Children's Mercy Hospital has launched a next-generation sequencing-based test that assesses the coding regions of 514 genes implicated in more than 750 severe childhood-onset diseases.
In a platform presentation at the American Society of Human Genetics conference last month, Sarah Soden, medical director of the Center for Pediatric Genomic Medicine at CMH, presented data from 107 patients with neurodevelopmental disorders who had been screened with either the panel, exome sequencing, or whole-genome sequencing.
Children's Mercy is now offering the customized panel — dubbed TaGSCAN for Targeted Gene Sequencing and Customized Analysis — as a commercial diagnostic test. Additionally, it has a research protocol to provide exome sequencing, and under a National Institutes of Health grant is offering its rapid whole-genome sequencing test, STAT-seq, in the neonatal intensive care unit (CSN 9/25/2013).
Carol Saunders, director of laboratory compliance, test interpretation, and reporting, told Clinical Sequencing News that within the next three to six months, CMH plans to launch an expanded version of the TaGSCAN test that includes an additional 25 genes plus the entire mitochondrial genome.
The current version of TaGSCAN costs $3,200 or less, and has a turnaround time of six to eight weeks.
The assay multiplexes 11 samples on Illumina's HiSeq 2000. Because the 11 samples do not fill the entire flow cell, Saunders said that exomes are also run in conjunction with the test. The expanded version is being validated on the MiSeq, the lower throughput of which should help reduce turnaround time to around two weeks, Saunders said.
The lab provides customized analysis of the assay, said Saunders, which also impacts turnaround time. While full analysis typically takes six to eight weeks, some physicians are ordering the test specifically for one or two genes, which may result in a turnaround time of four weeks, she added.
Genes are analyzed based on the patient's phenotype. "There are some phenotypic terms that get plugged into the analysis pipeline that are more or less specific than others," Saunders said. For instance, terms such as developmental delay or hypotonia will pull up a lot of genes, while including susceptibility to a specific bacterial infection will result in a more limited gene set. "It's highly individual for each patient in terms of the number of variants we analyze," she said.
Currently, test uptake is around 25 per month, but Saunders said now that the test is available outside of CMH, she expects uptake to increase.
At last month's ASHG meeting, Soden presented data from 107 neurodevelopmental patients, 37 percent of whom received a diagnosis from one of the three sequencing-based tests. Three out of four patients tested with whole-genome sequencing, 27 of 56 tested with exome sequencing, and 10 of 47 patients tested with the customized panel received diagnoses. Additionally, the team identified candidate genes in nine additional patients tested with exome sequencing. In 10 cases, the diagnosis changed the clinical management of the patient.
For instance, there was one case of a child that had been diagnosed with lactic acidemia, said Soden, but sequencing identified a deletion of the TBX1 gene, which is located in the 22q11 region that is associated with Di George syndrome, a condition that can cause developmental delays, heart abnormalities, and facial malformations.
The patient had previously been placed on medication to treat lactic acidemia and had also been given mitochondrial supplements because the presumed reason for the elevated levels of lactic acid was thought to be a mitochondrial disorder, Soden said. But, Soden noted, the TBX1 diagnosis identified that the patient did not have a primary mitochondrial disorder , so the medication and mitochondrial supplements were stopped and the patient was referred to endocrine, ENT, and cardiac specialists.
"That's the kind of case where we see a real shift in an understanding of the etiology and a change in treatment," she said.
In a second case, sequencing of a child with intractable epilepsy and macrocephaly identified a mutation in the mTOR gene, making her eligible for a rapamycin trial. While the patient passed away before the drug trial was started, "had we been able to enroll her and start treatment sooner, we may have been able to make a difference," Soden said.
In other cases, the sequencing-based test enabled a diagnosis without having to do an invasive muscle biopsy, Saunders said. For instance, in one case doing a muscle biopsy would have been a "major undertaking because it was a really small neonate who wasn't doing very well at all," Saunders said. Ultimately, TaGSCAN was able to provide a diagnosis, but the prognosis was so poor that the test, rather than pointing to treatment options, helped the family make end of life decisions, Saunders said.
Saunders added that diagnoses with TaGSCAN have also pointed to treatments such as a bone marrow transplant, creatine supplement, and prophylactic antibiotics.
Additionally, she said, a diagnosis can still be helpful even in cases where it doesn't change clinical management.
"Depending on the length of the diagnostic odyssey for the individual family, some people are just so happy just to have an answer and have that all come to an end," Saunders said.
A "molecular diagnosis [might also] clarify the recurrence risk for the family," she added, enabling couples to make informed decisions about having additional children. Even a negative result from TaGSCAN, at the very least, is "a quick way to cross off a lot of things inexpensively," she said.
While the exome and whole-genome sequencing cases had significantly higher diagnostic rates than the panel, Saunders said that the TaGSCAN panel is "a good first step." Additionally, the panel is commercially available and less expensive than exome or whole-genome sequencing.
Currently, CMH is doing exome sequencing under a research protocol, Saunders said, and is sequencing proband-parent trios. That additional data also contributes to the higher diagnostic rate of exome sequencing, she said.
Some of the patients that did not receive a diagnosis via the TaGSCAN test may be eligible for exome sequencing, she added. "There's a process where physicians can nominate patients for exome sequencing." Nominated patients have to meet certain criteria, including having a genetic disorder, and must go through an informed consent process before receiving exome sequencing. There is a review process that includes input from Saunders, genetic counselors, clinical geneticists, and others to review each patient individually and determine whether he or she is eligible for exome sequencing.
Soden added that sometimes a patient will not be eligible for exome or whole-genome sequencing because the disorder appears to be one of the triplet repeat disorders, like Fragile X syndrome, or caused by large insertions or deletions.
Such abnormalities are difficult to detect with short-read next-gen sequencing technology. "We wouldn't do an exome in a patient that most likely had Fragile X," Soden told CSN. "We wouldn't want to roll them over into exome sequencing until something like that had been ruled out."
Additionally, because TaGSCAN is now a commercially available test, not all cases for which it is ordered have "had the baseline workup or are as suggestive of a genetic disease," Soden said.
"When we choose whether to roll [a patient] over into exome, we look at all those things; whereas for TaGSCAN, a physician can just order it," she added.