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Preliminary Results Show Some Promise for Scripps Exome Sequencing Molecular Autopsy Approach


NEW YORK (GenomeWeb) – Sequencing DNA from deceased people can identify genetic alterations that may have played a role in their death in at least some individuals, according to a new study by a team from the Scripps Translational Science Institute.

Genomics-based strategies to identify a molecular cause in cases of unexplained sudden deaths is a nascent but growing area of interest among researchers.

About 11,000 individuals under 45 die suddenly and unexpectedly each year from conditions including sudden infant death, pulmonary embolism, aortic aneurysm, and sudden cardiac death (SCD). Knowing the cause of these deaths can be important for family members who may share inherited physical or genetic features that put them at risk for a similar fate or for other complications. Hence, attention has grown toward developing post-mortem genetic testing strategies that can address this need.

Most efforts to date have used relatively focused genetic techniques, limiting analyses to a set of genes associated with cardiac chanelopathies, epilepsy, or other known cardiac disorders that could explain a sudden death in an otherwise healthy individual.

For example, the Montreal Heart Institute's Cardiovascular Genetics Center said recently that it tests cases referred from coroners using the targeted NGS panel it has developed.

In contrast, the Scripps team, led by Ali Torkamani, assistant professor and director of drug discovery at STSI, has been working to measure how effective broader, whole-exome sequencing can be as a molecular autopsy tool employed through collaboration with working medical examiners.

In a letter published this week in JAMA, the Scripps researchers reported preliminary results from their effort in an initial 25 cases, all aged 45 or younger, who suffered a sudden unexpected death between October 2014 and November 2015 and were subsequently referred to Scripps by the medical examiner.

When possible, the investigators also sequenced exomes from saliva samples from these individuals' parents. They categorized any mutations that they found as either a likely cause of death (a mutation that has been previously reported or is otherwise expected in a gene related to sudden cardiac death); a plausible cause of death (a mutation of unknown significance in an SCD gene); or a speculative cause of death (a mutation previously reported in other disorders that might be expected to play a role in an unexplained death).

Overall, the researchers determined a likely cause of death in four cases via their sequencing-based molecular autopsy method. The group also found a plausible cause in six probands and a speculative cause in seven. The eight remaining individuals had no exome mutations that fell into one of these three categories.

Counted together, the likely and plausible findings, which occurred for 10 of the 25 study subjects, represent a diagnosis rate of about 40 percent.

Torkamani told GenomeWeb this week that that rate is consistent with what other studies have found and hints at the potential clinical benefit of more widespread use of genetics in cases of sudden death.

Compared to sequencing in cases of rare diseases — in which molecular diagnoses are possible about 25 percent of the time — the 40 percent rate seen in the postmortem results so far looks good, he said.

"Also, when you do get a positive finding [in the postmortem setting] there is a lot more in terms of actionably of that finding than in rare disease," Torkamani said. "In rare disease, you get a diagnosis and that's basically it most of the time. In this case, the dead person doesn't get any benefit obviously, but the family definitely does. They'll know if they are at risk, and for many conditions underlying sudden death you can intervene — either with watchful waiting or with actual interventions like drugs or defibrillators in arrhythmia or blood thinners for embolisms."

Some investigators looking at molecular autopsy methods have had more limited success, though. For example, researchers from a Texas-based consortium reported a study earlier this year in Genome Research in which they sequenced 64 genes associated with sudden death in 351 deceased infants and young people. They found that only about four percent of cases had a reportable genetic variant contributing to sudden death.

In the Scripps study, among the five individuals with a mutation determined to be a likely cause of death, only two had clinical autopsy findings that actually corroborated this genetic diagnosis.

But Torkamani said that this doesn't necessarily detract from the molecular results. It really reflects the limitations of standard clinical autopsies in the case of sudden deaths and the fact that so few of the sudden death cases could be explained through physical or clinical findings at all.

Interestingly, most of the genetic findings in the study were variants of unknown significance inherited from relatives not affected by sudden death and present at population frequencies incompatible with full disease penetrance, Torkamani and his coauthors reported.

For example, among the 10 likely and plausible cases, seven appeared to have inherited the mutation in question from live, apparently unaffected relatives.

According to the study authors, this observation of likely and plausible pathogenic variants in unaffected relatives is consistent with other large-scale studies that have found clinically relevant variants in living relatives of SCD cases.

The Scripps results now suggest that similar patterns may be at work in non-SCD sudden death as well, although Torkamani and his colleagues cautioned that the findings from the study so far can't definitively be linked to sudden death.

Torkamani told GenomeWeb that his team has already continued their work beyond the 25 subjects reported in their JAMA letter and have analyzed about 40 subjects in total.

The group is now also hoping to expand the program by involving other medical examiners nationwide. The more cases the group is able to sequence, the better their rate of positive findings might be, as knowledge about the genetic contributors to sudden death and the disorders that precipitate it are uncovered.

This could also have important implications for living people, he added. "These conditions that cause sudden death can also [influence] chronic diseases. The genetics are overlapping, so findings in this study could have further-reaching implications."

Despite growing interest, the actual practice of postmortem genetic testing is still limited both in scope and the number of medical examiners who embrace it. According to Torkamani, a recent survey found that 60 percent of MEs have never ordered a genetic test.  And when testing is done, it's most often limited to specific genes known to play a role in arrhythmias and other cardiovascular disorders.

By expanding their study, the Scripps investigators are hoping to spread information about the potential added value of an exome-sequencing based approach.

For truly widespread use, though, Torkamani said that postmortem genetic testing may need to become reimbursable by insurance.

"Clinical autopsies were at some point covered by insurance and they aren’t really anymore, which is one reason why the rates have fallen off," he said. "But I think there is a decent case to be made here that molecular autopsy should be a reimbursable genetic test because it has direct relevance to living individuals."

In the meantime, Torkamani said, there may be individuals who want to know who are willing to pay for it themselves. Though new commercial companies offering sequencing for living people have abounded over the last half decade, there doesn't seem to yet be a market for self-paid postmortem genetics.

That said, commercial groups may be interested. Testing firm Invitae recently got involved, saying last year that it would work with the Sudden Death in the Young (SDY) registry, providing genetic testing in 10 US regions for 900 cases where the cause of death could not be determined by clinical autopsy.