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NEJM Review Outlines Basics of Diagnostic Genome, Exome Sequencing for Clinicians

NEW YORK (GenomeWeb) – Signaling that genome sequencing is starting to reach mainstream medicine, a review published in the New England Journal of Medicine today provides the nuts and bolts of diagnostic genome and exome sequencing for physicians that might not be familiar with this type of clinical test.

The article, authored by Les Biesecker of the National Human Genome Research Institute and Robert Green of Brigham and Women's Hospital and Harvard Medical School, focuses on clinical genome and exome sequencing, CGES, for the diagnosis of rare genetic disorders and does not touch upon tumor sequencing or sequencing of healthy individuals.

"It is important to understand the basis of this testing and how to select the patients most likely to benefit from it," the authors wrote, noting that CGES has a success rate of about 25 percent.

The test is most appropriate for patients suspected to have a Mendelian or single-gene disorder where candidate gene tests have come back negative. Prior to ordering CGES, clinicians should gather the patient's family history, evaluate their phenotype, scour the literature and databases for related known disorders, and obtain informed consent.

Depending on the assumed inheritance pattern — for example, dominant, recessive, or de novo — it may be necessary to also sequence family members, such as parents, siblings, or more distant relatives.

Because of the underlying technology, the test is best at detecting single-nucleotide substitutions and small indels but not as good at uncovering other types of variants, such as copy number variants, repeats, epigenetic changes, or chromosomal aneuploidy.

Test results "vary widely," the authors cautioned, ranging from a single causative variant to multiple candidates to no plausible variant explaining the disorder.

While positive findings "are highly accurate," the test often misses variants in certain areas of the genome. "For this reason, CGES is not yet a substitute for targeted sequencing of suspected genes or gene panels that have been optimized for a particular condition," the authors wrote.

Determining the clinical validity of the results — whether or not a variant indeed causes the disease — is still a challenge.

The literature is riddled with incorrect assignment of pathogenicity, "a problem that is in part due to the conflation of association with causation," and clinicians need to be aware that a so-called pathogenic variant may not be disease-causing after all, according to the authors. Obtaining such a false-positive result is more likely with CGES than with other tests because thousands of genes are analyzed simultaneously.

Positive CGES results can be clinically useful in several ways. In a minority of cases, they lead to a treatment or management strategy "that dramatically changes the clinical outcome," the authors wrote.

If they don't, they can put an end to further diagnostic testing, help families assess the risk of recurrence in future children, and, for adult-onset diseases, lead to better screening or preventive therapy for siblings.

Pretest counseling is important, the authors pointed out, to set realistic expectations for the success of the test, how helpful the results may be, inform about the possibility of incidental findings, and to discuss cost.

Published prices for CGES tests range from $4,000 to $15,000 per patient, which they note is only two to four times the price of some single-gene tests, and reimbursement practices "vary widely."

Clinicians need to review the test results prior to communicating them to the patient and determine whether a positive result makes sense in the context of the patient's clinical history. If it does, patients should learn about the inheritance, penetrance, expressivity, prognosis, and, if possible, treatment and management for the condition.

In cases where the test identifies several candidate variants, additional research might be needed to find the causative one among them, if it is actually there.

Negative tests results could become positive over time as more knowledge accumulates, and while approaches for re-analyzing CGES data are not yet established, the authors predict they eventually will be. "How this will be done and how it will be reimbursed [is] not yet known," they wrote.

Regarding incidental findings, they pointed to the guidelines of the American College of Medical Genetics and Genomics that advise to analyze a minimum set of 56 genes involved in 24 disorders that are "highly medically actionable." An estimated 1 to 3 percent of patients receiving CGES testing will have such incidental findings, and ordering physicians "should be aware of this issue and should obtain consent and counsel patients appropriately."

Approaches for CGES today "are sure to evolve over time," the authors concluded, and such tests might enter other areas including neonatal medicine.