NEW YORK (GenomeWeb) – Sequenom has published a clinical validation study of its MaterniT Genome test, a noninvasive prenatal test that evaluates genome-wide chromosomal copy number status.
The retrospective, blinded study included plasma samples from over 1,000 pregnant women at an increased risk for fetal chromosomal aneuploidy and was published online this month in the American Journal of Obstetrics and Gynecology.
Abnormalities beyond trisomies 21, 18, 13, and sex chromosome aneuploidies "comprise more than 20 percent of all karyotype-level abnormalities in the general obstetric population," Sequenom CEO Dirk van den Boom said in a statement. As such, "the ability to non-invasively detect chromosomal and sub-chromosomal abnormalities across the genome is critical in clinical practice," he added.
Sequenom launched MaterniT Genome in the third quarter of last year and ran around 3,000 of the tests in the fourth quarter. The test is akin to a karyotyping test, screening for trisomies 21, 18, and 13; sex chromosome aneuploidies; and genome-wide copy number variants that are larger than 7 megabases and select deletions that are smaller than 7 megabases.
In the study, the Sequenom researchers compared the results of MaterniT Genome to an invasive microarray-based test, G-band karyotyping, or high-coverage sequencing.
Of the 1,222 samples originally sent for testing, 11 were excluded due to having no or insufficient microarray or karyotyping results and three were excluded due to confirmed mosaicism. Another 42 samples were non-reportable due to quality issues, like insufficient fetal fraction DNA, leaving 1,166 samples. Of those samples, 153 were positive for aneuploidy in either chromosome 21, 18, 13, X, or Y; while 43 had sub-chromosomal aneuploidies.
The researchers found that the test had an overall sensitivity and specificity of 97.7 percent and 99.9 percent, respectively, for copy number variants. For trisomies 21, 18, and 13, sensitivity and specificity were 100 percent; while for sex chromosomal aneuploidies, the test had had 100 percent sensitivity and 99.9 percent specificity.
In addition, the firm estimated the test had a positive predictive value between 68 percent and 83 percent, depending on the specific alteration, and a negative predictive value of "well over 99.9 percent," the authors wrote.
Sequenom uses a shotgun sequencing strategy for the MaterniT Genome test similar to the one it uses for its MaterniT21 test, with the main difference being that it sequences to higher coverage. In the study, Sequenom generated an average of 32 million reads per sample compared to around 15 to 17 million reads, on average, for the MaterniT21 Plus test with microdeletion analysis.
After sequencing, the reads were partitioned into 50-kilobase pair, non-overlapping segments and the reads per segment were counted and normalized to remove coverage, GC biases, and other artifacts.
To identify genome-wide CNVs, the team used a method called circular binary segmentation, which broke up each chromosome into contiguous regions of equal copy number. Next, they calculated z-scores for the genome-wide CNVs identified by circular binary segmentation as well as whole chromosomes — similar to the method used for the MaterniT21 test. To improve the specificity, the team used an informatics tool called bootstrap analysis, which provided additional confidence in the calls.
The test is geared toward older pregnant women who have a higher risk of fetal aneuploidy, women who have had an abnormal nuchal translucency, serum screen or ultrasound, women with a family history of fetal chromosomal aneuploidy, and women who may have concerns about such conditions.
Van den Boom said in the statement that the firm has so far ran more than 6,000 MaterniT Genome tests and has found that around 25 percent of samples with abnormal results had rare events that "would have been undetectable by other [cell-free] DNA testing methods."