and families of pediatric patients to navigate the landscape.
Dr. Gabriele Richard
“Testing options range from targeted variant testing and single-gene testing to exome and genome sequencing,” Gabriele Richard, MD, said at the annual meeting of the Society for Pediatric Dermatology. “It is not always easy to determine which testing is right.”
Increasingly, clinical genomic tests, including exome and genome sequencing, are used for patients with complex phenotypes, and possibly multiple disorders, who might have no diagnosis despite extensive prior testing, said Dr. Richard, medical director at Gaithersburg, Md.–based GeneDx., a molecular diagnostic laboratory that performs comprehensive testing for rare genetic disorders. These tests are also being used more for first-line testing in critically ill patients in the neonatal and pediatric intensive care units, and “have heralded a whole new era of gene and disease discovery,” she added.
Targeted variant testing is used for known familial variants, to test family members for carrier status and segregation, and to make a prenatal diagnosis, she said. Single-gene testing is available for most genes and has its place for conditions that can be clinically well-recognized, such as ichthyosis vulgaris, Darier disease, or Papillon-Lefèvre syndrome.
Specific tests for identifying gene deletions or duplications are exon-level microarrays, multiplex ligation-dependent probe amplification (MLPA), and chromosomal microarray analysis. “The latter has been successful in identifying diseases causing chromosomal abnormalities in over 10% of cases overall,” Dr. Richard said. An example of a skin disorder is X-linked ichthyosis caused by a deletion of the steroid sulfatase locus in more than 95% of affected males, she said.
“However, the current staple of molecular diagnostic testing is multigene next-generation sequencing (NGS) panels, which allow you to interrogate two to hundreds of genes concurrently, including sequencing and deletion duplication testing.” These tests are the most cost effective, she said, and are available for almost any genodermatosis or group of disorders with overlapping phenotypes, such as albinism or ichthyosis, epidermolysis bullosa and skin fragility, ectodermal dysplasia, or porphyria. According to Dr. Richard, the diagnostic outcomes of NGS panels mainly depend on test indication, panel size and gene curation, age of onset, and prevailing inheritance pattern of disorders.
Her recommended criteria for distinguishing the myriad of available NGS panels include checking gene content, technical sensitivity of sequencing and deletion/duplication analysis, quality of variant interpretation and reporting, turn-around time, and available familial follow-up testing. “If a family might consider future prenatal diagnosis, choose the lab that performs prenatal and diagnostic testing,” Dr. Richard said. “Equally important are client services such as ease of ordering, insurance coverage, and the ability to determine out-of-pocket cost to patients.”
Resources that enable consumers to compare panel content, methodology, turnaround time, and other parameters include the Genetic Testing Registry (GTR) operated by the National Center for Biotechnology Information, and Concert Genetics, a genetic testing company. The National Society of Genetic Counselors also offers a searchable database for finding a genetic counselor.
Exome sequencing includes the coding sequences of about 20,000 genes and has an average depth of 50 to about 150 reads. “It is a phenotype-driven test where only select variants are being reported fitting the phenotype,” Dr. Richard said. “The outcome of exome and genome sequencing much depends on optimization of bioinformatic pipelines and tools.” Besides small sequence variants, exome sequencing is able to identify a variety of different types of disease-causing variants, such as gene copy number variants seen in about 6% of positive cases, mosaicism, regions of homozygosity, uniparental disomy, and other unusual events and is cost effective.
Whole-genome sequencing, meanwhile, includes the entire genome, particularly noncoding regions, and has an average depth of more than 30 reads. “It’s based on single-molecule sequencing, has longer reads and more uniform coverage, compared to exome sequencing,” she said. “Higher cost, variant interpretation, and lack of coverage by payers are still presenting challenges for genome sequencing.” Genome sequencing can be done in a day or less.
According to diagnostic outcomes based on 280,000 individuals including 125,000 probands from GeneDx data, a definitive diagnosis was made in 26% of probands, of which 2.8% had more than one diagnostic finding and 1.8% had actionable secondary findings. In addition, 7% of the variants were found in candidate genes; 31% of probands had variants of uncertain significance, while 36% tested negative. “Nevertheless, the diagnostic yield of exome sequencing depends on the phenotype and cohort studied,” Dr. Richard continued.
At her company, she said, the highest positive rate is for multiple congenital anomalies (34%), skeletal system abnormalities (30%), and nervous system abnormalities (29%). Trio testing – the concurrent analysis of both biological parents and proband for all genes – “is a critical factor for success,” she added. “It not only improves the variant calling because we have three times the data and increases test sensitivity, it also provides more certain results, determines inheritance and allows for detection of parental mosaicism.”
According to Dr. Richard, trio testing has a one-third higher diagnostic rate than sequencing of the proband alone. Citing a published prospective study that compiled data from eight different exome- and genome-sequencing studies in critically ill neonates and children, trio testing made it possible to make a genetic diagnosis in up to 58% of children.
Whole-genome sequencing is estimated to have a 5%-10% higher diagnostic rate than exome sequencing. “However, we are still a ways away from using it as a routine diagnostic test for all test indications,” Dr. Richard said. “Automation, special bioinformatics algorithms and databases, and combination of genome sequencing with mRNA sequencing are being explored and built to further improve the diagnostic yield.”
Dr. Richard had no disclosures other than being an employee of GeneDx.