Genetic Test Detects Hundreds of Harmful Mutations in High-Risk Populations

Samara Rosenfeld
APRIL 26, 2019
DNA

Researchers have developed a new low-cost genetic test that has accurately identified more than 200 known disease-causing gene variations in two high-risk populations — the Old Order Amish and Old Order Mennonites of Lancaster County, Penn. — according to the findings of a study published in the Journal of Molecular Diagnostics.

The findings from the research team at Nemours Children’s Health System in Wilmington, Del., could help reduce morbidity and mortality from rare genetic disorders and reduce costs of care through early diagnosis of newborns.

“Without rapid diagnosis of newborns, children can have shorter lifespans or lasting disabilities, even after intensive, lengthy and costly medical care,” said Erin Crowgey, Ph.D., lead study author and associate director for bioinformatics at Nemours.

The team developed a custom next-generation sequencing gene test capable of identifying 168 unique genes, with a focus on 202 alleles associated with 162 different syndromes, to identify carriers of these variants in a simple blood test.

There were 63 subjects from the Clinic for Special Children that were consented using an approved IRB clinical registry and specimen banking protocol. Blood was collected and DNA was extracted.

A targeted gene panel was created using custom configuration of the ArcherDX Anchored Multiplexed Polymerase Chain Reaction technology, which detected 309 different gene variants.

In order to see the accuracy of the test, the researchers used an alternative method to validate all genetic variants. The team selected 48 samples based on prior whole exome sequencing results and an additional 15 samples to validate SMN1 and SMN2 copy number analyses.

The panel collectively detected 273 pathogenic single nucleotide or small insertion/deletion variants, 35 copy number variants and one chromosomal abnormality.

There was a 100% agreement between the two methods.

The study authors estimated that using this screening tool at a cost of approximately $165 per person could result in the savings of hundreds of thousands of dollars in healthcare costs annually.

“Robust, expanded screening and diagnostic testing in these populations for people who may carry these gene variants could potentially improve patient outcomes and reduce medical costs, through a single low-cost procedure,” Crowgey said.

Populations that are genetically isolated, such as the Old Order Amish and Old Order Mennonite communities, have an increased chance of specific autosomal recessive disorders. So, the authors suggested that the implementation of a community-wide carrier screening program could be beneficial.

They wrote that by identifying at-risk couples and performing the testing on cord blood for their children, it can be ensured that a majority of the children affected by a recessive genetic disease in such communities are identified as asymptomatic newborns.

Early diagnoses also help avoid lengthy and costly hospitalizations, which could save uninsured communities millions in healthcare dollars.

Diagnosis of asymptomatic newborns also ensures optimal timing for new therapeutics such as gene therapy.

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