CLARITY Challenge | Families & Results

CLARITY 1 Families & Results

 Family 1 (Foye)

AJ Foye (parents Sarah and Patrick Foye), is an 11-year-old currently in sixth grade. He was born with muscle weakness and was delayed in his motor development as an infant. Because of low muscle tone, he had difficulties with feeding as a baby, has curvature of the spine (treated with a brace) and is vulnerable to respiratory infections. He fatigues easily and requires breathing assistance at night with a nasal ventilator. He walks for limited distances (up to four city blocks) and uses a stroller or scooter for longer distances.

AJ was diagnosed with centronuclear myopathy, a rare muscle disease, based on a muscle biopsy at 13 months of age. AJ was also diagnosed with sensorineural hearing loss as an infant and wears hearing aids in both ears.

AJ appears to be the only member of his family with muscle weakness. He has tested negative for 13 genes previously associated with muscle weakness, including some discovered at Boston Children’s Hospital.

The CLARITY Challenge identified alterations in a gene called titin (TTN) as the likely cause of AJ’s muscle weakness, and six teams also identified mutations in a gene called GJB2 as the likely cause of AJ’s hearing loss. Both of these are recessive mutations, meaning that both of AJ’s parents are carriers for each of these genes, but are not themselves affected.

Since titin has previously been associated with heart problems, the finding suggests that Adam should be monitored more regularly with cardiac testing. The Foyes could also have prenatal testing for titin should they decide to have another child.

The titin gene encodes a spring-like protein that is part of the main contractile structure in muscles (known as the sarcomere).

Alan Beggs, PhD, CLARITY co-organizer and director of the Manton Center for Orphan Disease Research at Boston Children’s Hospital, notes that even if titin had been suspected previously, sequencing it individually in Adam’s family would have taken nine months, because of the gene’s enormous size. (Sequencing the entire genome at once, and ignoring everything except the gene of interest, is actually faster and cheaper.) Beggs now plans a research project to model the titin defect in zebrafish, allowing large-scale testing of drugs that might correct the defect.

 Family 2 (Burns)

The Burns family sought genetic testing after Liam Burns died 12 days after birth from multiple cardiac defects: an underdeveloped (hypoplastic) right heart, a narrowed artery to the lungs (pulmonary stenosis) and a block in electrical conduction (a type II atrioventricular block). Liam’s sister Eloise, born two years later, is a healthy baby with no heart problem

Three other family members also have right-sided heart defects of lesser, varying severity:

  • Liam’s 6-year-old first cousin has an arrhythmia known as right bundle branch block (RBBB) that does not cause any symptoms (her sister, 4, is free of heart problems).
  • Liam’s maternal aunt (the cousins’ mother) has RBBB that does not cause symptoms. Liam’s father Casey has a heart block and arrhythmia requiring a pacemaker, as well as structural defects (coarctation of the aorta and pulmonary stenosis).
  • Liam’s father and aunt (who are brother and sister) had a third sibling who died as a newborn from heart complications.

The CLARITY Challenge identified mutation of a gene called TRPM4 as the likely cause of the heart rhythm disturbances in the Burns family. It encodes a protein that acts as a gate, allowing electrical charges in and out of cells. Build-up and discharge of these charges is part of normal muscle function.

The cause of the family’s structural heart defects remains uncertain. They may also be caused by TRPM4, or the family may have an unrelated mutation in a different gene. The CLARITY team plans to investigate further in consultation with experts in cardiac genetics.

Family 3

The third child, a 7-year-old boy, was diagnosed with nemaline myopathy, another rare muscle disorder. His case is relatively mild, so he can breathe independently and walk with a walker, occasionally using a stroller or scooter for longer distances. In addition to muscle weakness, he was born with clubbed feet, pectus excavatum (sunken chest), osteoporosis and a dislocated elbow. His parents are unaffected.

The CLARITY Challenge did not lead to any firm gene identifications for this family. Mutations in seven different genes were cited as plausible possible causes, and the case was especially strong for four genes. Of these four, two genes have been linked with nemaline myopathy in the past, and two have not but were flagged by multiple teams. Whether those genes are actually connected to the disease remains to be seen with further research.

CLARITY Undiagnosed Families & Results

Alex Yiu, age 10, enjoys watching Curious George and Frozen on his iPad. He started life as a normally developing, active, happy-go-lucky child, but now has an unknown, progressive neurodegenerative condition.

When Alex was around 3½, his parents noticed awkward walking, and, at age 4, falling. At age 5, his speech began to decline, and he stopped walking entirely at age 6. By age 7, he lost arm and hand control and the ability to chew. He then lost trunk and neck control, developed swallowing problems and went from needing pureed foods to requiring tube feeding due to food aspiration. He has suffered very painful muscle spasms and has begun having seizures. The past year, Alex has had respiratory issues requiring breathing therapies and sometimes oxygen support.

Alex can no longer talk, but can indicate a yes/no with his eyes. Until last year, he was able to participate at grade level at school. For a while, he used an eye-gaze device to communicate through a tablet, but loss of head and neck control have made it hard for him to use it. Alex is now trying out a headset device that measures brainwaves.

The family has spent four years going to neurologists and research institutes in multiple states and internationally with many rounds of blood work and invasive testing. Alex applied to the National Institutes of Health's Undiagnosed Diseases Program, but the program felt it could not help him.

In the last six months, Alex's illness has progressed noticeably. He has been in the hospital nine times this year alone for G-tube placement surgery, seizures, respiratory distress, pneumonia and infection. He can no longer move himself in a wheelchair or sit or stand independently, and now requires 24-hour-care for all activities of daily living and monitoring of his oxygen levels.

"It's exhausting just to keep up with his medicines and his therapies," says his mother, Caroline Yiu. "We haven't had the time and energy to do a lot of research."

Alex has a sister Elaine who is healthy. The family went into the CLARITY Undiagnosed Challenge with cautious optimism. "Over the years, we've become more cynical about testing, we always have this hope, 'maybe this time they'll figure it out,'" Caroline says.

What CLARITY Undiagnosed found

Alex was found to have "variants of unknown significance" (VUS) in three different genes that seemed possibly related to his condition, but would require more work to establish as causative. None of the genes has ever been associated with any human disease.

Two of the three variants confirmed candidates identified by another multi-institution research team that had investigated Alex's case. One of these was a large deletion of DNA that included a gene called RUNX3, known to be involved in nervous system development and the formation of neurons. It was de novo, meaning the variant was present in Alex but not in either of his parents—it arose some time during Alex's early embryonic development.

The second finding involved two different variants in a gene called SLC26A1, one inherited from each of Alex's parents. The gene is involved in ion channels (gate-like structures that let charged molecules in and out of cells) that are important in the brain and liver. The variants have also been found in healthy people, making them weaker candidates than the other variants described above, but they have been found only in isolation, not combined as in Alex.

The third variant had also been noted by the earlier research team but had been ruled out. This variant, in a gene called GASK3, was also de novo. GASK3 is highly expressed (very active) in the brain and regulates several important processes in the body. It has been hypothesized to play a role in certain forms of memory impairment, including Alzheimer's disease, and may be involved in regulating other genes. One genetic pathway GASK3 is thought to regulate has been implicated in a disorder that presents similarly to Alex's.

For Alex's parents, the results are mainly confirmatory. "Our secret hope was that there would be a more 'for-sure' answer, something that the other teams missed," says Caroline. "But in a way, it is reassuring that all 26 international teams have looked at Alex's case, and two of the three genes they identified are ones that our core team has been focusing on."

Alex's parents now hope to have functional studies done to see whether the genetic variants are actually disease-causing and if so, what they do and how. They plan to share the findings with the other researchers who are investigating Alex's case and connect them with the Manton Center for Orphan Disease Research at Boston Children's for collaborative research.

"I'd really like to see if there are more patients out there," Caroline adds. "I can't imagine Alex is the only one in the world with something like this. If there were other patients we might be able to find more data, and maybe these families have found something that works for them. I'd also like to find more researchers that are doing studies on these genes, and see if we can add to what they're doing, and vice versa.

"To find the disease causing genes will help Alex and other children like him with diagnostics and treatments that would, we hope, offer an improved quality of life."

Jeremy Hobbs, age 7, weighed only 4 lbs, 3 oz at birth. No one knew why he was so small. He had very bad reflux and wasn't gaining weight. At three months, his parents noticed nystagmus, or wobbling of his eyes. By 4 months he had gone completely blind.

The MRI showed delayed white matter development in his brain. His parents were told he probably had a leukodystrophy, but this was later ruled out and his white matter became more normal on subsequent MRIs.

Jeremy's main symptoms are severe low muscle tone (hypotonia) and weakness, as well as craniosynostosis, in which the plates that form the skull fuse too soon, putting pressure on the brain which has no space to expand. Jeremy has endured multiple operations to separate the skull bones and relieve the pressure. These have relieved his symptoms for a time and enabled his vision to come back, but his skull bones have repeatedly re-fused, causing the pressure in his head to return, so much that surgeons described his brain as "exploding" out of his skull.

The high pressure made Jeremy throw up, lose his vision and suffer terrible headaches. He became terrified of pain and has been diagnosed with post-traumatic stress disorder. "Every time he has a headache, he freaks out, thinking he will have to have surgery," says Angela Hobbs, Jeremy's mother.

Jeremy has had 38 surgeries to date, including urologic surgery and two heart operations to correct a blocked pulmonary valve. For unknown reasons, he has discrepancies in muscle strength on the two sides of his body, leading one leg to be shorter than the other.

Jeremy cannot speak, but does well in academics (he is in first grade) and can communicate with writing and with sign language. The family has visited multiple cities in search of answers. All genetic tests have come up negative. The doctors suspect some kind of metabolic disorder. Jeremy's two siblings are unaffected.

"We just want our son not to be in so much pain," says Angela. "We would love an answer and a treatment, if not a cure."

What CLARITY Undiagnosed found

For many of the other Challenge families, several teams reported the same variant. But for Jeremy, nearly every team had a different guess.

Since Jeremy has craniosynostosis, the teams tested for known craniofacial syndromes but, consistent with previous testing, he had no positive findings. However, one of the teams reported that Jeremy has a small genetic deletion in the gene EFNB1 that occurred in a "mosaic" pattern, affecting only some of his cells. Despite many prior genetic evaluations, including exome sequencing, this mutation was a new finding, likely because mosaic mutations are difficult to detect.

EFNB1 is known to cause craniofrontonasal dysplasia, a condition that includes craniosynostosis, asymmetry of the lower legs and hypotonia — all features Jeremy has. Interestingly, the condition is only reported in males with mosaicism of this gene. The diagnosis does not explain all of Jeremy's features, so it could represent an "expansion of phenotype," further describing a spectrum of a disorder.

The Hobbs have enrolled Jeremy in the Manton Center, which will seek to confirm the mutation in his blood, saliva and possibly a skin sample, and then to determine the degree of mosaicism, whether the mutation was inherited or de novo and its role in Jeremy's health problems.

Though many of Jeremy's physicians had suspected a metabolic disorder, none was identified in the Challenge.

"The Manton Center will try to figure out the implications of what the teams found and go from there," says Angie. "We were surprised to see that they found something and I'm curious to see where this goes. We're really glad for this opportunity. It would make a difference to be able to tell the doctors that there's a diagnosis, so they'll be less scared about treating him."

Jeff Lowe, age 64, was a world-renowned mountain climber who was on the cover of Sports Illustrated in 1978. Around 1998, he began having odd episodes where he would lose his balance and even fall unexpectedly—the onset of a progressive neurologic disorder that has gradually robbed him of his climbing life and landed him in a wheelchair. He got a power wheelchair in 2009, and today continues to live fully, mentor young climbers and enjoy the outdoors from the chair. Last summer he got a feeding tube and he uses supplemental oxygen at night. He spent nearly two and a half years on hospice but recently came off. Jeff has difficulty speaking, but is an excellent writer and communicates through a speaking device or his partner Connie interprets for him.

Amyotrophic lateral sclerosis (ALS) and multiple sclerosis have been ruled out. Initially, Jeff was diagnosed with multiple sclerosis and then olivopontocerebellar atrophy (OPCA), a rare condition involving the degeneration of neurons in specific areas of the brain, but in 2009, this diagnosis was withdrawn. Broadly, he is considered to have a motor neuron disease of unknown origin, but a new feeding formulation called Liquid Hope has allowed him to regain some strength.

"Everybody kind of makes up their own diagnosis—they need to write treatment orders," says Connie Self, his partner and caregiver. "Without a diagnosis, you fall through the cracks and can't get prescriptions and treatment approved."

Jeff and Connie are glad to be part of CLARITY Undiagnosed. "We thought it was a tremendous opportunity we could never get otherwise," says Connie. "We're hoping to learn something that would be helpful in terms of making Jeff more comfortable, and if there's something disease-altering, we'd be thrilled."

A documentary about Jeff's life and climbs, Jeff Lowe's Metanoia (narrated by Jon Krakauer) is currently making the rounds of film festivals all over the world.

What CLARITY Undiagnosed found

The CLARITY teams identified several different genetic variants, two of which were thought worth highlighting. One variant, reported by four teams, and considered by some to be "possibly pathogenic," was in a gene called CSF1R. Mutations of CSF1R are known to cause progressive loss of motor function and cognitive and behavioral changes. Although Jeff's mental functions are completely normal, this variant was considered a potential cause for his progressive weakness; however, it was ultimately ruled out because the particular change in Jeff's CSF1R gene is also found in about 1 in 1,000 healthy people.

Another variant, in a gene called AARS, was reported by a single team that had looked at DNA regions that can help control gene expression. Mutations in this gene have been reported to cause disorders ranging from problems with peripheral nerves, which Jeff does not have good evidence for, to defects in the brain. The CLARITY teams reported a unique type of AARS mutation in Jeff that is predicted to create a protein that is larger than normal. This does not appear to have been seen before, so the implications are unknown. However, this variant can now be looked for in Jeff's healthy brother and sister, and in additional unaffected individuals, to determine whether it correlates with disease.

For now, the family is submitting a new blood samples from Jeff to study his cells and see if they contain proteins with altered function. In addition, Jeff's physician has a collaborator who studies a gene associated with SCA36. Through a research collaboration with the Manton Center, that gene will be tested in Jeff.

The Challenge again ruled out a diagnosis of ALS.

"There also appears to be no smoking gun for Jeff's family, and that's good news," says Connie. "We're feeling positive about what they learned, and it makes sense what they learned."

Jeff notes that his interest in CLARITY Undiagnosed goes far beyond his own disease process. Connie agrees.

"We know this has to be of value to medicine, we're so excited to have been a part of this," she says. "We're grateful for any and all information and excited for the future of medicine. We feel this collaborative effort is so important. Usually medicine is competitive, but we need to get over that! The more people collaborate, the more information can move quickly. Now that NIH has a database and this information is going to be collected, maybe we will have more knowledge that can help a lot of undiagnosed people."

Katia Moritz, 48, is a clinical psychologist and creator/director of the forthcoming documentary, Undiagnosed, which has been following the patients in the CLARITY Undiagnosed Challenge for the past three years and is filming parts of the Challenge.

Katia was healthy until undergoing an endoscopy in 2010. Almost immediately on waking, she had flu-like symptoms, low-grade fever, pain in her upper right quadrant and a feeling of being impaled by a sharp object. The symptoms became episodic, lasting 72 hours on average. No evidence has been found of any endoscopy complication, such as infection, that would explain her symptoms.

Over time, Katia has begun experiencing other problems: swallowing difficulties, a feeling that her esophagus is swollen, debilitating headaches, visual disturbances, pain behind her eyes, muscle fatigue and cramping, hair loss, strong urges to sleep and blood-flow problems in her extremities accompanied by a burning sensation and mottled, purplish skin. She has been diagnosed with a carnitine deficiency, autonomic and peripheral neuropathy, a spinal hemangioma, pulmonary changes and esophageal and vocal cord dysfunction. The muscle problems are getting worse and Katia now sometimes has difficulty breathing.

Katia hopes the CLARITY Undiagnosed Challenge, together with her film, will help raise awareness, give hope and change how the medical community approaches rare, hard-to-diagnose conditions. "For myself, the goal is to learn more about my condition and where I can go for help, what to do next," she says.

What CLARITY Undiagnosed found

The Challenge found no potential new genes, but had two confirmatory findings and helped rule out a gene identified previously.

The teams first affirmed that Katia is a carrier for a variant in GBA, the gene associated with Gaucher disease, whose major symptoms include an enlarged liver and spleen, anemia, easy bruising caused by a decrease in blood platelets, lung disease, and bone problems such as pain, fractures and arthritis.

Katia was also confirmed to be a carrier for familial Mediterranean fever. Caused by the gene MEFV, this is an episodic inflammatory disorder that is often accompanied by fever and sometimes rash or headache. It is traditionally a recessive condition, requiring two genetic changes (one from each parent) to cause symptoms, but in rare cases, symptoms can present from only one genetic change. Another genetic change was found in NLRP3 which may be involved in the same pathway as MEFV and modify its effects in Katia.

One genetic change that had previously been reported to Katia was ruled out through the Challenge. A DCTN1 variant had been reported as causative of a rare condition called Perry syndrome, but the variant is actually found somewhat commonly in the healthy population.

Because the symptoms seemed to begin soon after endoscopy, many of the teams looked for pharmacogenomic variants — differences in genes involved in metabolizing drugs — thinking that the anesthesia for the procedure might have triggered her symptoms. Although some teams found genetic differences, the judges did not deem the findings plausible, since adverse anesthesia reactions would be expected to be constant, not episodic. So whether the endoscopy could have triggered something as yet unknown, or whether the timing was simply coincidental, is still unknown.

Katia is enrolled with the Manton Center, which will further analyze her sequencing results. Based on her clinical picture, it was recommended she see a rheumatologist.

Dominic and Bridget Nuccitelli both passed away in infancy after cardiorespiratory arrest, Dominic in 2001 and Bridget in 2007. Their development had been slow, they had low muscle tone, making them somewhat "floppy" and neither gained weight well. Each had distinctive features—such as Bridget having multiple birthmarks, large soft spots on the top and back of her head, and a very small jaw (micrognathia). Despite these, doctors hoped they just had a slight delay and that they would catch up with their peers, as they still appeared somewhat in normal range on most counts. Since Bridget was born prematurely, that was thought to account for her delays.

At times, though, they were listless and became more floppy. Dominic's physicians in the ICU suggested he might have a mitochondrial disease, and one mentioned a specific mitochondrial disorder known as Barth syndrome. After Bridget's crisis event, doctors were more suspicious of a mitochondrial or possibly metabolic disorder.

Six living siblings each have varying symptoms that are chronic but not currently life-threatening; their parents, Marie and Chris Nuccitelli, call them "quirks." The children's symptoms include hypotonia, motor difficulties, temperature regulation issues, developmental delays, sleep disturbances and immune deficiencies. One son has leg, neck and shoulder dystonia—muscle tightness that gave the appearance one side of his body had grown taller than the other. A daughter has milder dystonia, most often noticed in her hands, aggravated by writing. Several siblings have neurologic symptoms in response to viral infections. A son has multiple food allergies and, along with three sisters and Marie, eosinophilic esophagitis, an allergic reaction that inflames the esophagus. The same son and another daughter have micrognathia, macrocephaly (an enlarged head) and difficulty swallowing. Marie and Chris have various symptoms, too.

It's been hard finding a doctor that feels able to care for them, as one specialist's field of expertise often doesn't cover all the issues. The result is a lot of referrals. "We get bounced around a lot," says Marie. "I can't even keep track any more of all the doctors we've seen." Many of the specialists suspect a metabolic or mitochondrial DNA abnormality, because these can cause a broad range of symptoms of variable severity. However, mitochondrial DNA and metabolic tests have thus far come back conclusively negative.

The family hopes the CLARITY Undiagnosed Challenge will have more to say about possible mitochondrial mutations. If mutations are found in mitochondrial DNA (as opposed to DNA in the cell nucleus), the family "quirks" would only be passed on by the girls, not the boys. "My dream would be just to know, 'this is how your children died, this is how it may or may not be affecting the rest of you,'" Marie says. "There's always that question of, 'is there going to be another crisis event? Is there a day when another one of my children stops breathing?' For me it's important to have a genetic answer that's evidence-based. We wouldn't have to keep doing all these tests that are stressful and taxing financially."

What CLARITY Undiagnosed found

Sequencing of Dominic, Bridget, their parents and one sister identified genetic alterations, or variants, in three genes (CACNB2, DSP and CSRP3) that have been linked to heart arrhythmias. Arrhythmias can vary in severity, with the most severe cases resulting in sudden cardiac death. Marie carries two of these variants and Chris has one; Dominic and Bridget each inherited one variant from each parent. The two affected genes in Dominic and Bridget are known to be involved in ion channels responsible for sodium and calcium flow in and out of cells, which can regulate the heart's rhythm. All three findings are considered variants of uncertain significance (VUS) since it hasn't been established whether they actually alter the genes' function, or are benign changes in the genes.

Marie and Chris are interested in investigating the family's cardiac health further, noting that they and two of their sons had previously been found to have unusual patterns on EKGs. The boys were sent for echocardiograms, but beyond that they were not referred for further follow-up.

In addition to the heart-related genes, a variant was found in the gene TNFRSF13B, known to be involved in common variable immune deficiency (CVID), a group of disorders that impair the immune system. This variant could potentially explain the IgA deficiency in two children, as well as the eosinophilic esophagitis (affecting Marie and four children), but without further testing its effect on gene function is unclear and it is still considered a VUS.

Investigations of a genetic cause for the dystonia in two of the children, as well as other family symptoms, found no variants of potential relevance.

Marie and Chris feel participating in the Challenge was worthwhile, even though it yielded no definitive answers. "It gave us some things that are a little more substantive to consider, rather than just guessing," says Marie. And as Chris put it, "We're still lost in the wilderness, but now we have a compass so we have a little bit better idea of where we're going."

The family now has the opportunity to enroll in the Manton Center study to investigate how the variants discovered by the challenge affect the genes' function.