Low-cost Test Can Screen for Chromosome 15 Disorders Like Angelman

Marta Figueiredo, PhD avatar

by Marta Figueiredo, PhD |

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A new low-cost molecular test can accurately distinguish people with Angelman syndrome from those without the disease and those with other chromosome 15 imprinting disorders, a study shows.

While the test cannot identify about 10% of Angelman cases, these findings highlight the feasibility of using it in newborn screening for this and other chromosome 15 imprinting disorders, the researchers noted.

Still, further studies are needed to confirm the diagnostic value of the test.

The study, “Feasibility of Screening for Chromosome 15 Imprinting Disorders in 16 579 Newborns by Using a Novel Genomic Workflow,” was published in the journal JAMA Network Open.

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Each person inherits two copies of every gene — one from each biological parent. While most cells in the body use both gene copies to produce proteins, some cells depend only on one of the copies, due to a mechanism called genomic imprinting.

Genomic imprinting is the process by which one copy of a gene — either the maternal or the paternal copy — is silenced, or turned off, by a chemical tag called methylation. This suppresses a gene’s activity without changing its sequence.

Chromosome 15 imprinting disorders, including Angelman, Prader-Willi syndrome (PWS), and chromosome 15 duplication syndrome (Dup15q), are caused by deletions, duplications, or other changes in genes located at the same region of chromosome 15 and that undergo genomic imprinting.

While they are distinct conditions, chromosome 15 imprinting disorders share some features, including intellectual disability, behavioral problems, and social communication deficits.

Given that each condition is associated with a specific, abnormal pattern of methylation in a specific region of chromosome 15 — called the promoter of the SNRPN gene — methylation analysis in this region has been proposed as potential diagnostic tool for newborn screening of chromosome 15 imprinting disorders.

Such early diagnosis “could prevent the diagnostic odyssey, reducing medical costs and the significant stress and anxiety currently experienced by families while they await a diagnosis,” the study stated.

Now, an international team of researchers developed a new high-throughput, low-cost screening test, called methylation-specific quantitative melt analysis (MS-QMA), to quantify abnormal levels of SNRPN promoter methylation.

To validate it, the researchers first assessed the test’s ability to correctly identify 109 PWS patients, 48 Angelman patients, nine people with Dup15q, and 1,190 people with typical neurological development by analyzing their DNA samples.

Results showed that SNRPN promoter-targeted MS-QMA correctly ruled out all but one unaffected case and correctly identified 99% of PWS cases, 93.8% of Angelman patients, and 77.8% of Dup15q patients.

All cases identified as Angelman or PWS actually had the disease (100% positive predictive value), while 87.5% of those with a positive test for Dup15q had the condition. Nearly all (about 99.9%) of those with a negative test for either disease had normal neurodevelopment.

After confirming the test’s high sensitivity and specificity for these conditions, the team evaluated whether it could be used for newborn screening by analyzing newborn blood spots from 16,579 infants from the general population.

SNRPN promoter methylation analysis using MS-QMA identified 92 cases (0.55%) with values outside the normal range, which were referred for confirmatory genetic testing. Such additional testing confirmed the presence of Angelman syndrome in two cases, PWS in two cases, and Dup15q in one case.

Using more stringent Angelman- and PWS-specific thresholds dropped the number of positive MS-QMA results to nine samples (0.05%), but these did not include the Dup15q case, suggesting that such conservative cut-offs may miss people with Dup15q.

These results provided frequency estimates of 1 in 8,290 newborns for both Angelman and PWS, and 1 in 16,579 for Dup15q. These estimates are consistent with previous reports for Angelman syndrome.

However, because Angelman is caused by mutations in the maternal UBE3A gene, it can often show normal SNRPN promoter methylation patterns, and as such could not be differentiated by MS-QMA from general population controls. This “suggests that the [Angelman syndrome] estimates provided might not be totally accurate,” the researchers wrote.

In addition, the test showed relatively high positive predictive values for Angelman, with 67% of those identified as positive for Angelman being confirmed by additional genetic testing.

While lower positive predictive values were seen for PWS (33%) and the combined detection of all three chromosome 15 imprinting disorders (44%), these were still within the range reported for many tests of conditions included in state-sponsored newborn screening programs, the team noted.

High positive predictive values are important for newborn screening as they ensure a lower number of false-positive results that have to be repeated, which may incur more costs, the collection of a new sample, and increased psychological stress for families.

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Moreover, in this study, the cost of simultaneously testing a sample for the three conditions was less than $4, or less than $1.3 per condition per infant, and this type of test can be used to simultaneously screen for other rare disorders with distinct methylation signatures.

“Screening for all chromosome 15 imprinting disorders at a population scale was feasible using quantitative analysis of SNRPN promoter methylation, with the reagent cost, sample requirements, prevalence, and [positive predictive value] estimates compatible with screening for other conditions in the state sponsored programs,” the researchers wrote.

Should these findings be confirmed in larger prospective studies, “this workflow could ensure that early interventions for these disorders are uniformly available to most infants from birth as part of state-sponsored newborn screening programs,” they concluded.