Researchers Develop Fast, Low-Cost, and Non-invasive Prenatal Screening Test for SMA

Chinese researchers have developed a fast, low-cost, and non-invasive maternal blood test for prenatal screening of spinal muscular atrophy (SMA).

This method may be a safer alternative to traditional invasive prenatal screenings for families with a history of SMA and other high-risk populations, with the ability to identify affected fetuses within the first trimester.

The study, “Development and validation of a haplotype‐free technique for non‐invasive prenatal diagnosis of spinal muscular atrophy,” was published in the Journal of Clinical Laboratory Analysis.

SMA is mainly caused by the complete loss of exon 7 in the SMN1 gene, which leads to a reduction in levels of the SMN protein. Exons are the sections of a gene that contain the information to generate proteins.

Loss of exon 7 can occur due to large DNA deletions or gene conversion from SMN1 to SMN2, a second SMN gene which differs from SMN1 in only one nucleotide — the building blocks of DNA.

SMA is inherited in an autosomal recessive manner, meaning a child must acquire two defective copies of the SMN1 gene — one from the father and one from the mother — to develop the disease.

While people with only one mutated SMN1 copy do not develop the disease, they can still transmit the mutated gene to their children. They are called carriers.

The discovery of circulating cell-free fetal DNA (cffDNA) in maternal blood has led to the development of various non-invasive prenatal testing, and avoids the 1:100 chance for miscarriage associated with invasive sampling methods.

In pregnant women, cffDNA are DNA fragments generated mainly from the natural death of specific placental cells. Fetal DNA fraction, or the percentage of cffDNA in maternal peripheral blood, is generally at an average of 13% (ranging from 3% to 30%).

Chinese researchers in the study sought to develop a non‐invasive prenatal test to screen for spinal muscular atrophy and validate its performance.

Their test is based on specific probes — or DNA fragments used to search for a particular gene or DNA sequence — a highly sensitive and specific method called droplet digital PCR (ddPCR), and a newly developed algorithm to determine SMN1 copy number.

The generated probes were designed to specifically detect the DNA region of the SMN1 gene containing the nucleotide that differs from SMN2. This way, the test is able to detect not only the deletion of exon 7 but also any SMN1-to-SMN2 gene conversion.

In ddPCR, a single blood sample is divided into 20,000 droplets, and detection of the DNA sequences of interest occurs in each, which increases the statistical power of the detection while reducing costs.

The validity of the test was evaluated in 17 women who were SMA carriers and seeking SMA prenatal diagnosis for their male fetuses. The women were at 16 to 22 weeks of gestation, and seen at the Hunan Jiahui Genetics Hospital, in Changsha, China.

Fetal DNA fraction was determined based on the relative proportion of chromosome-Y (the male chromosome) sequences detected.

Two sets of tests were conducted, one with all 17 women (test set A) and another included 10 randomly selected women from the group (test set B). One sample in each set of the tests was determined as an unclassified result.

The results were then compared to those of standard genetic testing of fetal DNA extracted from the amniotic fluid of these women.

The concordance rate between results of the new test and standard fetal DNA testing was 94.12% in test set A (16 out of 17) and 90% in set B (9 out of 10), which went to 100% when considering only the classifiable results — those where fetal SMN1 copy number could be quantified to either accept or reject the hypothesis of an SMA diagnosis.

The data suggests that the new test produced consistent and accurate results. In addition, it is fast (taking about six hours) and low-cost (under $600 for eight samples), the team said.

The researchers also noted that, compared with other non-invasive prenatal testing for SMA, the test does not require additional genetic data from both parents and detection of SMN1 exon 7 loss caused by both possible genetic events.

The test “has the potential to be utilized for first‐trimester prenatal diagnosis in affected families, as well as prenatal screening in high‐risk population alternative to carrier screening,” they said.

Among the test limitations are the inability to detect subtle mutations in the SMN1 gene other than the loss of exon 7, and the male-specific fetal fraction determination method, which the researchers noted may be overcome with alternative methods that cover both genders.

Future studies in a larger population are required to confirm the validity of this new test, they said.