Doctor checking a newborn baby with a stethoscope

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Whole-exome sequencing (WES) on its own isn’t sufficient in detecting rare metabolic disorders in newborns, but it may be useful as a secondary diagnostic tool. Researchers in California reported that tandem mass spectrometry (MS/MS) outperformed WES on sensitivity and specificity, although results varied by type of disorder. They chronicled their findings in Nature Medicine.

Clinicians have relied on MS/MS to screen newborns for rare inborn errors of metabolism panels (IEMs). Sequencing, however, has received growing attention for detecting rare disorders in otherwise healthy babies. “There is a lot of enthusiasm for sequencing, including statements that all babies should have their genome sequenced at birth,” said Jennifer Puck, MD, professor of pediatrics at the University of California, San Francisco (UCSF) and co-senior author of the study. However, sequencing hasn’t been rigorously compared with other methods for screening healthy individuals. “The aim of the study was to scientifically determine how exome sequencing would stack up against MS/MS,” an established test with a good track record, Puck told CLN Stat.

California has a biobank of millions of stored leftover newborn dried blood spots. These samples had already been screened by MS/MS and could be studied by exome sequencing under strict controls, Puck explained. “The biobank had the dried blood spots from all the infants born in the state, including those who were found by MS/MS to have very  rare metabolic disorders. It even had the rare cases missed by MS/MS and diagnosed later by clinical symptoms.”

Puck and her colleagues included data on 1,334 inborn IEM cases from 4.5 million infants born in California over a 10-year period. Investigators assessed mutations in 78 genes associated with 48 metabolic disorders that newborns are screened for in California.

Compared with MS/MS, whose overall sensitivity was 99% and 99.8%, respectively, the sequencing method yielded a sensitivity of only 88%, with a somewhat higher specificity, at 98.4%. This means that WES would have missed 160 cases in the IEM cohort, while misidentifying nearly 8,000 infants per year that would have needed an urgent evaluation by a specialist.

Several factors explain why WES didn’t perform as well as the older MS/MS method. “In some instances our DNA exome sequencing and analysis failed to find mutations in the genes known to cause these disorders, causing low sensitivity,” Puck said. “Not sequencing whole genomes would miss noncoding mutations, but in a small sample this was not a major reason. Exome sequence coverage wasn’t uniformly great, and there could be genes not yet known that we didn’t look at.”

California’s diverse population also contains many variations in the genome, she continued. Any analysis that flags unknown rare variants will generate many referrals for infants without disease, causing poor specificity, noted Puck. That said, WES did find mutations in cases that MS/MS had missed. In particular there were some cases for which MS/MS did not give a clear result and sequencing found mutations that could have cleared up some of these very quickly.

While these disorders were too rare to statistically prove WES’ superiority, as an adjunct it could be very beneficial in quickly solving difficult cases, said Puck.

“Following identification of infants with abnormal analytes on MS/MS, the metabolic centers to which these infants are referred would likely find exomes invaluable for suggesting a definitive diagnosis by identifying pathogenic variants,” said Steven Brenner, PhD, professor at UC Berkeley, a member of UCSF's Institute for Human Genetics, and co-senior author of the study. “Deep sequencing could facilitate rapid and precise clinical resolution for newborns with positive MS/MS on newborn screening,” added Brenner.

Sequencing also might identify treatable conditions that go unrecognized until it’s too late for an intervention, Brenner continued. Many treatable disorders aren’t part of newborn screening because they’re not amenable to MS/MS testing, Brenner continued. “Our findings suggest that, after careful vetting, sequencing might enable screening for hundreds of treatable genetic diseases that currently can’t be detected through biochemical testing.”

According to Puck and colleagues, the study is the largest of its kind to sequence an entire population of IEM-affected cases to assess WES’ capabilities as a screening tool in an unbiased manner.