Dataset Information

Count-based size-correction analysis of maternal plasma DNA for improved noninvasive prenatal detection of fetal trisomies 13, 18, and 21.

ABSTRACT:

Purpose

Our goal was to derive more sensitive and accurate Z-scores based on combined DNA count- and size-based algorithms to advance molecular diagnostics for noninvasive prenatal testing of fetal trisomies.

Methods

We included 180 cases at high risk for fetal aneuploidy who underwent amniotic fluid cytogenetic analysis. We calculated their traditional count-based Z-scores, as well as their 100-, 130- and 150-, and 166-bp size-corrected Z-scores, and determined each Z-score's reliability based on its comparison to the cases' cytogenetic results.

Results

We detected for trisomies 13, 18, or 21 among the 180 cases in our study by amniotic testing and DNA sequence analysis. None trisomies 13 was detected, while 1 case of trisomies 18 and 3 cases of trisomies 21 were found. The sensitivity, specificity, and accuracy of traditional count-based Z-scores were 75%, 98.86%, and 98.33%, respectively, while these rates increased to 80%, 99.43%, and 99.44% with a count-based 100- and 166-bp size correction. Moreover, the sensitivity, specificity, and accuracy of count-based Z-scores with 130- and 150-bp size corrections were 100%, and neither of these algorithms yielded false positive trisomies, unlike other evaluated size correction Z-scores.

Conclusions

Count-based Z-scores with 130- and 150-bp size corrections more robustly predict fetal trisomies than count-based methods alone or those combined with other size-correction cutoffs, such as 166 bp. These testing parameters may enhance the utility of DNA sequence-based methods for noninvasive prenatal detection of fetal trisomies.

SUBMITTER: Zhang L

PROVIDER: S-EPMC5527261 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Publications

Count-based size-correction analysis of maternal plasma DNA for improved noninvasive prenatal detection of fetal trisomies 13, 18, and 21.

Zhang Li L Zhu Qian Q Wang He H Liu Shanling S

American journal of translational research 20170715 7

<h4>Purpose</h4>Our goal was to derive more sensitive and accurate Z-scores based on combined DNA count- and size-based algorithms to advance molecular diagnostics for noninvasive prenatal testing of fetal trisomies.<h4>Methods</h4>We included 180 cases at high risk for fetal aneuploidy who underwent amniotic fluid cytogenetic analysis. We calculated their traditional count-based Z-scores, as well as their 100-, 130- and 150-, and 166-bp size-corrected Z-scores, and determined each Z-score's rel ...[more]

PMID: 28804563

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Project description:BackgroundPregnant people have a risk of carrying a fetus affected by a chromosomal anomaly. Prenatal screening is offered to pregnant people to assess their risk. Noninvasive prenatal testing (NIPT) has been introduced clinically, which uses the presence of circulating cell-free fetal DNA in the maternal blood to quantify the risk of a chromosomal anomaly. At the time of writing, NIPT is publicly funded in Ontario for pregnancies at high risk of a chromosomal anomaly.MethodsWe completed a health technology assessment, which included an evaluation of clinical benefits and harms, value for money, budget impact, and patient preferences related to NIPT. We performed a systematic literature search for studies on NIPT for trisomies 21, 18, and 13, sex chromosome aneuploidies, and microdeletions in the average-risk or general population. We evaluated the cost-effectiveness of traditional prenatal screening, NIPT as a second-tier test (performed after traditional prenatal screening), and NIPT as a first-tier test (performed instead of traditional prenatal screening). We also conducted a budget impact analysis to estimate the additional costs of funding first-tier NIPT. We interviewed people who had lived experience with NIPT and people living with the conditions NIPT screens for, or their families.ResultsThe pooled clinical sensitivity of NIPT in the average-risk or general population was 99.5% (95% confidence interval [CI] 81.8%-99.9%) for trisomy 21, 93.1% (95% CI 75.9%-98.3%) for trisomy 18, and 92.7% (95% CI 81.6%-99.9%) for trisomy 13. The clinical specificity for any trisomy was 99.9% (95% CI 99.8%-99.9%). Compared with traditional prenatal screening, NIPT was more accurate in detecting trisomies 21, 18, and 13, and decreased the need for diagnostic testing. We found limited evidence on NIPT for sex chromosome aneuploidies or microdeletions in the average-risk or general population. Positive NIPT results should be confirmed by diagnostic testing.Compared with traditional prenatal screening, second-tier NIPT detected more affected fetuses, substantially reduced the number of diagnostic tests performed, and slightly reduced the total cost of prenatal screening. Compared with second-tier NIPT, first-tier NIPT detected more affected cases, but also led to more diagnostic tests and additional budget of $35 million per year for average-risk pregnant people in Ontario.People who had undergone NIPT were largely supportive of the test and the benefits of earlier, more accurate results. However, many discussed the need for improved pre- and post-test counselling and raised concerns about the quality of the information they received from health care providers about the conditions NIPT can screen for.ConclusionsNIPT is an effective and safe prenatal screening method for trisomies 21, 18, and 13 in the average-risk or general population. Compared with traditional prenatal screening, second-tier NIPT improved the overall performance of prenatal screening and slightly decreased costs. Compared with second-tier NIPT, first-tier NIPT detected more chromosomal anomalies, but resulted in a considerable increase in the total budget. Interviewees were generally positive about NIPT, but they raised concerns about the lack of good informed-choice conversations with primary care providers and the quality of the information they received from health care providers about chromosomal anomalies.

Project description:ObjectiveTo identify pregnancies at increased risk for trisomy 13, trisomy 18 or triploidy attributable to low fetal fraction (FF).MethodsA FF-based risk (FFBR) model was built using data from more than 165 000 singleton pregnancies referred for single-nucleotide polymorphism (SNP)-based non-invasive prenatal testing (NIPT). Based on maternal weight and gestational age (GA), FF distributions for normal, trisomy 13, trisomy 18 and triploid pregnancies were constructed and used to adjust prior risks for these abnormalities. A risk cut-off of ≥ 1% was chosen to define pregnancies at high risk for trisomy 13, trisomy 18 or triploidy (high FFBR score). The model was evaluated on an independent blinded set of pregnancies for which SNP-based NIPT did not return a result, and for which pregnancy outcome information was gathered retrospectively.ResultsThe evaluation cohort comprised 1148 cases, of which approximately half received a high FFBR score. Compared with rates expected based on maternal age (MA) and GA, cases with a high FFBR score had a significantly increased rate of trisomy 13, trisomy 18 or triploidy combined (5.7% vs 0.7%; P < 0.001) and also of unexplained pregnancy loss (14.7% vs 10.4%; P < 0.001). For cases that did not receive a high FFBR score, the incidence of a chromosomal abnormality or pregnancy loss was not significantly different from that expected based on MA and GA. In this study cohort, the sensitivity of the FFBR model for detection of trisomy 13, trisomy 18 or triploidy was 91.4% (95% CI, 76.9-98.2%) with a positive predictive value of 5.7% (32/564; 95% CI, 3.9-7.9%).ConclusionsFor pregnancies with a FF too low to receive a result on standard NIPT, the FFBR algorithm identified a subset of cases at increased risk for trisomy 13, trisomy 18 or triploidy. For the remainder of cases, the risk of a fetal chromosomal abnormality was unchanged from that expected based on MA and GA. © 2018 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of the International Society of Ultrasound in Obstetrics and Gynecology.

Dataset Information

Count-based size-correction analysis of maternal plasma DNA for improved noninvasive prenatal detection of fetal trisomies 13, 18, and 21.

Purpose

Methods

Results

Conclusions

Publications

Count-based size-correction analysis of maternal plasma DNA for improved noninvasive prenatal detection of fetal trisomies 13, 18, and 21.

Similar Datasets

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