Noninvasive Prenatal Testing of Rare Autosomal Aneuploidies by Semiconductor Sequencing

Abstract

Rare autosomal aneuploidies (RAAs) can cause miscarriage or other pregnancy complications and lead to inconsistent results of noninvasive prenatal testing (NIPT), but many NIPT providers have not yet started to provide related services. Our aim was to develop a semiconductor sequencing platform (SSP)-based method for detecting RAAs when pregnant women performed NIPT. Fifty-three aneuploidy samples with verified karyotyping or array comparative genomic hybridization (aCGH) results were collected and subjected to RAAs detection using an SSP to develop a method by genomic sequencing. Various trisomies on all chromosomes other than chromosomes 17 and 19, four multiple aneusomies, one monosomy and five sex chromosome abnormalities were got by our method which can directly identify RAAs via a z-score. Then, artificial mixtures of 10% and 5% DNA were created by adding fragmented fifty-three tissue samples and used in an NIPT simulation to develop a bioinformatics analysis method which can use in NIPT. And the results were in accordance with those of karyotyping and aCGH. Therefore, our method has potential for use in NIPT. Finally, 23,823 clinical plasma samples were tested to verify the performance of our approach. Karyotyping or aCGH was performed on the positive clinical samples. In total, 188 of 23,823 clinical samples were positive (T2, n = 1; T7, n = 1; T13, n = 15; T18, n = 45; T21, n = 125; and multiple aneusomies, n = 1) and verified by karyotyping or aCGH; no sample was a false negative. Several false positives were detected, one of which showed maternal copy number variation (CNV). One case of multiple aneusomies was caused by a maternal tumor. The method developed enables detection of RAAs without increasing costs.

Non-invasive prenatal testing to detect chromosome aneuploidies in 57,204 pregnancies

“…For RCA analysis, chromosome 7 aneuploidy accounted for the largest proportion of NIPT-positive cases on both platforms (Table 2). According to the previous studies, T7 is the most frequently detected chromosomal abnormality [7, 10], which was consistent with our results. However, only one case was confirmed as a true positive among 57,204 cases, and the most common reason for early abortion is the existence of a major fetal chromosomal abnormality [10].…”

“…According to the previous studies, T7 is the most frequently detected chromosomal abnormality [7, 10], which was consistent with our results. However, only one case was confirmed as a true positive among 57,204 cases, and the most common reason for early abortion is the existence of a major fetal chromosomal abnormality [10]. The chromosome 22 aneuploidy case was detected on the Proton platform, perhaps due to the long reads and deeper sequencing leading to an unexpected harvest, but neither NGS platform is currently optimized for detecting RCAs.…”

“…Some publications even revealed RCAs are less rare than previously thought and are often associated with poor obstetric outcomes [8]. Multiple groups have emphasized the importance of detecting RCAs for monitoring pregnancy health and minimizing the frequency of false-positive and false-negative NIPT results [9, 10].…”