by insurers. Organizations such as MyGene2 and larger, national organizations, such as the Centers for Mendelian Genomics (CMG) and the Undiagnosed Diseases Network (UDN), are using the approach to help diagnose rare diseases, and to end what clinicians call the “diagnostic odyssey” for hundreds of families every year. “Exome sequencing has really been revealing,” says Robert Kliegman, a neonatologist and rare disease specialist at Children’s Hospital of Wisconsin in Milwaukee.
Helpful as it’s been, however, exome sequencing only resolves 25 percent to 50 percent of undiagnosed cases. Researchers and clinicians are now exploring new tools, such as whole-genome sequencing and RNA analysis, developing better techniques to analyze sequence data, and finding ways to get patients with the same diseases connected faster. This effort is making rare disease diagnosis likely to experience another revolution in the next decade.
Exome explosion
About 15 years ago, Kliegman and his colleagues started noticing a huge unmet need at Children’s Hospital of Wisconsin. Families would end up there after years of searching for a diagnosis, and there was no system in place to settle their cases. Then chair of the pediatrics department at the Medical College of Wisconsin (MCW), Children’s Hospital’s academic partner, Kliegman began bringing together specialists to discuss undiagnosed cases in detail. But the team wasn’t galvanized until it came up against the case of Nic Volker, a young boy with severe inflammatory bowel disease. By the time Volker turned four, his intestines were dotted with holes, he’d had a colostomy, and he mainly ate through a feeding tube. The hospital’s gastrointestinal specialist couldn’t make sense of the disease, leaving Volker’s doctors with no options beyond treating his symptoms.
In 2009, at the request of Volker’s pediatrician, a team at MCW sequenced the boy’s exome. The $75,000 bill was covered by funds raised by Howard Jacob, the founding director of MCW’s genetics center, who hadn’t expected to implement exome sequencing there for at least another five years. Analysis of Volker’s genetic data picked up more than 16,000 gene variants, and four months of sifting through those variants revealed that a mutation in X-linked inhibitor of apoptosis protein (XIAP), a gene on the long arm of the X chromosome, was the likely culprit behind his illness.1 XIAP mutations were already associated with X-linked lymphoproliferative disease, an immunodeficiency disorder that leaves boys unable to fight off Epstein-Barr virus. Because the gene only affects immune cells, a cord blood transplant to replace Volker’s immune cell progenitors was enough to essentially cure him, says Kliegman. The case became nationally renowned as the first time DNA sequencing saved a patient’s life.
