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NIPT Should Be Broadened Beyond Most Common Trisomies, New Study Suggests

NEW YORK (GenomeWeb) – Based on a new study, a team of Swiss researchers has made a case for expanding noninvasive prenatal testing beyond the three common trisomies — T21, T18, and T13 — and sex-chromosome anomalies to which many current NIPT assays limit themselves.

Because of the significantly lower sensitivity that NIPT technologies have to detect rarer aneuploidies and other conditions, such expansion has been a controversial proposition. However, in their new study — published yesterday in Genetics in Medicine — the authors presented evidence that with better false positive and false negative rates, including these additional targets makes sense.

The team — from Swiss genomics and pathology labs Aurigen, Genesupport, Fasteris, and the Swiss Institute of Bioinformatics — began its exploration of NIPT's ability to detect a larger class of abnormalities based on growing evidence that a substantial fraction of clinically relevant aneuploidies are missed by more restricted detection schemes.

For example, common trisomies comprise only about 75 percent of aneuploidies detected by karyotyping in Down syndrome screen-positive cases, the Swiss team wrote.

According to the authors, the main aneuploidy classes missed are rare autosomal trisomies and sub-chromosomal anomalies, specifically disease-causing copy-number variations.

Studies that have followed the outcomes of pregnancies have confirmed that rare pathogenic aneuploidies, like T22 mosaicism, are overlooked by tests that set their boundaries only around T21, 18, and 13. In additional to fetal mosaic trisomies, uniparental disomy is also a source of fetal pathology, and even placental trisomies account for a low but significant risk of issues like fetal growth restriction, according to the Swiss research team.

Where CNVs are concerned, there are estimates that alterations longer than 400 kilobases account for almost 15 percent of disease burden in children affected by intellectual disability. While CNVs have posed a more challenging target in NIPT than chromosomal aneuploidy, recent advances have shown that cfDNA testing can be extended to include reliable CNV detection.

Despite some research that has called into question the ease and reliability of calling subchromosomal alterations in NIPT, US-based companies like Natera and Sequenom have recently expanded their menus to include microdeletions, including 22q11.2 (DiGeorge syndrome), 1p36 deletion syndrome, Angelman syndrome, Cri-du-chat syndrome, and Prader-Willi syndrome.

The Swiss study authors previously published a validation of their own cfDNA screening approach, covering a broader array of anomalies, including not just common trisomies and sex-chromosome anomalies (SCAs) but also rare autosomal trisomies and CNVs.

In their new study, the investigators reported on their testing of a series of 6,388 consecutive singleton pregnancies with nearly complete follow-up to compare NIPT results to post-delivery diagnoses or confirmatory tests.

Unlike their earlier study, the team also integrated fetal fraction measurements and a fetal cfDNA enrichment procedure in this work, using the latter in conjunction with signal statistical methods to determine the main sources of false negative results, to stratify the likelihood of true positive versus false positive results, and to establish the detection threshold for recurrent pathogenic CNVs.

Overall, 258 out of 6,388, or about four percent of the samples, were considered abnormal or likely abnormal, comprising 119 common trisomies, 53 SCAs, 50 rare autosomal trisomies, and 36 CNVs. The other 6,130 samples were deemed normal or likely normal.

In addition to the 119 common trisomies classified as abnormal or likely abnormal, there were also 15 cases rated as having unknown clinical significance based on statistical scores below the cutoff threshold.

Of the 53 SCAs, 38 were monosomy X, 10 triple X syndrome, and 5 Klinefelter syndrome.

According to the authors, CNVs were most frequent in two genomic regions known to undergo recurrent rearrangements and to overlap with well-known genomic disorders. They found two deletions and two duplications of the DGS region 22q11.2, and two deletions and two duplications of the 16p13.11 region.

Based on their tracking of follow-up test results and pregnancy outcomes, the researchers determined false positive and negative rates for all classes of alterations.

The group reported both very high detection rates and very low false positive rates for the common trisomies. Overall, only two false negatives were recorded, both for T18, one caused by a low fetal fraction and the other due to likely fetal mosaicism.

Consistent with their earlier technical validation study, the authors wrote, there was similar performance for sex chromosome abnormalities. Accuracy was also similar for rare autosomal trisomies, the authors wrote, with positive predictive values closely reflected by CVS data.

After initially taking a genome-wide approach to CNV detection, the authors wrote that their data in these 6,000 cases supports a narrower screening strategy, because there is a lack of data on phenotypic consequences for most if not all non-recurrent CNVs.

Overall, based on the results, the group recommended cfDNA-based NIPT screening should be extended to include detection of rare autosomal triosomies and CNVs limited to those associated with well-characterized genomic disorders, which will likely expand with time.