SAN DIEGO (GenomeWeb) – Whether to use a gene panel or sequence the entire exome is an ongoing debate with each option having its own advantages and drawbacks and also depending on the disorder being studied, researchers said at the American Society of Human Genetics meeting, held here this week.
While exome sequencing is more comprehensive than gene panels, it may add to cost and may not even completely cover the genes of interest. However, even in well-phenotyped cases, exome sequencing can uncover an unexpected molecular diagnosis.
Renkui Bai, the director of mitochondrial disorder testing services at GeneDx, presented on his firm's experience using a mitochondrial gene panel, exome sequencing, and sequencing of the entire mitochondrial genome to diagnose suspected cases of mitochondrial disease.
Deciding what test to use to diagnose a suspected mitochondrial disorder can be challenging because mitochondrial disorders are extremely heterogeneous, he said during the presentation.
The group evaluated 635 cases by whole mitochondrial genome sequencing, 669 with a 140-gene panel, and 200 cases with exome sequencing. Mitochondrial genome sequencing led to a diagnosis or probable diagnosis in only 11.7 percent of cases, while the gene panel led to a likely diagnosis in 39.9 percent of cases, and exome sequencing yielded a likely diagnosis in about 30 percent of cases. Bai's team also found that sequencing trios had a higher diagnostic rate than singletons — trio sequencing yielded a diagnosis in 32 percent of cases and a possible diagnosis in 14.5 percent of cases, while singleton sequencing diagnosed 25 percent with candidate genes found in an additional 4 percent.
Despite the panel's higher diagnostic rate, exome sequencing still has some advantages, he said. Notably, only 33 percent of the mutations identified by exome sequencing would have been found with the gene panel. Another 5 percent were in known mitochondrial disease genes that had not yet been added to the panel and 3 percent were in other genes related to mitochondrial pathways. However, 59 percent were in known disease genes not associated with mitochondrial disorders.
"There were overlapping disorders that would have been missed by just doing a mitochondrial gene panel," he said.
However, he said for patients with a definite mitochondrial disorder, panel testing is still more sensitive — around 40 percent compared to 30 percent sensitivity with exome sequencing. But panel sensitivity drops dramatically, to around 8 percent, for patients that have a "possible" mitochondrial disorder.
"The majority of patients with a possible mitochondrial disorder have mutations in non-mitochondrial genes," he said.
He said that he now recommends that patients for whom there is strong evidence of a mitochondrial disorder should receive a targeted gene panel plus sequencing of the mitochondrial gene, but patients without such strong evidence may be better served by exome sequencing.
Bradford Powell, a clinical assistant professor at the University of North Carolina, Chapel Hill, said one way to offer both the benefits of exome sequencing and panel sequencing is to sequence the whole exome of patients, but analyze panels based on the patient's phenotype.
Powell is co-investigator on UNC's NCGENES, a National Institutes of Health Clinical Sequencing Exploratory Research project that aims to understand the diagnostic yield and clinical utility of exome sequencing, among other goals.
For the project, the group has developed gene lists for a range of disorders including hereditary cancer, cardiovascular disease, retinopathies, and neurological disorders. The group sequences the whole exomes of the individuals, but then first evaluates those set lists to try and find the causative variant. Limiting the scope of genes helps reduce the bioinformatics load and also "reduces our need to look at off-target variants," reducing the possibility of uncovering incidental findings, Powell said.
So far, the group has sequenced around 300 individuals out of the 750 it plans to sequence in total.
Another advantage of panels is that they can provide better coverage of all the exons on the panel compared to exome sequencing, where coverage is often incomplete, Lee-Jun Wong, director of Baylor College of Medicine's Medical Genetics Laboratory, said during a presentation.
For certain disorders, she said, panels have diagnostic rates approaching 90 percent. Some of Baylor's panels with high diagnostic rates include its 66-gene non-syndromic retinitis pigmentosa panel, which has a diagnostic rate of 82 percent, and its nine-gene usher syndrome panel, which has a diagnostic rate of 94 percent.
Meantime, Madhuri Hegde, executive director of the Emory Genetics Laboratory, said that researchers are making progress on developing a medical exome that will have complete coverage of the exons of around 4,600 medically relevant genes.
Emory began offering the medical exome in March, which it designed in collaboration with Avni Santani, scientific director of the Molecular Genetics Laboratory at the Children's Hospital of Philadelphia, and Birgit Funke, director of clinical research and development at Harvard University's Laboratory of Molecular Medicine.
According to Hegde, panels can be designed to cover the entire targeted regions well, but typical exome capture kits completely miss or poorly cover between 11 percent and 20 percent of known clinically relevant exons.
She said that with the medical exome Emory now offers, 98 percent of the exons within those 4,600 genes are covered completely. "So there are still some that are not properly covered," she said. In addition, she added that the limitations are not unique to exome sequencing but to next-gen sequencing, in general.
"Current NGS assays are not optimal for highly homologous regions, triplet repeats, or structural variants," she said. These just happen to be compounded when doing exome sequencing versus targeted sequencing, because often when a lab designs a targeted panel, it is familiar with the genes on the panel and is aware of potential issues. "But this knowledge does not exist when [sequencing] every gene," Hegde added.