Sensitivity Of Non-invasive Prenatal Testing Research Articles

Značaj NIPT U kombinaciji sa serumom bez DNK ćelija, estriolom, AFP i nivoom b-HCG U prepoznavanju trizomije 21 i 18 u drugom trimestru

Background: This study aimed to evaluate the clinical application value of noninvasive prenatal testing from DNA (NIPT) and serum screening for screening in detecting fetal trisomy 21 and 18. Methods: As a retrospective analysis, we collected data from 1383 women (singleton pregnancy) who underwent serum screening and noninvasive prenatal testing from DNA (NIPT) in our department from May 2015 to September 2017 and calculated the diagnostic value of the two methods. Results: In 1383 cases, the sensitivity of serum screening to trisomy 21 and 18 was 76.9%, specificity 74.7%, PPV 2.9%, NPV 99.7%, and AUC 0.758 (95% CI: 0.625-0.891). The sensitivity of noninvasive prenatal testing from DNA (NIPT) to trisomy 21 and 18 was 100%, specificity 99.8%, PPV 81%, NPV 100%, and AUC 0.999 (95% CI: 0.000-1.000). Conclusion: Serum screening can detect high-risk pregnant women in time, but the incidence of false positives and negatives is high; the accuracy of noninvasive prenatal testing from DNA (NIPT) is high, which can effectively reduce the rate of defective babies.

Retrospective analysis for 424 330 first-line screening results of non-invasive prenatal testing in Hebei province

Objective: To evaluate the effect of noninvasive prenatal testing (NIPT) as first-line screening in fetal chromosome aneuploidy screening practice, and to provide evidence for the prevention and control strategy of birth defects. Methods: Since July 2019, Hebei province had carried out the NIPT project providing first-line screening for eligible pregnant women in the area (except for those who were not applicable). Pregnant women with high risk received genetic counseling, prenatal diagnosis and intervention guidance. Low risk and false-positive ones received continuous detection and moved to prenatal diagnosis center for counseling and diagnosis if abnormities were discovered. All pregnant women were followed up to learn about pregnancy outcomes and newborn health status. Detection results and clinical data of pregnant women participating the NIPT project from July 2019 to July 2020 were collected. The detection results and effect of NIPT were analyzed. Results: (1) Basic information of the screened population: A total of 424 330 pregnant women were screened, and 423 596 were successfully detected, with a success rate of 99.83% (423 596/424 330). The age of pregnant women was (28.8±4.5) years old; the gestational age of screening was (16.6±2.3) weeks; the proportion of advanced-age pregnant women (≥35 years old) was 10.18% (43 132/423 596); in vitro fertilization-embryo transfer (IVF-ET) rate was 1.58% (6 713/423 596); the twin rate was 1.38% (5 849/423 596); the proportion of primipara was 34.23% (144 977/423 596). (2) Screening results and detection performance: totally, 325, 73 and 20 pregnant women were diagnosed with trisomy 21, 18 and 13; the sensitivity were 99.39%, 100.00% and 100.00%; the specificity were 99.98%, 99.99% and 99.98%; the positive predictive value were 75.76%, 68.87% and 21.51%, respectively. Besides, 249 190 pregnant women were received supplementary reports as well, and 255, 10 and 9 were confirmed for sex chromosome aneuploidy, other autosomal aneuploidy and deletion/duplication syndrome; the positive predictive value were 37.78%, 6.06% and 32.14%, respectively. The sensitivity of NIPT for target trisomy (trisomy 21, 18 and 13) screening in advanced-age, IVF-ET and twin pregnant women were 99.29%, 100.00% and 90.00%, respectively; the specificity were 99.93% for all; the positive predictive value were 82.25%, 61.54% and 69.23%, respectively. Conclusions: NIPT has a significant effect and good performance in the first-line screening of fetal chromosome aneuploidy in the whole population, which might provide reference for the improvement of birth defect prevention and control strategy.

The accuracy and feasibility of noninvasive prenatal testing in a consecutive series of 20,626 pregnancies with different clinical characteristics.

BackgroundTo evaluate the accuracy and feasibility of noninvasive prenatal testing (NIPT) according to the results of NIPT and pregnancy outcomes with different indications.MethodsBetween October 2014 and December 2020, 20,626 pregnant women who received NIPT were included in this study. The positive predictive value (PPV) of trisomy 21, 18, and 13 (T21, T18, T13), sex chromosome abnormalities (SCAs), other chromosomal aneuploidies, and chromosomal microdeletion/microduplication were calculated. The positive results of NIPT were confirmed by amniocentesis, Karyotype analysis, and chromosome microarray analysis (CMA).ResultsIn total, 263 positive cases (263/20,626, 1.28%) were detected by NIPT, of which T21, T18, and T13 were 69, 26, and 9 cases, respectively. Sex chromosome abnormalities (SCAs), other chromosomal aneuploidies, and copy number variants (CNVs) were 69, 12, and 38 cases, respectively. There were true positive in 49 of T21, 13 of T18, 1 of T13, 32 of SCAs, 1 of other chromosomal aneuploidies, and 15 of CNVs. The NIPT sensitivity of T21, T18, T13, SCAs, other chromosomal aneuploidies, and CNVs was all 100%, the specialty was 99.90%, 99.94%, 99.96%, 99.82%, 99.95%, 99.89%, and the PPV was 71.01%, 50.00%, 11.11%, 46.38%, 8.33%, 39.47%, respectively. The PPV was high in T21, moderate in T18 and SCAs, and low in T13 and other chromosomal abnormalities.ConclusionNIPT has high accuracy, specificity and and can effectively avoid the occurrence of birth defects, but it cannot replace prenatal diagnosis. The accuracy, specificity, and sensitivity of NIPT in detecting sex chromosomes, chromosome microdeletion/microduplication, and other chromosomal abnormalities should be improved.

Application analysis of noninvasive prenatal testing for fetal chromosome copy number variations in Chinese laboratories

Objective: To investigate the general situation, detection range, testing reagents, and clinical performance of non-invasive prenatal testing (NIPT) for fetal chromosomal copy number variations (CNVs) in Chinese laboratories. Methods: The National Center for Clinical Laboratories of the National Health Commission designed a questionnaire for the detection of CNVs by NIPT, which included the investigation of whether the laboratory has carried out NIPT to detect CNVs and its testing scope, reagents/platforms, intended uses, screening populations and clinical performance. The questionnaires were distributed to 355 laboratories in 31 provinces, autonomous regions, and municipalities across the country on October, 2020. Further, the feedbacks were statistical analyzed. Results: Two hundred and twenty-eight laboratories had performed NIPT to detect CNVs, including 116 types of CNVs, and more than 95% of laboratories chose to detect the CNVs of 5p15 deletion, 22q11.2 deletion, 1p36 deletion, and 15q11.2 deletion. All testing reagents used were laboratory-developed tests and were based on massive parallel sequencing, the minimum amount of sequencing data was 3-15 M reads, the detection limit of fetal fraction was 3%-5%, and the minimum size of variants that can be detected was 1-5 Mb. The proportion of laboratories that apply CNVs testing for daily project, voluntary requirements of patients, and scientific research were 58.8% (134/228), 57.5% (131/228), and 20.6% (47/228), respectively. One hundred and thirty-four laboratories were fully or partially aware of the clinical performance of NIPT to detect microdeletion/microduplication syndromes, and the laboratories' declared sensitivity of NIPT for Cri du Chat syndrome, 22q11.2 deletion syndrome, 1p36 deletion syndrome, and Angelman syndrome were 50.0%-100%, 60.0%-100%, 50.0%-100%, and 33.3%-100%, and the positive predictive values were 9.0%-50.0%, 18.0%-100%, 20.0%-30.0%, and 20.0%. Conclusion: The detection of CNVs by NIPT in Chinese laboratories need to be standardized. Laboratories should detect CNVs with clear clinical significance in accordance with the guidelines, conduct performance validation of the reagents, then perform NIPT test and provide adequate interpretation after mastering the clinical performance sufficiently.

Performance of cell-free DNA sequencing-based non-invasive prenatal testing: experience on 36,456 singleton and multiple pregnancies

BackgroundThis paper describes the clinical practice and performance of cell-free DNA sequencing-based non-invasive prenatal testing (NIPT) as a screening method for fetal trisomy 21, 18, and 13 (T21, T18, and T13) and sex chromosome aneuploidies (SCA) in a general Italian pregnancy population.MethodsThe AMES-accredited laboratory offers NIPT in maternal blood as a screening test for fetal T21, T18, T13 and SCA. Samples were sequenced on a NextSeq 550 (Illumina) using the VeriSeq NIPT Solution v1 assay.ResultsA retrospective analysis was performed on 36,456 consecutive maternal blood samples, including 35,650 singleton pregnancies, 800 twin pregnancies, and 6 triplet pregnancies. Samples were tested between April 2017 and September 2019. The cohort included 46% elevated-risk and 54% low-risk patients. A result indicative of a classic trisomy was found in 356 (1%) of singleton or twin samples: 254 T21, 69 T18, and 33 T13. In addition, 145 results (0.4%) were indicative of a SCA. Of the combined 501 screen-positive cases, 484 had confirmatory diagnostic testing. NIPT results were confirmed in 99.2% (247/249) of T21 cases, 91.2% (62/68) of T18 cases, 84.4% (27/32) of T13 cases, and 86.7% (117/135) of SCA cases. In the 35,955 cases reported as unaffected by a classic trisomy or SCA, no false negative cases were reported. Assuming that false negative results would be reported, the sensitivity of NIPT was 100.00% for T21 (95% Cl 98.47–100.0), T18 (95% Cl 94.17–100.0), and T13 (95% Cl 87.54–100.0). The specificities were 99.99% (95% Cl 99.98–100.0), 99.98% (95% Cl 99.96–100.0), 99.99% (95% Cl 99.97–100.0), and 99.95% (95% Cl 99.92–99.97) for T21, T18, T13, and SCA, respectively.ConclusionThis retrospective analysis of a large cohort of consecutive patients who had whole-genome sequencing-based NIPT for classic trisomies and SCA shows excellent detection rates and low false positive rates.

Next-generation sequencing: a follow-up of 36,913 singleton pregnancies with noninvasive prenatal testing in central China

PurposeTo evaluate the noninvasive prenatal testing (NIPT) results of 36,913 cases in Jiangxi province of central China and explore its application value in prenatal screening and diagnosis.MethodsThis retrospective analysis included 36,913 singleton pregnant women who underwent NIPT because of moderate-/high-risk pregnancy or voluntary requirements between January 2017 and December 2019 in our hospital. Chromosomal abnormalities such as trisomies 21, 18, and 13 (T21, T18, T13) and sex chromosome aneuploidies (SCAs) were judged by standard Z-score analysis. Positive NIPT results were confirmed by amniocentesis and karyotyping. Pregnancy outcomes were followed up via telephone interview.ResultsA total of 1.01% (371/36,913) positive cases were detected by NIPT, comprising 137, 46, 31, and 157 cases of T21, T18, T13, and SCAs, respectively. A total of 116 of T21, 27 of T18, 13 of T13, and 51 of SCAs were confirmed to be true positive; all normal cases that had been followed up were verified to be true negative. The NIPT sensitivity in T21, T18, T13, and SCAs was 100.00% individually, whereas the specificity was 99.94% (36,488/36,509), 99.95% (36,579/36,598), 99.95% (36,594/36,612), and 99.72% (36,472/36,574), respectively. Furthermore, the negative predictive values of T21, T18, T13, and SCAs were all 100%, while the positive predictive values were 84.67%, 58.70%, 41.94%, and 33.33%, respectively.ConclusionNIPT is highly sensitive and has a low false positive rate in testing clinically significant fetal aneuploidies of general reproductive women. However, this technique cannot substitute for amniocentesis and karyotyping, and detailed genetic counseling is also essential for the high-risk group of NIPT.

Clinical Application of Cell-Free DNA Sequencing-Based Noninvasive Prenatal Testing for Trisomies 21, 18, 13 and Sex Chromosome Aneuploidy in a Mixed-Risk Population in Iran

Purpose: To report the clinical experience and performance of plasma cell-free DNA sequencing-based noninvasive ­prenatal testing (NIPT) as a screening method in detecting trisomy 21, 18, 13 (T21/T18/T13) as well as sex chromosome aneuploidy (SCA) in a mixed-risk population in Iran. Methods: In a 2-year period between January 1, 2015, and December 31, 2016, over 150 medical centers in Iran offered NIPT as clinical screening tests for fetal T21, T18, T13 and SCA. All NIPT positive cases were recommended to undergo invasive prenatal diagnosis. Results: 11,414 maternal blood samples were received for NIPT, for which 11,223 samples obtained NIPT results. Among 11,213 cases with confirmatory results, 94 T21, 39 T18, 8 T13, 15 XO, 6 XXX, 3 XYY, 5 XXY and 11,042 euploid cases were detected. The overall sensitivity of NIPT was 98.90, 100.00, 100.00, 90.91, 100.00, 100.00 and 100.00%, and specificities were 99.96, 99.97, 99.99, 99.96, 99.98, 100.00 and 99.99% for detecting T21, T18, T13, XO, XXX, XYY and XXY, respectively. Conclusion: With a stringent protocol, our prospective large-scale multicentric nationwide study demonstrated that NIPT showed excellent performance as screening test for the detection of fetal T21, T18, T13 and SCA in mixed-risk pregnancies in Iran.

Comparison of Efficiencies of Non-invasive Prenatal Testing, Karyotyping, and Chromosomal Micro-Array for Diagnosing Fetal Chromosomal Anomalies in the Second and Third Trimesters.

In this study, we aimed to compare the efficiency of non-invasive prenatal testing (NIPT), karyotyping, and chromosomal micro-array (CMA) for the diagnosis of fetal chromosomal anomalies in the second and third trimesters. Pregnant women, who underwent amniocenteses for prenatal genetic diagnoses during their middle and late trimesters, were recruited at the Prenatal Diagnosis Center of Taizhou City. Maternal blood was separated for NIPT, and amniotic fluid cells were cultured for karyotyping and CMA. The diagnostic efficiency of NIPT for detecting fetal imbalanced anomalies was compared with karyotyping and CMA. A total of 69 fetal chromosomal imbalances were confirmed by CMA, 37 were diagnosed by NIPT and 35 were found by karyotyping. The sensitivities of NIPT and karyotyping for diagnosing aneuploidy were 96.3% and 100% respectively. Only one mosaic sexual chromosome monosomy was misdiagnosed by NIPT, whereas the sensitivity of NIPT and karyotyping was 70% and 30%, respectively, for detecting pathogenic deletions and duplications sized from 5–20 Mb. Taken together, our results suggest that the efficiency of NIPT was similar to the formula karyotyping for detecting chromosome imbalance in the second and third trimesters.

Enrichment of fetal and maternal long cell-free DNA fragments from maternal plasma following DNA repair.

ObjectiveCell‐free DNA (cfDNA) fragments in maternal plasma contain DNA damage and may negatively impact the sensitivity of noninvasive prenatal testing (NIPT). However, some of these DNA damages are potentially reparable. We aimed to recover these damaged cfDNA molecules using PreCR DNA repair mix.MethodscfDNA was extracted from 20 maternal plasma samples and was repaired and sequenced by the Illumina platform. Size profiles and fetal DNA fraction changes of repaired samples were characterized. Targeted sequencing of chromosome Y sequences was used to enrich fetal cfDNA molecules following repair. Single‐molecule real‐time (SMRT) sequencing platform was employed to characterize long (>250 bp) cfDNA molecules. NIPT of five trisomy 21 samples was performed.ResultsSize profiles of repaired libraries were altered, with significantly increased long (>250 bp) cfDNA molecules. Single nucleotide polymorphism (SNP)‐based analyses showed that both fetal‐ and maternal‐derived cfDNA molecules were enriched by the repair. Fetal DNA fractions in maternal plasma showed a small but consistent (4.8%) increase, which were contributed by a higher increment of long fetal cfDNA molecules. z‐score values were improved in NIPT of all trisomy 21 samples.ConclusionPlasma DNA repair recovers and enriches long cfDNA molecules of both fetal and maternal origins in maternal plasma.

Non-invasive Prenatal Testing: A Unique Approach with Single Nucleotide Polymorphism

AbstractThe purpose of this review is to demonstrate the unique properties of a single nucleotide polymorphism (SNP)-based approach in non-invasive prenatal testing (NIPT). The identification of cell free fetal DNA in the plasma of pregnant women led to the development of NIPT. This can be performed with either a quantitative approach (massively parallel shotgun sequencing, chromosome selective sequencing) or a qualitative approach (SNP-based). NIPT tests have been shown to have superior performance as a screen for common fetal chromosome abnormalities compared with maternal serum screening. At low fetal fractions, NIPT sensitivity falls, particularly when quantitative methods are used. A SNP-based approach allows both accurate assessment of fetal fraction, and a robust test performance at lower fetal fractions. The ability of the SNP-based approach to screen for vanishing twins and maternal copy number variants reduces false positives; and the ability to make high confidence calls at lower fetal fraction, minimizes discordance between the NIPT result and the true fetal status.

Specificity and Sensitivity of NIPT for Prenatal Screening of Down Syndrome in 100 Pregnant Women from Tonekabon, Iran

Down syndrome is one of the most common genetic disorders, with a prevalence of one in 600 live births. There are numerous methods for diagnosis of this syndrome before birth such as non-invasive prenatal testing (NIPT). This test evaluates positive and negative predictive values of Down syndrome screening as well as determining the gender of the fetus. Data were collected from 100 pregnant women who visited obstetrics and gynecology clinic of Tonekabon Hospital, Tonekabon, Iran. The average age of pregnant women was 35.9 and the average gestational age was 12 to 13 weeks. About 40% of participating mothers had a history of previous pregnancies (32%), 45% of mothers had no history of live births and none of them had a family history of developing Down syndrome. According to the results, 56 percent of babies were male and 44 percent were female and none of the fetuses had Down syndrome. Results of the present study also indicated that NIPT sensitivity and specificity in the diagnosis of Down syndrome and also the baby's gender were 100%. The positive and negative predictive values were also 100% as well. This study has shown that NIPT as a diagnostic test is used to detect Down syndrome in all pregnancies, including high-risk pregnancies such as cases with high maternal age. Another important issue which has to be taken into account is a source of support such as Insurance coverage for the test.

Knowledge and future preference of Chinese women in a major public hospital in Hong Kong after undergoing non-invasive prenatal testing for positive aneuploidy screening: a questionnaire survey.

BackgroundDespite the non-invasive nature of non-invasive prenatal testing (NIPT), there is still a need for a separate informed consent process before testing. The objectives of this study are to assess (a) knowledge and preferences of Chinese women in a major public hospital in Hong Kong who underwent NIPT, and (b) whether their knowledge and preferences differ depending on womens’ characteristics and sources of information.MethodsSetting: prenatal diagnosis and counselling clinic.Between February 2012 and September 2013, a questionnaire survey was distributed to all women who underwent NIPT after positive aneuploidy screening. As a pilot study, ten knowledge questions were designed based on the rapid response statement on Prenatal Detection of Down Syndrome using Massively Parallel Sequencing from the International Society for Prenatal Diagnosis in 2011. The source of women’s knowledge and their preferences were also evaluated. While conventional screening was publicly funded, NIPT was not. Differences between subgroups were compared using chi square tests and logistic regression analysis.ResultsOf 152 women who underwent NIPT, 135 (88.8 %) completed their questionnaires. More than 90 % of women recognised the possibility of false positive and false negative results. Slightly more than 70 % of women knew the inferior sensitivity of NIPT compared to an invasive test, and the possibility of an uninformative test result, but were not aware of the complicated aspects of NIPT. Pregnant women with an advanced level of education or those who underwent NIPT before 15 weeks provided answers that was more accurate by around 10-20 % in two to three knowledge questions than those without. These associations were confirmed by multivariate logistic regression analysis. The women received information on NIPT largely from their private doctors (47.4 %) and web (41.5 %). In their future pregnancies, more women would opt for NIPT (a self-financed item) after positive screening (‘free’ in a public hospital) (57.8 %) than as a primary screening (30.4 %).ConclusionsIt is feasible to use a questionnaire based on the ISPD statement on NIPT to assess women’s knowledge of the test. The Chinese women who underwent NIPT recognised the limitations, but did not understand the complicated aspects. More information should be provided by health care professionals in order to facilitate an informed choice by patients. More women preferred NIPT as a contingent test than as a primary screening probably because of its high cost.

Noninvasive Prenatal Test Raises Concern Over Screening Strategies and the Role of Ultrasound

Noninvasive Prenatal Test Raises Concern Over Screening Strategies and the Role of Ultrasound