Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study

Abstract

Objectives To validate the clinical efficacy and practical feasibility of massively parallel maternal plasma DNA sequencing to screen for fetal trisomy 21 among high risk pregnancies clinically indicated for amniocentesis or chorionic villus sampling. Design Diagnostic accuracy validated against full karyotyping, using prospectively collected or archived maternal plasma samples. Setting Prenatal diagnostic units in Hong Kong, United Kingdom, and the Netherlands. Participants 753 pregnant women at high risk for fetal trisomy 21 who underwent definitive diagnosis by full karyotyping, of whom 86 had a fetus with trisomy 21. Intervention Multiplexed massively parallel sequencing of DNA molecules in maternal plasma according to two protocols with different levels of sample throughput: 2-plex and 8-plex sequencing. Main outcome measures Proportion of DNA molecules that originated from chromosome 21. A trisomy 21 fetus was diagnosed when the z score for the proportion of chromosome 21 DNA molecules was >3. Diagnostic sensitivity, specificity, positive predictive value, and negative predictive value were calculated for trisomy 21 detection. Results Results were available from 753 pregnancies with the 8-plex sequencing protocol and from 314 pregnancies with the 2-plex protocol. The performance of the 2-plex protocol was superior to that of the 8-plex protocol. With the 2-plex protocol, trisomy 21 fetuses were detected at 100% sensitivity and 97.9% specificity, which resulted in a positive predictive value of 96.6% and negative predictive value of 100%. The 8-plex protocol detected 79.1% of the trisomy 21 fetuses and 98.9% specificity, giving a positive predictive value of 91.9% and negative predictive value of 96.9%. ConclusionMultiplexed maternal plasma DNA sequencing analysis could be used to rule out fetal trisomy 21 among high risk pregnancies. If referrals for amniocentesis or chorionic villus sampling were based on the sequencing test results, about 98% of the invasive diagnostic procedures could be avoided.

Women’s and health professionals’ preferences for prenatal tests for Down syndrome: a discrete choice experiment to contrast noninvasive prenatal diagnosis with current invasive tests

“…5 The technology underpinning noninvasive prenatal diagnosis (NIPD) for Down syndrome has advanced rapidly and several large scale validity studies have now been conducted to evaluate testing based on massively parallel sequencing. [6][7][8] Moreover, the first NIPD tests for Down syndrome are now available commercially in some countries 9 and considerations for more widespread implementation are being debated. 10 Validation of NIPD for Down syndrome using sequencing approaches is, however, ongoing and the test is not yet considered fully diagnostic as the small, but significant rate of false positives means an invasive test is still required to confirm a positive result.…”

Targeted next-generation sequencing as a comprehensive test for patients with and female carriers of DMD/BMD: a multi-population diagnostic study

“…The sequencing depth of a mutated exon would be out of the range of the Gaussian distribution, but lie within the range after rectification by the theoretical CFs. 21 However, due to inevitable inter-batch differences and variability of targeted NGS approaches, some falsepositive results were intermingled with true CNVs. Therefore, we used the intra-batch ratio to further distinguish the CNVs from falsepositive results (step 3).…”

On the future of genetic risk assessment

“…To put this into perspective, the Down syndrome risk for children of 37 years old mothers is also about 0.5 %, and there is consensus in our society that this justifies prenatal diagnosis, in spite of the small, but measurable risk that this intervention will induce an abortion (reliable non-invasive prenatal tests are under development, but so far, only for excluding Down syndrome, e.g. see Chiu et al 2011;Papageorgiou et al 2011). In contrast, preconceptual carrier testing for severe recessive disorders is a non-invasive procedure that can be done on blood, hair roots or even buccal smear of the parents.…”