By Julia Karow
Researchers at Baylor College of Medicine, in collaboration with Life Technologies, provided another example this week of how whole-genome sequencing can provide not only a molecular diagnosis for patients with rare genetic disorders but can also point to effective treatments that their doctors would otherwise not have considered.
In a paper published in Science Translational Medicine today, the researchers, led by Matthew Bainbridge and Richard Gibbs at the Human Genome Sequencing Center at Baylor, describe how sequencing the genomes of the teenage twins of Life Technologies' chief information officer, Joe Beery, led them to a simple drug that helped improve the symptoms of their disease, dopa-responsive dystonia, a movement disorder.
Baylor is now taking steps to make whole-genome sequencing available to other patients with inherited disorders who could benefit from it. If all goes according to plan, Baylor hopes to be able to accept the first patient samples for whole-genome analysis in a CLIA-certified laboratory this fall, according to Jim Lupski, a professor of molecular and human genetics as well as of pediatrics at Baylor, who was involved in the study.
The story of the Beery twins, Noah and Alexis, started when they were diagnosed with cerebral palsy at age two — as it turned out, an incorrect diagnosis. Three years later, based on Internet research by their mother, they were diagnosed with dopa-responsive dystonia and successfully treated with L- dihydroxyphenylalanine, or L-DOPA, a precursor of dopamine, which improved many of their symptoms.
But other symptoms persisted over the years, and about 18 months ago, the girl started to develop severe breathing problems. When Linh Hoang, director of genomic medicine at Life Tech, heard about his colleague's children, he said he recognized "that the condition would be very amenable to next-generation sequencing." The twins had tested negative for mutations in two genes known to cause dystonia, GCH1 and TH, for which clinical genetic testing was available.
Hoang put the family in touch with the Baylor researchers, who have been collaborating with Life Tech on other projects and maintain a fleet of the company's SOLiD sequencers. Life Tech agreed to support the study, which was approved by Baylor's institutional review board, with reagents.
Lupski said that it was not clear at the time whether the twins' remaining symptoms resulted from their L-DOPA treatment or from the underlying disease, and they hoped to get clues to this from a molecular diagnosis. "After exhausting the clinically available tests at the time, we sought to see if we could find the potential genetic susceptibility locus by virtue of sequencing the whole genome," he said.
Baylor researchers sequenced the twins' genomes on the SOLiD 4 platform, generating 50-base reads from 1-kilobase mate-pair libraries, which they aligned to the human reference genome. On average, they covered each child's genome about 30-fold. They called about 2.5 million single nucleotide variants in each sibling, about 1.6 million of which they shared. The scientists then filtered those variants for rare, protein-altering mutations, leaving them with 77.
Assuming that the twins suffered from a recessive disorder, the researchers then honed in on genes that contained homozygous or heterozygous mutations in both alleles, leaving three candidate genes, and they annotated those with known functional data and disease associations. They also used array-CGH to look for copy number variants but did not find any potentially pathogenic ones for dystonia.
Two of the three candidate genes had no known function. The third gene, SPR, encodes an enzyme that helps produce a cofactor, BH4, which is required not only for making dopamine, but also serotonin and noradrenaline. In fact, SPR had been previously associated with dopa-responsive dystonia in a small number of patients, but no clinical genetic test was available for it. "What happens often in medical genetics and the practice of medicine is, there are discoveries, but then there is time until there are clinically available tests for these problems," Lupski said.
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The SPR mutations were validated by Sanger sequencing, and further testing of family members showed that the twins had inherited a nonsense mutation from their mother and a missense mutation from their father, while their unaffected brother did not inherit either mutation.
The results suggested that the children could benefit from treatment with 5-hydroxytryptophan, or 5-HTP, a precursor of serotonin, in addition to L-DOPA. "The key is that two neurotransmitter pathways are involved here, versus a single one," Lupski explained, "so you have to not only try to correct the disturbance in synthesis of dopamine but see if you can also do some treatment of the pathway to serotonin synthesis." Other treatment options included serotonin reuptake inhibitors, he said. "Those options were not available until you made a specific molecular diagnosis when the genome sequence came in," he said.
After just a few weeks on the new drug, overseen by the family's local pediatric neurologist, both children's symptoms improved markedly. The girl's breathing got better, allowing her to resume athletics, and the boy's handwriting became more legible. In addition, both children's sleep and focus at school improved.
Lupski said he believes that whole-genome sequencing could benefit many patients like the Beery twins. "You are obviously going to hear a bit of a biased opinion from someone who is a practicing clinical geneticist and who has seen it work, but my opinion is, this is going to be as big a revolution to clinical genetics as whole-genome array technology has been for copy number determination," he said, adding that the technology will improve the level of resolution.
"I could conceive of this being applied similar to the way MRI has been applied to the brain to try and resolve changes in the brain that you could not see before by previous methodologies," he said. To get there, though, the cost of a whole-genome sequencing test would need to drop to "a reasonable cost" of $1,000 or so. He did not mention how much it cost Baylor to conduct the study.
Lupski conceded that ethical concerns, for example about incidental findings or false positive results, need to be considered and that there are "still lots of things to be ironed out" regarding the clinical use of whole-genome sequencing.
Nevertheless, he said, "there are thousands and thousands of people and families out there with similar situations, where [genome sequencing] may be playing a key role in making a specific etiologic diagnosis and furthermore, may actually enable different treatment options that had not been thought of before."
This could extend to a patient's family members — for example, the twins' mother and maternal grandmother were diagnosed with fibromyalgia, which perhaps resulted from the SPR nonsense mutation they carry. Interestingly, Lupski said, the only drug approved by the US Food and Drug Administration for fibromyalgia is a serotonin reuptake inhibitor. "Maybe the information goes beyond the individual sitting in front of you — if you are willing to think that way, [you will try to] maximize the utilization of this information."
"I feel there will come a day when the genome sequence may become as integral to the family record as the family history is," he said. "And it's just a different family history, much more refined and potentially much more helpful for your thought process to investigate the different differential diagnoses at hand."
To start the process, Baylor is gearing up to open a CLIA-approved whole-genome sequencing laboratory this fall. If all goes according to plan, the lab will announce at the annual American Society of Human Genetics meeting in October that it is ready to take its first samples. Lupski said the lab will build on the experience Baylor has gained from sequencing Jim Watson's genome in 2007 — the first human genome sequenced using a next-generation sequencing platform, from 454 Life Sciences — as well as from sequencing his own genome last year, which identified the underlying mutation of an inherited disorder he suffers from, Charcot-Marie-Tooth syndrome (IS 3/16/2010).
Whole-genome sequencing will also make economic sense for diagnosing heterogeneous genetic diseases, he said, because some gene panel tests cost as much today as sequencing the whole genome would. For example, Charcot-Marie-Tooth disease can be caused by mutations in 41 different genes, he said, but the current clinical test only analyzes six genes and costs $11,000.
"There will probably be obstacles thrown up in front of us to do this," he said. "But it is our goal to provide the best genetic testing that we can out there for the patients and families in need."
The Beery family certainly agrees. Concluding his talk at a Life Tech seminar at the Advances in Genome Biology and Technology meeting earlier this year, Joe Beery said that to obtain the genome sequence data that helped change his children's lives, "I would give everything I have."
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