Exome Sequencing as a Diagnostic Tool
Since it involves a tiny subset of human genes, exome sequencing is faster and more economical than whole genome sequencing
More information, fewer genes
Human protein-coding genes number about 180,000 and constitute the exome, which is about one percent of the genome. Exome (or whole-exome) sequencing therefore identifies only genes with the potential to influence protein expression, including protein abnormalities implicated in disease. Since it involves a tiny subset of human genes, exome sequencing is faster and more economical than whole-genome sequencing—hence the method’s value in both basic research and diagnostic medicine.
Exome sequencing is primarily used to identify hereditary diseases, including those that follow a Mendelian or polygenetic etiology—for example, Alzheimer’s disease. Because it is relatively new and focuses broadly, exome sequencing has not yet been adopted as a tool to monitor a patient’s progress through a course of treatment, either in standard clinical practice or in clinical trials. In those instances, targeted analysis for treatment-induced genetic changes is more economical and practical. Armed with exome sequencing data, physicians can then home in on specific responses using more targeted tests.
For example, last year, OneOme (Minneapolis, MN) teamed with Rainbow Genomics to provide genomic services to patients in the Far East. Under the arrangement, OneOme’s RightMed® pharmacogenomic test will be offered alongside Rainbow Genomics’ whole-exome sequencing test services.
RightMed uses genomics to predict drug responses, with the potential to improve outcomes by reducing side effects and rehospitalization rates. The RightMed test will be offered both as a stand-alone and coupled with exome sequencing for pediatrics, cancer, cardiovascular conditions, and other tests for adult genetic conditions. It covers 22 genes and more than 340 medications for more than 28 medical indications.
OneOme, codeveloped and exclusively licensed with the Mayo Clinic, has developed the RightMed comprehensive test, an end-to-end solution that includes sample collection, pharmacogenomic testing services, data analysis, clinical interpretation, and interactive reporting.
In addition to end-to-end pharmacogenomic evaluation, OneOme generates a comprehensive report from thirdparty exome data—for example, from Rainbow Genomics.
Why two test platforms?
Exome sequencing provides that raw information about unique variations in a patient’s DNA, which clinicians must then interpret to assess the patient’s risks and conditions. “Typically the interpretation is focused on hereditary diseases and risks. To that data OneOme adds targeted pharmacogenomic analysis and interpretation based on the exome sequence,” says Paul Owen, CEO. “OneOme’s interpretation service analyzes 23 genes—98 alleles—that have known clinical impact, to assess how a patient metabolizes many commonly prescribed medications.”
OneOme takes raw exome information from Rainbow Genomics and subjects it to their pharmacogenomic algorithms to generate the RightMed pharmacogenomic report. This report describes how patients respond to more than 340 medications based on exomic variants.
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“Adding pharmacogenomic interpretation to exome sequencing allows more-informed medication decisions, helping to reduce adverse drug reactions, increase drug effectiveness, and reduce medication trial and error,” Owen explains. “Combining the two tests is less about an additional layer of validation and more about providing immediate clinical impact or actionably for the health care provider and patient.”
Homing in: exome libraries
Agilent Technologies (Santa Clara, CA) has been expanding its next-generation DNA sequencing capabilities, particularly within the exome market. In 2017, the company introduced a target enrichment product, SureSelect Clinical Research Exome V2, containing one thousand more additional diseaserelevant targets than the previous version had.
According to Agilent, the new release “delivers a curated, annotated list of included genes, as well as evidence for disease relevance.”
Exome V2 builds on Agilent’s target enrichment technology with the addition of 1,099 disease-associated genes, more than 75,000 splice sites of noncoding exons, 12,000 previously reported deep intronic variants, and 800 variants in promoter regions. These targets were identified in collaboration with Emory University and the Children’s Hospital of Philadelphia.
“Next-generation sequencing—NGS—has accelerated the pace of discovery, particularly the discovery of new genes associated with diseases,” explains Chitra Kotwaliwale, PhD, senior global product manager for the NGS Technology Group at Agilent.
But as the number of disease-associated genes increases, curating this information is impractical for one group. That is what Agilent is striving for with Exome V2.
Because whole-genome sequencing is costly and most disease mutations reside in genes, sequencing exons generally provides the most valuable information at the lowest cost. To enrich just exons from the rest of the genome via its SureSelect exome sequencing workflow, Agilent creates exome “bait” libraries, which are short biotinylated RNA sequences that hybridize to their target sequence and enrich them over the rest of the genome.
Agilent states, “When coupled with Agilent’s SureSelectQXT workflow, the new exome enables researchers to create enriched libraries in just one day, with as little as 3.5 hours of hands-on time.” Producing libraries through conventional selection and sequencing takes about 24 hours.
Where the exome fits
Pharmacogenomics is rapidly expanding due to the advances in next-generation sequencing and gene-amplification methodologies. In the past, pharmacogenomic tests looked only for single genetic variants. Now, says Owen, “with knowledge of more drug-gene interactions identified and validated, a more comprehensive panel is the ideal approach. It is somewhat analogous to the sequencing advances whereby the technology and analysis advanced from sequencing a single gene or locus to sequencing an exome or full genome.” Exome sequencing has several advantages compared with traditional diagnostics, targeted genetic analysis, and whole-genome sequencing. One is higher diagnostic yield—the likelihood that a test will establish a diagnosis. Another is the ability to make one or more diagnoses that a physician unfamiliar with a particular disorder might miss. “Whole-exome sequencing removes a lot of the guesswork,” says David Everman, MD, a clinical geneticist at the Greenwood Genetic Center (Greenville, SC).
Whole-exome sequencing is now fully mainstreamed within clinical genetics, particularly for conditions not readily diagnosed by history and physical examination followed by standard tests. Yet the approach is far from a panacea.
“One hurdle to achieving more routine clinical implementation of this technology is the relatively high cost of testing and whether the method is cost-effective to implement on a larger scale,” says Everman.
Another obstacle, according to Agilent’s Kotwaliwale, is that while exome sequencing identifies many genetic variants, pinpointing the precise variant that causes diseases remains a challenge. “Furthermore,” she says, “variable reimbursement means that exome sequencing is not available to everyone yet.”
For additional resources on next-generation sequencing, including useful articles, visit www.labmanager.com/ngs