Expanding the Scope of Non-invasive Prenatal Testing to Detect Fetal Chromosomal Copy Number Variations

Abstract

Non-invasive prenatal testing (NIPT) for common fetal trisomies is effective. However, the usefulness of cell-free DNA testing to detect other chromosomal abnormalities is poorly understood. We analyzed the positive rate at different read depths in next-generation sequencing (NGS) and identified a strategy for fetal copy number variant (CNV) detection in NIPT. Pregnant women who underwent NIPT by NGS at read depths of 4–6 M and fetuses with suspected CNVs were analyzed by amniocentesis and chromosomal microarray analysis (CMA). These fetus samples were re-sequenced at a read depth of 25 M and the positive detection rate was determined. With the increase in read depth, the positive CNV detection rate increased. The positive CNV detection rates at 25 M with small fragments were higher by NGS than by karyotype analysis. Increasing read depth in NGS improves the positive CNV detection rate while lowering the false positive detection rate. NIPT by NGS may be an accurate method of fetal chromosome analysis and reduce the rate of birth defects.

The accuracy of cell‐free DNA screening for fetal segmental copy number variants: A systematic review and meta‐analysis

“…Twenty-five of the 63 included studies (39.7%) involved predominately high-risk cohorts. 15,26,28,29,31,35,37,39,41,42,45,51,54,56,57,59,60,62,65,67,71,[73][74][75]78 Six inclusions (9.5%) were validation studies assessing novel cfDNA technologies or algorithms. 15,29,31,39,47,49 Seventeen studies (27.0%) reported cfDNA screening outcomes for 22q.11.2 syndrome (16 reporting PPV 12,14,26,27,30,38,40,47,56,60,65,68,69,73,76,83 and three reporting sensitivity and specificity 39,60,76 ), inc...…”

Cell-Free Fetal DNA and Non-Invasive Prenatal Diagnosis of Chromosomopathies and Pediatric Monogenic Diseases: A Critical Appraisal and Medicolegal Remarks

“…On the contrary, Kaseniit et al, in a 2018 study, reported how, with proper algorithm design and extensive testing, NIPT can achieve high specificity also for CNV alterations [ 52 ]. Songchan et al, in a 2021 study, highlight how an adequate analysis as an NGS method, can be very valid as long as the depth of reading is adequate; this in fact allows us to reduce the percentage of false positives and consequently increase the specificity of the test [ 48 ].…”

“…A major issue with CNV lies in the fact that many alterations detected, in the case of a shallow NGS sequencing, risk not being confirmed and are therefore false positives. Instead, using NGS sequencing of adequate depth could provide an adequate method to detect CNVs with relatively advantageous costs [ 48 ].…”

Prenatal Silver-Russell Syndrome in a Chinese Family Identified by Non-Invasive Prenatal Testing

“…Indeed, CNVs identified by NIPT could be larger or smaller in size than those detected by CMA [Li et al, 2016]. NIPT can provide a good indication of chromosomal imbalances, but the detection is influenced by read counts, type of algorithm, and fetal fraction [Chen et al, 2021]. For a positive NIPT result, further diagnostic investigation is needed to identify the genomic position of chromosomal imbalances at higher precision, and CMA should be performed as a gold standard to confirm the presence of CNVs reported by NIPT.…”