Noninvasive prenatal testing for chromosome aneuploidies and subchromosomal microdeletions/microduplications in a cohort of 42,910 single pregnancies with different clinical features.
Chen Yibo,Yu Qi,Mao Xiongying,Lei Wei,He Miaonan,Lu Wenbo
Human genomics
BACKGROUND:Since the discovery of cell-free DNA (cfDNA) in maternal plasma, it has opened up new approaches for non-invasive prenatal testing. With the development of whole-genome sequencing, small subchromosomal deletions and duplications could be found by NIPT. This study is to review the efficacy of NIPT as a screening test for aneuploidies and CNVs in 42,910 single pregnancies. METHODS:A total of 42,910 single pregnancies with different clinical features were recruited. The cell-free fetal DNA was directly sequenced. Each of the chromosome aneuploidies and the subchromosomal microdeletions/microduplications of PPV were analyzed. RESULTS:A total of 534 pregnancies (1.24%) were abnormal results detected by NIPT, and 403 pregnancies had underwent prenatal diagnosis. The positive predictive value (PPV) for trisomy 21(T21), trisomy 18 (T18), trisomy 13 (T13), sex chromosome aneuploidies (SCAs), and other chromosome aneuploidy was 79.23%, 54.84%, 13.79%, 33.04%, and 9.38% respectively. The PPV for CNVs was 28.99%. The PPV for CNVs ≤ 5 Mb is 20.83%, for within 5-10 Mb 50.00%, for > 10 Mb 27.27% respectively. PPVs of NIPT according to pregnancies characteristics are also different. CONCLUSION:Our data have potential significance in demonstrating the usefulness of NIPT profiling not only for common whole chromosome aneuploidies but also for CNVs. However, this newest method is still in its infancy for CNVs. There is still a need for clinical validation studies with accurate detection rates and false positive rates in clinical practice.
10.1186/s40246-019-0250-2
Non-invasive prenatal screening versus prenatal diagnosis by array comparative genomic hybridization: a comparative retrospective study.
Sotiriadis Alexandros,Papoulidis Ioannis,Siomou Elisavet,Papageorgiou Elena,Eleftheriades Makarios,Papadopoulos Vasilios,Alexiou Maria,Manolakos Emmanouil,Athanasiadis Apostolos
Prenatal diagnosis
OBJECTIVE:To calculate the proportion of array comparative genomic hybridization (aCGH) pathogenic results, that would not be detectable by non-invasive prenatal screening (NIPS). METHODS:This is a comparative study using data from 2779 fetuses, which underwent invasive prenatal diagnosis, and the samples were analyzed using aCGH. The simulated NIPS assay would test for trisomies 21, 18, 13, monosomy X, 47, XXX, 47, XYY, and 47, XXY. Indications for invasive testing were grouped into categories and the absolute, relative rates of pathogenic/likely pathogenic results of aCGH analysis that would not be detectable by NIPS were calculated. RESULTS:The expected rate of aCGH-detected abnormalities that would not be detectable by NIPS was 28.0% (95% CI 14.3-47.6) for nuchal translucency (NT) 95 to 99th centile; 14.3% (95% 5.0-34.6) for NT > 99th centile; 34.2% (95% CI 21.1-50.1) for high-risk first-trimester results (regardless of NT); 52.4% (95% CI 32.4-71.7) for second-trimester markers; and 50.0% (95% CI 26.8-73.2) for advanced maternal age. The overall rate of aCGH pathogenic/likely pathogenic results was 5.0% and 44.0% (95% CI 36.0-52.2) of them would not be detected by NIPS. CONCLUSIONS:Approximately half of the abnormal aCGH results would not be detectable by standard NIPS assays, highlighting the necessity of pre-test counseling, and illustrating the limitations of NIPS. © 2017 John Wiley & Sons, Ltd.
10.1002/pd.5051
[Application analysis of noninvasive prenatal testing for fetal chromosome copy number variations in Chinese laboratories].
Shi J P,Tan P,Li J M,Zhang R
Zhonghua yi xue za zhi
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. 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. 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%. 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.
10.3760/cma.j.cn112137-20210125-00238
Factors affecting cell-free DNA fetal fraction: statistical analysis of 13,661 maternal plasmas for non-invasive prenatal screening.
Hou Yaping,Yang Jiexia,Qi Yiming,Guo Fangfang,Peng Haishan,Wang Dongmei,Wang Yixia,Luo Xiaohui,Li Yi,Yin Aihua
Human genomics
BACKGROUND:The identification of cell-free fetal DNA (cffDNA) facilitated non-invasive prenatal screening (NIPS) through analysis of cffDNA in maternal plasma. However, challenges regarding its clinical implementation become apparent. Factors affecting fetal fraction should be clarified to guide its clinical application. RESULTS:A total of 13,661 pregnant subjects with singleton pregnancies who undertook NIPS were included in the study. Relationship of gestational age, maternal BMI, and maternal age with the cffDNA fetal fraction in maternal plasmas for NIPS was investigated. Compared with 13 weeks (12.74%) and 14-18 weeks group (12.73%), the fetal fraction in gestational ages of 19-23 weeks, 24-28 weeks, and more than 29 weeks groups significantly increased to 13.11%, 16.14%, and 21.17%, respectively (P < 0.01). Compared with fetal fraction of 14.54% in the maternal BMI group of < 18.5 kg/m, the percentage of fetal fraction in the group of 18.5-24.9 kg/m (13.37%), 25-29.9 kg/m (12.20%), 30-34.9 kg/m (11.32%), and 35-39.9 kg/m (11.57%) decreased significantly (P < 0.01). Compared with the fetal fraction of 14.38% in the group of 18-24 years old, the fetal fraction in the maternal age group of 25-29 years old group (13.98%) (P < 0.05), 30-34 years old group (13.18%) (P < 0.01), 35-39 years old group (12.34%) (P < 0.01), and ≥ 40 years old (11.90%) group (P < 0.01) decreased significantly. CONCLUSIONS:The percentage of fetal fraction significantly increased with increase of gestational age. Decreased fetal fraction with increasing maternal BMI was found. Maternal age was also negatively related to the fetal fraction.
10.1186/s40246-019-0244-0
Performance of semiconductor sequencing platform for non-invasive prenatal genetic screening for fetal aneuploidy: results from a multicenter prospective cohort study in a clinical setting.
El Khattabi L Allach,Brun S,Gueguen P,Chatron N,Guichoux E,Schutz S,Nectoux J,Sorlin A,Quere M,Boudjarane J,Tsatsaris V,Mandelbrot L,Schluth-Bolard C,Dupont J M,Rooryck C,
Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology
OBJECTIVE:To validate and evaluate the performance metrics of the high-throughput semiconductor sequencing platform, Ion Proton®, in non-invasive prenatal genetic screening (NIPS) for common fetal aneuploidies in a clinical setting. METHODS:This prospective cohort study included 2505 pregnant women from eight academic genetics laboratories (695 high risk for trisomy 21 (risk ≥ 1/250) pregnancies in a validation study, and 1810 such pregnancies, without ultrasound anomalies, in a real-life NIPS clinical setting). Outcome was available for all cases in the validation cohort and for 521 in the clinical cohort. Cell-free DNA from plasma samples was sequenced using the Ion Proton sequencer, and sequencing data were analyzed using the open-access software, WISECONDOR. Performance metrics for detection of trisomies 21, 18 and 13 were calculated based on either fetal karyotype result or clinical data collected at birth. We also evaluated the failure rate and compared three methods of fetal fraction quantification (RASSF1A assay, and DEFRAG and SANEFALCON software). RESULTS:Results from both cohorts were consistent and their gestational age was not significantly different so their data were combined to increase the sample size for analysis. Sensitivities and specificities, respectively, were as follows: for trisomy 21, 98.3% (95% CI, 93.5-99.7%) and 99.9% (95% CI, 99.4-100%); for trisomy 18, 96.7% (95% CI, 80.9-99.8%) and 100% (95% CI, 99.6-100%); and for trisomy 13, 94.1% (95% CI, 69.2-99.7%) and 100% (95% CI, 99.6-100%). Our failure rate was 1.2% initially and as low as 0.6% after retesting some of the failed samples. Fetal fraction estimation by the RASSF1A assay was consistent with DEFRAG results, and both were adequate for routine diagnosis. CONCLUSIONS:We describe one of the largest studies evaluating Ion Proton-based NIPS and the first clinical study reporting pregnancy outcome in a large series of patients. This platform is highly efficient in detecting the three most common trisomies. Our protocol is robust and can be implemented easily in any medical genetics laboratory. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.
10.1002/uog.20112
Estimation of Detection Rates of Aneuploidy in High-Risk Pregnancy Using an Approach Based on Nuchal Translucency and Non-Invasive Prenatal Testing: A Cohort Study.
Khalil Asma,Mahmoodian Negar,Kulkarni Abhijit,Homfray Tessa,Papageorghiou Aris,Bhide Amar,Thilaganathan Basky
Fetal diagnosis and therapy
OBJECTIVES:The aim was to investigate aneuploidy detection using an approach based on nuchal translucency (NT) and non-invasive prenatal testing (NIPT). METHODS:This was a cohort study including 5,306 high-risk pregnancies with NT measurements and chorionic villus samples (CVS) tested for full karyotype. RESULTS:The fetal karyotype was normal in 4,172 (78.6%) cases and abnormal in 1,134 (21.4%), including 1,009 with a likely clinically significant adverse outcome. Universal CVS with full karyotyping would lead to the diagnosis of all clinically significant abnormalities. A policy of relying solely on NIPT would have led to the diagnosis of 88.9% of clinically significant abnormalities. A strategy whereby NIPT is the main method, with CVS reserved for cases with NT ≥3.0 mm, would require CVS in 21.7% of cases, identify 94.8% of significant abnormalities and avoid miscarriage in 41 pregnancies compared to CVS for all. CONCLUSIONS:A policy of NIPT for increased-risk cases and CVS with full karyotype if the NT was ≥3.0 mm reduced the risk of miscarriage yet still identified 95% of clinically significant aneuploidy.
10.1159/000381182
Prenatal testing in pregnancies conceived by in vitro fertilization with pre-implantation genetic testing.
Arian Sara E,Erfani Hadi,Westerfield Lauren E,Buffie Alexandra,Nassef Salma,Gibbons William E,Van den Veyver Ignatia B
Prenatal diagnosis
OBJECTIVE:Women with pregnancies resulting from in vitro fertilization (IVF) with normal pre-implantation genetic testing for aneuploidy (PGT-A) are advised to undergo prenatal screening and testing during pregnancy. It is not well known how many follow these recommendations. Our objective was to study prenatal testing decisions made by women with pregnancies conceived through IVF with PGT-A. METHODS:We performed a retrospective review of women who received genetic counseling during pregnancies conceived through IVF with normal PGT-A. We excluded those who received genetic counseling preconceptionally prior to IVF. Statistical analysis included descriptive statistics and after testing for normality by the Kolmogorov-Smirnov test, independent t test, Mann-Whitney U test, or Chi-square/Fisher's exact test. RESULTS:Data from 83 women were included. Of these, 53 (63.9%) had at least one of the following prenatal tests: first trimester combined screening (16.9%), non-invasive prenatal screening (NIPS) (45.8%), second trimester serum screening (6%), and invasive diagnostic testing (6%). 10.8% had more than one of the above tests and 36.1% declined all tests. CONCLUSION:Almost two-thirds of women who were pregnant after IVF with normal PGT-A had prenatal aneuploidy screening or testing. Future prospective studies with larger cohorts are needed to further ascertain decision making in this population.
10.1002/pd.5711
Non-invasive prenatal testing for fetal chromosomal abnormalities by low-coverage whole-genome sequencing of maternal plasma DNA: review of 1982 consecutive cases in a single center.
Lau T K,Cheung S W,Lo P S S,Pursley A N,Chan M K,Jiang F,Zhang H,Wang W,Jong L F J,Yuen O K C,Chan H Y C,Chan W S K,Choy K W
Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology
OBJECTIVE:To review the performance of non-invasive prenatal testing (NIPT) by low-coverage whole-genome sequencing of maternal plasma DNA at a single center. METHODS:The NIPT result and pregnancy outcome of 1982 consecutive cases were reviewed. NIPT was based on low coverage (0.1×) whole-genome sequencing of maternal plasma DNA. All subjects were contacted for pregnancy and fetal outcome. RESULTS:Of the 1982 NIPT tests, a repeat blood sample was required in 23 (1.16%). In one case, a conclusive report could not be issued, probably because of an abnormal vanished twin fetus. NIPT was positive for common trisomies in 29 cases (23 were trisomy 21, four were trisomy 18 and two were trisomy 13); all were confirmed by prenatal karyotyping (specificity=100%). In addition, 11 cases were positive for sex-chromosomal abnormalities (SCA), and nine cases were positive for other aneuploidies or deletion/duplication. Fourteen of these 20 subjects agreed to undergo further investigations, and the abnormality was found to be of fetal origin in seven, confined placental mosaicism (CPM) in four, of maternal origin in two and not confirmed in one. Overall, 85.7% of the NIPT-suspected SCA were of fetal origin, and 66.7% of the other abnormalities were caused by CPM. Two of the six cases suspected or confirmed to have CPM were complicated by early-onset growth restriction requiring delivery before 34 weeks. Fetal outcome of the NIPT-negative cases was ascertained in 1645 (85.15%). Three chromosomal abnormalities were not detected by NIPT, including one case each of a balanced translocation, unbalanced translocation and triploidy. There were no known false negatives involving the common trisomies (sensitivity=100%). CONCLUSIONS:Low-coverage whole-genome sequencing of maternal plasma DNA was highly accurate in detecting common trisomies. It also enabled the detection of other aneuploidies and structural chromosomal abnormalities with high positive predictive value.
10.1002/uog.13277
Fetal fraction evaluation in non-invasive prenatal screening (NIPS).
Hestand Matthew S,Bessem Mark,van Rijn Peter,de Menezes Renee X,Sie Daoud,Bakker Ingrid,Boon Elles M J,Sistermans Erik A,Weiss Marjan M
European journal of human genetics : EJHG
An important factor in quality control of non-invasive prenatal screening (NIPS) or testing (NIPT) is a sufficient percentage of fetal DNA to avoid false-negative results. Here we evaluate 14,379 shallow whole-genome sequenced diagnostic NIPS samples, as well as negative controls, for both technical and biological factors that can influence fetal fraction and its assessment. Technically, bioinformatics analyses can have a profound impact on fetal fraction determination. We found best performance for fetal fraction determination with the Y chromosome based tool DEFRAG for male fetuses and the count based tool SeqFF for female fetuses. Biologically, gestational age of up to 21 weeks and maternal age had no influence on fetal fraction, while an increase in weight and BMI had a negative influence on fetal fraction. While a trend was observed, no statistically significant difference in fetal fraction was found between trisomy and normal samples. Overall, these results confirm the influence of biological factors and give insight into technical factors that can affect fetal fractions in NIPS.
10.1038/s41431-018-0271-7
Accuracy of non-invasive prenatal testing using cell-free DNA for detection of Down, Edwards and Patau syndromes: a systematic review and meta-analysis.
Taylor-Phillips Sian,Freeman Karoline,Geppert Julia,Agbebiyi Adeola,Uthman Olalekan A,Madan Jason,Clarke Angus,Quenby Siobhan,Clarke Aileen
BMJ open
OBJECTIVE:To measure test accuracy of non-invasive prenatal testing (NIPT) for Down, Edwards and Patau syndromes using cell-free fetal DNA and identify factors affecting accuracy. DESIGN:Systematic review and meta-analysis of published studies. DATA SOURCES:PubMed, Ovid Medline, Ovid Embase and the Cochrane Library published from 1997 to 9 February 2015, followed by weekly autoalerts until 1 April 2015. ELIGIBILITY CRITERIA FOR SELECTING STUDIES:English language journal articles describing case-control studies with ≥ 15 trisomy cases or cohort studies with ≥ 50 pregnant women who had been given NIPT and a reference standard. RESULTS:41, 37 and 30 studies of 2012 publications retrieved were included in the review for Down, Edwards and Patau syndromes. Quality appraisal identified high risk of bias in included studies, funnel plots showed evidence of publication bias. Pooled sensitivity was 99.3% (95% CI 98.9% to 99.6%) for Down, 97.4% (95.8% to 98.4%) for Edwards, and 97.4% (86.1% to 99.6%) for Patau syndrome. The pooled specificity was 99.9% (99.9% to 100%) for all three trisomies. In 100,000 pregnancies in the general obstetric population we would expect 417, 89 and 40 cases of Downs, Edwards and Patau syndromes to be detected by NIPT, with 94, 154 and 42 false positive results. Sensitivity was lower in twin than singleton pregnancies, reduced by 9% for Down, 28% for Edwards and 22% for Patau syndrome. Pooled sensitivity was also lower in the first trimester of pregnancy, in studies in the general obstetric population, and in cohort studies with consecutive enrolment. CONCLUSIONS:NIPT using cell-free fetal DNA has very high sensitivity and specificity for Down syndrome, with slightly lower sensitivity for Edwards and Patau syndrome. However, it is not 100% accurate and should not be used as a final diagnosis for positive cases. TRIAL REGISTRATION NUMBER:CRD42014014947.
10.1136/bmjopen-2015-010002
Increasing maternal age is not a significant cause of false-positive results for monosomy X in non-invasive prenatal testing.
Sandow Rhiannon,Scott Fergus P,Schluter Philip J,Rolnik Daniel L,Menezes Melody,Nisbet Deborah,McLennan Andrew C
Prenatal diagnosis
OBJECTIVE:The accuracy of cell-free DNA aneuploidy screening varies by the chromosome assessed. The positive predictive value is consistently low for monosomy X (MX), at less than 30%. This study aims to investigate maternal age and other possible predictors of false-positive MX screening results in order to guide pre-test and post-test counselling. METHODS:A total of 52 499 NIPT samples were tested over 69 months, across three specialist obstetric services. Outcome data were available for 96 out of 107 cases high risk for MX. Cytogenetic outcomes were compared to clinical and demographic data to look for trends that may indicate higher likelihood of a false-positive NIPT result. RESULTS:The likelihood of a false-positive MX result significantly increased with the absence of ultrasound features suggestive of MX and with lower PAPP-A levels. Non-significant trends towards false-positive results were identified with increased maternal age, increased body mass index and Caucasian ethnicity. CONCLUSION:Maternal age is not a reliable predictor of a false-positive result. Assessment of ultrasound findings and placental serology in the first trimester is important for appropriate post-test counselling and should continue to be a part of screening even when NIPT is used as a first-tier screening test.
10.1002/pd.5790
Non-invasive prenatal testing for aneuploidy: current status and future prospects.
Benn P,Cuckle H,Pergament E
Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology
Non-invasive prenatal testing (NIPT) for aneuploidy using cell-free DNA in maternal plasma is revolutionizing prenatal screening and diagnosis. We review NIPT in the context of established screening and invasive technologies, the range of cytogenetic abnormalities detectable, cost, counseling and ethical issues. Current NIPT approaches involve whole-genome sequencing, targeted sequencing and assessment of single nucleotide polymorphism (SNP) differences between mother and fetus. Clinical trials have demonstrated the efficacy of NIPT for Down and Edwards syndromes, and possibly Patau syndrome, in high-risk women. Universal NIPT is not cost-effective, but using NIPT contingently in women found at moderate or high risk by conventional screening is cost-effective. Positive NIPT results must be confirmed using invasive techniques. Established screening, fetal ultrasound and invasive procedures with microarray testing allow the detection of a broad range of additional abnormalities not yet detectable by NIPT. NIPT approaches that take advantage of SNP information potentially allow the identification of parent of origin for imbalances, triploidy, uniparental disomy and consanguinity, and separate evaluation of dizygotic twins. Fetal fraction enrichment, improved sequencing and selected analysis of the most informative sequences should result in tests for additional chromosomal abnormalities. Providing adequate prenatal counseling poses a substantial challenge given the broad range of prenatal testing options now available.
10.1002/uog.12513
The importance of determining the limit of detection of non-invasive prenatal testing methods.
Fiorentino Francesco,Bono Sara,Pizzuti Francesca,Mariano Martina,Polverari Arianna,Duca Sara,Sessa Mariateresa,Baldi Marina,Diano Laura,Spinella Francesca
Prenatal diagnosis
OBJECTIVE:Several non-invasive prenatal testing (NIPT) methods, which analyze circulating fetal cell-free DNA (cfDNA) in maternal plasma, suggest a fetal fraction (FF) ≥ 4% for a reportable result, with the assumption that fetal aneuploidies may not be detectable at lower FF. This study determined the actual limit of detection (LOD) of a massively parallel sequencing-based NIPT method and evaluated its performance in testing samples with low FF. METHOD:An experimental model, involving the creation of artificial plasma mixtures with a final aneuploid FF ranging from 1% to 4%, simulated samples at different proportions of fetal cfDNA. We then analyzed 7103 blood samples, from pregnant women undergoing NIPT, to assess the impact of low FF on the performance of cfDNA testing. RESULTS:Detection of common aneuploidies in samples with an FF as low as 2% is well within the ability of this technology. Of 105 pregnancies confirmed chromosomally abnormal, 25 (23.8%) involving a 2% < FF < 4% were consistently detected. These high-risk pregnancies would have not been identified using the suggested 4% FF cut-off. CONCLUSION:This study underscores the importance of determining the actual LOD for each specific NIPT methodology. It may reduce the incidence of test cancelations and shorten the time required for the diagnosis of aneuploidy. © 2016 John Wiley & Sons, Ltd.
10.1002/pd.4780
Detection of fetal chromosomal anomalies: does nuchal translucency measurement have added value in the era of non-invasive prenatal testing?
Lichtenbelt K D,Diemel B D M,Koster M P H,Manten G T R,Siljee J,Schuring-Blom G H,Page-Christiaens G C M L
Prenatal diagnosis
OBJECTIVES:The objective of this study is to determine what percentage of fetal chromosomal anomalies remains undetected when first trimester combined testing is replaced by non-invasive prenatal testing for trisomies 13, 18, and 21. We focused on the added clinical value of nuchal translucency (NT) measurement. METHODS:Data on fetal karyotype, ultrasound findings, and pregnancy outcome of all pregnancies with an NT measurement ≥3.5 mm were retrospectively collected from a cohort of 25,057 singleton pregnancies in which first trimester combined testing was performed. RESULTS:Two hundred twenty-five fetuses (0.9 %) had an NT ≥3.5 mm. In 24 of these pregnancies, a chromosomal anomaly other than trisomy 13, 18, or 21 was detected. Eleven resulted in fetal demise, and ten showed fetal ultrasound anomalies. In three fetuses with normal ultrasound findings, a chromosomal anomaly was detected, of which one was a triple X. CONCLUSIONS:In three out of 25,057 pregnancies (0.01%), non-invasive prenatal testing and fetal ultrasound would have missed a chromosomal anomaly that would have been identified by NT measurement. © 2015 John Wiley & Sons, Ltd.
10.1002/pd.4589
Fetal sex determination in twin pregnancies using non-invasive prenatal testing.
Villela Darine,Che Huiwen,Van Ghelue Marijke,Dehaspe Luc,Brison Nathalie,Van Den Bogaert Kris,Devriendt Koen,Lewi Liesbeth,Bayindir Baran,Vermeesch Joris Robert
NPJ genomic medicine
Non-invasive prenatal testing (NIPT) is accurate for fetal sex determination in singleton pregnancies, but its accuracy is not well established in twin pregnancies. Here, we present an accurate sex prediction model to discriminate fetal sex in both dichorionic diamniotic (DCDA) and monochorionic diamniotic/monochorionic monoamniotic (MCDA/MCMA) twin pregnancies. A retrospective analysis was performed using a total of 198 twin pregnancies with documented sex. The prediction was based on a multinomial logistic regression using the normalized frequency of X and Y chromosomes, and fetal fraction estimation. A second-step regression analysis was applied when one or both twins were predicted to be male. The model determines fetal sex with 100% sensitivity and specificity when both twins are female, and with 98% sensitivity and 95% specificity when a male is present. Since sex determination can be clinically important, implementing fetal sex determination in twins will improve overall twin pregnancies management.
10.1038/s41525-019-0089-4
Non-invasive prenatal test to screen common trisomies in twin pregnancies.
Molecular cytogenetics
OBJECTIVES:Recent years have witnessed a shift from invasive methods of prenatal screening to non-invasive strategies. Accordingly, non-invasive prenatal testing (NIPT) using cell-free fetal DNA in maternal plasma has gained a considerable deal of interest from both geneticists and obstetricians. Efficacy of this method in identification of common aneuploidies has been extensively assessed in singleton pregnancies. However, a limited number of studies have addressed the twin pregnancies. In this context, the present study is aimed at identification of the efficacy of NIPT in twin pregnancies. METHODS:NIPT was performed on twin pregnancies to screen trisomies 13, 18 and 21. Pregnant women referring to Nilou Clinical Laboratory between March 2016 and December 2018 were included in this research. RESULTS:In the current study, a total 356 twin pregnancies were screened in search for trisomies 13, 18 and 21. 6 cases exhibited positive NIPT results in which the presence of trisomies 13, 18 and 21 was confirmed by fetal karyotype in 1, 2 and 2 cases, respectively. One twin pregnancy showed normal karyotype. The combined false-positive rate for these trisomies was 0.28%. No false negative case was observed. The combined sensitivity and specificity of NIPT in twin pregnancies were 100 and 99.7%, respectively. CONCLUSION:The results of the current study verify the feasibility, sensitivity and specificity of NIPT in twin pregnancies.
10.1186/s13039-020-0475-8
Clinical performance of non-invasive prenatal served as a first-tier screening test for trisomy 21, 18, 13 and sex chromosome aneuploidy in a pilot city in China.
Liu Yanhui,Liu Hailiang,He Yi,Xu Wanfang,Ma Qiulin,He Yuzhen,Lei Wei,Chen Guoquan,He Zheng,Huang Jiayi,Liu Jianan,Liu Yuanru,Huang Quanfei,Yu Fubing
Human genomics
BACKGROUND:Cell-free fetal DNA (cffDNA) has opened up new approaches for non-invasive prenatal testing (NIPT), and it is often used as the second-tier test for high-risk pregnant women in detecting trisomy (T) 21, T18, and T13 after serum biochemistry screening. This study aims to discuss the clinical performance of NIPT as an alternative first-tier screening test for pregnant women in detecting T21, T18, T13, and sex chromosome aneuploidies (SCAs) in China. METHODS:A total of 42,924 samples were recruited. The cell-free plasma DNA was directly sequenced. Each of the chromosome aneuploidies of PPV was analyzed. A total of 22 placental samples were acquired, including 14 FP and 8 TP samples. The placental verification of FP NIPT results was performed. RESULTS:Among 42,924 samples, 281 (0.65%) positive cases, including 87 of T21, 31 of T18, 22 of T13, and 141 of SCAs were detected. For the detection of T21, the positive predictive value (PPV) was 78.46%, for trisomy 18, 62.96%, for trisomy 13, 10.00%, for SCAs, 47.22% in the total samples. For trisomy 21, the PPV was 86.67%, for trisomy 18, 80.00%, for trisomy 13, 20.00%, for SCAs, 56.52% in advanced maternal age (AMA) women. The PPV of T21 increased with age. For T18, the PPV showed an overall upward trend. For T13 and SCAs, PPV was raised first and then lowered. Placental verification of false positive (FP) NIPT results confirmed confined placental mosaicism(CPM) was the reason for false positives. CONCLUSIONS:This study represents the first time that NIPT has been used as a first-tier screening test for fetal aneuploidies in a pilot city with large clinical samples in China. We propose that NIPT could replace serum biochemistry screening as a first-tier test.
10.1186/s40246-020-00268-2
[Preliminary analysis of the cause for the failure of non-invasive prenatal testing using cell-free fetal DNA derived from peripheral maternal blood].
Zhang Bin,Shen Cong,Wang Huiyan,Cai Zhengmao,Lu Beiyi,Zhang Xiaoqing,Yu Bin,Wang Ting
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics
OBJECTIVE:To explore the cause of failure of non-invasive prenatal testing (NIPT) using cell-free fetal DNA from peripheral maternal blood. METHODS:A total of 31 832 cases of NIPT were retrospectively analyzed. The clinical data of pregnant women were analyzed and the outcome of pregnancy was followed up. RESULTS:Among the 31 832 cases, 200 patients have failed for the first NIPT test. Second test has succeeded in 171 (85.9%) of 199 cases, while 28 cases (14.1%) still yielded no effective results. This gave rise for a total failure rate of 0.088%. Of the 28 cases, 11 (39.2%) were due to high content of total free DNA and could not be sequenced, 17 (60.7%) were found to have the fetal DNA content of less than 4%. Among the 171 cases which have obtained a valid result, NIPT showed that there were 4 patients with high risk of trisomy 21, 18 cases with high risk of 18 trisomy and 1 case with high risk of 13 trisomy. Karyotyping analysis of the amniocytic chromosomes has identified 3 cases with 47,XN,+21, 1 case with 46,XN,rob(21;21), 1 case with 47,XN,+18, while the 13 trisomy case was found to be false positive. For the 28 cases with failed NIPT retest, 14 had normal delivery, with no anomaly noticed in the neonates. Nine patients had opted for artificial abortion during middle or late pregnancy due to maternal factors (4 cases) or fetal factors (5 cases). Four patients developed complications of pregnancy. One case was in good condition upon follow-up. Four cases were lost during follow-up. Of the 11 pregnant women who had failed the NIPT test due to high content of total free DNA, 6 (54.5%) had opted for artificial abortion during midterm pregnancy, which was significantly higher than that of pregnant women with low free DNA content (17.6%). CONCLUSION:Failure of NIPT testing should attract attention from researchers. Failure of single NIPT test should not be regarded as a high risk signal for fetal chromosomal aneuploidies. For those where the test has failed again, genetic counseling and strengthened perinatal care should be provided for the pregnant women.
10.3760/cma.j.issn.1003-9406.2018.03.005
[False positive non-invasive prenatal testing results due to vanishing twins].
Yu Ting,Li Shuo,Zhao Wei,Yu Dongyi
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics
OBJECTIVE:To explore the mechanism and duration of false positive results of non-invasive prenatal testing (NIPT) caused by vanishing twins. METHODS:To detect the variation of cell-free fetal DNA fraction before and after the fetal death and explore its influence on the results of NIPT at different gestational weeks. Prenatal diagnosis was also carried out on amniotic fluid sample derived from the survivor twin. After birth, the two placentas and papyraceous fetus were obtained to ascertain the definitive genetic diagnosis and pathological changes through fluorescence in situ hybridization, fluorescence quantitative PCR and histopathological examination. Eight cases of vanishing twins leading to discordant NIPT results were reviewed for determining the duration of this influence. RESULTS:The vanishing twin has led to immediate flooding of cfDNA into the maternal plasma due to necrotic cytotrophoblasts, which in turn caused increased release of fetal DNA in a short time. However, this did not change the NIPT result for a period of time. The tissue and chorionic villi of perished fetus presented extensive degenerative necrosis. CONCLUSION:The false positive NIPT result caused by vanishing twins may be attributed to continuous release of DNA fragments into the maternal plasma by the fetuses. The influence of the vanished fetuses, which may lead to discordant NIPT results, can last for at least 7-8 weeks but no more than 12-14 weeks during the first and second trimester.
10.3760/cma.j.issn.1003-9406.2019.04.009
The Effect of Freezing on Non-invasive Prenatal Testing.
Xie Xiaolei,Li Fuguang,Tan Weihe,Yin Weiguo,Chen Feiyan,Guo Xiaoyan
Scientific reports
Plasma cryopreservation is unavoidable in China, due to technical specifications requiring storage of additional plasma at -80 degrees for three years. However, the effect of freezing on non-invasive prenatal testing (NIPT) is still uncertain. We collected 144 euploid pregnant samples, 22 on trisomy 21, 4 on trisomy 13, and 3 on trisomy 18, by massively parallel sequencing before and after freezing. Compared with the success rate of 100% of fresh samples, the detection success rates of trisomy 21, trisomy 13 and euploidy in frozen samples by NIPT were 95.45%, 75% and 95.14%, respectively. Of these, 9 cases of frozen sample sequencing failed, with 8 cases being due to high GC content. The chromosome 21 (chr21) z-value of the frozen trisomy 21 samples was lower than that of fresh samples. Meanwhile, freezing reduced the male positive foetal cell-free DNA (cfDNA) fraction, which was accompanied by an increase in the Unimap-GC level in the massively parallel sequencing data and a decrease in the Unique reads/Total reads ratio. Laboratory freezing reduced the chr21 z-value of foetal trisomy 21, which can be explained by a reduction in the foetal cfDNA fraction and effective Unique reads for NIPT analysis. The Unimap-GC content of the serum samples after freezing was higher, which can lead to failure of NIPT detection.
10.1038/s41598-019-42980-7
[Data analysis of non-invasive prenatal testing based on special loci in cell-free fetal DNA].
Xuan Liming,Kong Lingyin,Xia Yingying,Mao Yan,Shen Jingjing,Zhu Yijun,Xue Yongfeng,Sun Danfeng,Liu Huimin,Liang Bo
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics
OBJECTIVE To analyze the data of non-invasive prenatal testing based on specific loci of circulating cell-free fetal DNA (cffDNA). METHODS Selected loci of target chromosomes were analyzed by sequence capture and sequencing. Meanwhile, 600 loci were selected from other chromosomes for determining the concentration of cffDNA. RESULTS A total of 768 specific loci were captured on chromosomes 21 and 18, and used to determine whether the two were abnormal. When the minimum concentration of detected cffDNA was set at 3% and the threshold of Z score was set to [-6,6], the specificity of the analysis was 99.37% and the sensitivity was 100%. CONCLUSION A reliable, convenient and low-cost analytical method has been developed. The method requires less sequencing data for non-invasive prenatal testing, and can accurately detect abnormalities of fetal chromosomes 21 and 18, and simultaneously determine the concentration of cffDNA.
10.3760/cma.j.issn.1003-9406.2018.01.012
Efficiency of non-invasive prenatal screening in pregnant women at advanced maternal age.
Zhu Hui,Jin Xiaoxiao,Xu Yuqing,Zhang Weihua,Liu Xiaodan,Jin Jinglei,Qian Yeqing,Dong Minyue
BMC pregnancy and childbirth
BACKGROUND:Non-invasive prenatal screening (NIPS) is widely used as the alternative choice for pregnant women at high-risk of fetal aneuploidy. However, whether NIPS has a good detective efficiency for pregnant women at advanced maternal age (AMA) has not been fully studied especially in Chinese women. METHODS:Twenty-nine thousand three hundred forty-three pregnant women at AMA with singleton pregnancy who received NIPS and followed-up were recruited. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), receiver operating characteristic (ROC) curves and the Youden Index for detecting fetal chromosomal aneuploidies were analyzed. The relationship between maternal age and common fetal chromosomal aneuploidy was observed. RESULTS:The sensitivity, specificity, PPV, NPV of NIPS for detecting fetal trisomy 21 were 99.11, 99.96, 90.98, and 100%, respectively. These same parameters for detecting fetal trisomy 18 were 100, 99.94, 67.92, and 100%, respectively. Finally, these parameters for detecting trisomy 13 were 100, 99.96, 27.78, and 100%, respectively. The prevalence of fetal trisomy 21 increased exponentially with maternal age. The high-risk percentage incidence rate of fetal trisomy 21 was significantly higher in the pregnant women at 37 years old or above than that in pregnant women at 35 to 37 years old. (Youden index = 37). CONCLUSION:It is indicated that NIPS is an effective prenatal screening method for pregnant women at AMA.
10.1186/s12884-021-03570-6
Evaluation of droplet digital PCR for non-invasive prenatal diagnosis of phenylketonuria.
Yan Yousheng,Wang Fang,Zhang Chuan,Jin Xiaohua,Zhang Qinhua,Feng Xuan,Hao Shengju,Gao Huafang,Ma Xu
Analytical and bioanalytical chemistry
This study was carried out to establish a non-invasive prenatal diagnosis method for phenylketonuria (PKU) based on droplet digital PCR (ddPCR) and to evaluate its accuracy by comparison with conventional invasive diagnostic methods. A total of 24 PKU pedigrees that required prenatal diagnosis were studied, in which the genetic mutations in the probands and parents were unambiguous. Prenatal diagnosis of sibling fetuses was performed using traditional invasive prenatal diagnostic methods as a standard. At the same time, cell-free DNA (cfDNA) was extracted from maternal plasma and the fetal genes contained within were typed and quantified using ddPCR method. Invasive prenatal diagnosis determined that 3 of the 24 fetuses were affected, 8 of them were normal, and 13 were heterozygous carriers of pathogenic mutations. Successful non-invasive prenatal diagnosis analysis of PAH gene mutations was performed for 8 of the families using ddPCR method. Non-invasive prenatal diagnosis results were consistent with the results of the invasive prenatal diagnoses and no false positive or false negative results were found. In conclusion, this study is the first to establish non-invasive prenatal diagnosis of PKU based on ddPCR. The method showed high sensitivity and specificity from cfDNA, indicating that ddPCR is a reliable non-invasive prenatal diagnosis tool for PKU diagnosis. Graphical abstract.
10.1007/s00216-019-02087-4
Analyzing false-negative results detected in low-risk non-invasive prenatal screening cases.
Lin Ying,Liang Dong,Wang Yan,Li Hang,Liu An,Hu Ping,Xu Zhengfeng
Molecular genetics & genomic medicine
BACKGROUND:The non-invasive prenatal screening (NIPS) has been introduced into clinical practice with a high sensitivity and specificity. Although the false-negative results are inevitable and important, limited false-negative NIPS results have been reported and studied previously. In this study, we aim to report and analyze false-negative results detected in the NIPS cases with a low-risk result. METHODS:NIPS was performed using whole-genome massively parallel shotgun sequencing for screening common trisomies, rare autosomal aneuploidies, and subchromosome copy number variants. All the NIPS cases with a low-risk result performed in our center in 2017 were followed-up using medical records and telephone interview at 3 months after delivery. Fetal ultrasound results and available genetic diagnostic testing results were collected for pregnancies with adverse outcomes. The genetic diagnostic testing referred to chromosomal microarray analysis or fluorescent in situ hybridization on amniotic fluid cells, fetal skin tissue, neonatal peripheral blood, or available placental biopsies. RESULTS:By following-up 10,975 low-risk results, we found 166 NIPS cases with adverse pregnancy outcomes, in which eight cases had diagnostic testing. Among them, four false-negative cases were confirmed, including one trisomy 18 caused by placental mosaicism, one mosaic tetrasomy 12p, and 2 microdeletion/microduplication cases. CONCLUSION:Our results revealed that mosaicism contributes to a major cause of false negative in NIPS, and highlighted the importance of ultrasound in identifying these false-negative results.
10.1002/mgg3.1185
Aneuploidy screening by non-invasive prenatal testing in twin pregnancy.
Fosler L,Winters P,Jones K W,Curnow K J,Sehnert A J,Bhatt S,Platt L D
Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology
OBJECTIVES:To describe our experience with non-invasive prenatal testing (NIPT) in twin pregnancy. METHODS:Two sets of maternal blood samples from twin pregnancies were analyzed at our laboratory using NIPT: 115 stored samples from pregnancies with known outcome (Clinical Study A) and 487 prospectively collected samples for which outcomes were requested from providers (Clinical Study B). NIPT was used to screen for the presence of fetal aneuploidy on chromosomes 13, 18, 21, X and Y in all cases, and results were compared with outcomes when known. RESULTS:In Clinical Study A, all 115 samples were classified correctly by NIPT: three cases of trisomy 21 (one fetus affected), one of monochorionic trisomy 18 (both fetuses affected) and 111 euploid. In Clinical Study B, a NIPT result was reported for 479 (98.4%) of the 487 samples. Aneuploidy was detected or suspected in nine (1.9%) cases: seven cases of trisomy 21 detected, one case of trisomy 21 suspected and one case with trisomy 21 detected and trisomy 18 suspected. Information on aneuploidy outcome was available for 171 (35.7%) cases in Clinical Study B. Of the nine cases with aneuploidy detected or suspected, six were confirmed to be a true positive in at least one twin based on karyotype or birth outcome and two were suspected to be concordant based on ultrasound findings; the one known discordant result was for the aneuploidy suspected case. No false negatives were reported. CONCLUSION:NIPT performed well in the detection of trisomy 21 in twin pregnancy, with a combined false-positive frequency for trisomies 13, 18 and 21 of 0% for Clinical Study A and 0.2% for Clinical Study B. © 2016 Illumina. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
10.1002/uog.15964
Predicting fetoplacental chromosomal mosaicism during non-invasive prenatal testing.
Brison Nathalie,Neofytou Maria,Dehaspe Luc,Bayindir Baran,Van Den Bogaert Kris,Dardour Leila,Peeters Hilde,Van Esch Hilde,Van Buggenhout Griet,Vogels Annick,de Ravel Thomy,Legius Eric,Devriendt Koen,Vermeesch Joris R
Prenatal diagnosis
OBJECTIVE:Non-invasive prenatal detection of aneuploidies can be achieved with high accuracy through sequencing of cell-free maternal plasma DNA in the maternal blood plasma. However, false positive and negative non-invasive prenatal testing (NIPT) results remain. Fetoplacental mosaicism is the main cause for false positive and false negative NIPT. We set out to develop a method to detect placental chromosomal mosaicism via genome-wide circulating cell-free maternal plasma DNA screening. METHOD:Aneuploidy detection was combined with fetal fraction determination to enable the detection of placental mosaicism. This pipeline was applied to whole genome sequencing data derived from 19 735 plasma samples. Following an abnormal NIPT, test results were validated by conventional invasive prenatal or postnatal genetic testing. RESULTS:Respectively 3.2% (5/154), 12.8% (5/39), and 13.3% (2/15) of trisomies 21, 18, and 13 were predicted and confirmed to be mosaic. The incidence of other, rare autosomal trisomies was ~0.3% (58/19,735), 45 of which were predicted to be mosaic. Twin pregnancies with discordant fetal genotypes were predicted and confirmed. CONCLUSION:This approach permits the non-invasive detection of fetal autosomal aneuploidies and identifies pregnancies with a high risk of fetoplacental mosaicism. Knowledge about the presence of chromosomal mosaicism in the placenta influences risk estimation, genetic counseling, and improves prenatal management.
10.1002/pd.5223
Non-invasive prenatal testing (NIPT) by low coverage genomic sequencing: Detection limits of screened chromosomal microdeletions.
Kucharik Marcel,Gnip Andrej,Hyblova Michaela,Budis Jaroslav,Strieskova Lucia,Harsanyova Maria,Pös Ondrej,Kubiritova Zuzana,Radvanszky Jan,Minarik Gabriel,Szemes Tomas
PloS one
To study the detection limits of chromosomal microaberrations in non-invasive prenatal testing with aim for five target microdeletion syndromes, including DiGeorge, Prader-Willi/Angelman, 1p36, Cri-Du-Chat, and Wolf-Hirschhorn syndromes. We used known cases of pathogenic deletions from ISCA database to specifically define regions critical for the target syndromes. Our approach to detect microdeletions, from whole genome sequencing data, is based on sample normalization and read counting for individual bins. We performed both an in-silico study using artificially created data sets and a laboratory test on mixed DNA samples, with known microdeletions, to assess the sensitivity of prediction for varying fetal fractions, deletion lengths, and sequencing read counts. The in-silico study showed sensitivity of 79.3% for 10% fetal fraction with 20M read count, which further increased to 98.4% if we searched only for deletions longer than 3Mb. The test on laboratory-prepared mixed samples was in agreement with in-silico results, while we were able to correctly detect 24 out of 29 control samples. Our results suggest that it is possible to incorporate microaberration detection into basic NIPT as part of the offered screening/diagnostics procedure, however, accuracy and reliability depends on several specific factors.
10.1371/journal.pone.0238245
[Impact of confined placental mosaicism on non-invasive prenatal testing and pregnancy outcomes].
Wu Xiaoqing,Huang Hailong,Chen Xuemei,Chen Xiaolan,Shen Qingmei,He Deqin,Xu Liangpu
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics
OBJECTIVE:To assess the impact of confined placental mosaicism (CPM) on non-invasive prenatal testing (NIPT) and pregnancy outcomes. METHODS:Copy number variation sequencing (CNV-seq) and single nucleotide polymorphism array (SNP-array) were carried out on placental specimen sampled from eight pregnancies with confirmed false-positive NIPT results. The impact of CPM on NIPT and pregnancy outcomes were analyzed based on the laboratory tests and clinical characteristics. RESULTS:Five of the eight cases with false-positive NIPT results were proven to be CPM involving trisomy 9, 13, 21, 22, and X, respectively. The mosaic ratios for different placental regions have varied from 4% to 80%. Two fetuses with confirmed CPM showed fetal growth restriction (FGR) and additional ultrasound abnormalities, 1 fetus showed only FGR. The remaining two fetuses showed normal growth. CONCLUSION:NIPT is highly sensitive to CPM, whilst CPM is an important cause for false-positive NIPT result. CPM may be associated with FGR. Investigation of the presence of CPM is important for both pre- and post-test genetic counseling and management of the pregnancy.
10.3760/cma.j.cn511374-20200803-00574
[Influence of maternal chromosomal abnormalities on non-invasive prenatal testing for fetal sex chromosome aneuploidies].
Yuan Pei,Zhang Bin,Liu Jianbing,Wang Huiyan,Lu Beiyi,Zhou Qin,Yu Bin,Cai Zhengmao
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics
OBJECTIVE:To study the influence of maternal sex chromosomal abnormalities on the prediction of fetal sex chromosome abnormalities (SCAs) by non-invasive prenatal testing (NIPT). METHODS:Thirty-six pregnant women with a prediction for fetal SCAs by NIPT were verified as false positive after prenatal diagnosis using amniotic fluid samples. With informed consent, these women were subjected to chromosomal karyotyping or copy number variations (CNVs) analysis through high-throughput sequencing. RESULTS:Sex chromosomal abnormalities were found in 8 women, which yielded an abnormal rate of 22.22% (8/36). Among these, 3 had sex chromosome aneuploidies (47, XXX), 4 had sex chromosome mosaicisms, and 1 carried structural chromosomal abnormalities. Reanalysis of the results of NIPT were consistent with the maternal CNVs by large. With the ratio of cffDNA (ChrX)/cffDNA was more than 2, 6 of the eight women were found to harbor sex chromosome abnormalities, and the fetal karyotype was normal. However, with a ratio of less than 2, only 2 of the 38 pregnant women had sex chromosome abnormalities, and 10 of the fetuses were confirmed as positive. CONCLUSION:The presence of maternal sex chromosomal abnormalities can greatly influence the result of NIPT, which may also be an important reason for false prediction for fetal SCAs by NIPT. When NIPT indicates abnormal SCAs, it is necessary to analyze maternal sex chromosomes. The ratio of cffDNA(ChrX)/cffDNA may help to determine the source of abnormal signals.
10.3760/cma.j.issn.1003-9406.2020.06.005
[Clinical characteristics and prenatal diagnosis of fetuses with sex chromosomal aneuploidies detected by non-invasive prenatal testing during early and midterm pregnancies].
Luo Xiaojin,Guo Yanyun,Wei Fengxiang,Hu Liang,Pei Yuanyuan,Cong Xiaoyi,Liu Xiaoyi,Chen Jing,Li Gaochi,Chen Hanbiao,Guo Li,Chen Zheng
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics
OBJECTIVE:To analyze the indication, karyotyping result, ultrasound finding, pregnancy decision and follow-up of fetuses with sex chromosome aneuploidies (SCA) detected by non-invasive prenatal testing (NIPT) during early and midterm pregnancies. METHODS:The results of 225 singleton pregnancies with fetal SCA detected by NIPT were reviewed and analyzed. RESULTS:The 225 cases included 45,X (n=37), 47,XXY (n=74), 47,XXX (n=50), 47,XYY (n=56) and mosaicisms (n=8), among which 121 (53.8%) have opted to terminate the pregnancy, including 45,X (n=31), 47,XXY (n=61), 47,XXX (n=14), 47,XYY (n=12) and 3 mosaicisms. The remainder 104 (46.2%) have elected to continue with the pregnancy, among which three have opted to terminate due to abnormalities detected by ultrasonography, and two had spontaneous abortions. CONCLUSION:NIPT as a first-tier screening method can effectively detect fetal trisomies 21, 13 and 18 as well as SCA. The types of fetal SCA and presence of ultrasound abnormalities are critical factors for the termination of pregnancy.
10.3760/cma.j.cn511374-20200318-00174
Clinical Validation of Non-Invasive Prenatal Testing for Fetal Common Aneuploidies in 1,055 Korean Pregnant Women: a Single Center Experience.
Lee Da Eun,Kim Hyunjin,Park Jungsun,Yun Taegyun,Park Dong Yoon,Kim Minhyoung,Ryu Hyun Mee
Journal of Korean medical science
BACKGROUND:Non-invasive prenatal testing (NIPT) using cell-free fetal DNA from maternal plasma for fetal aneuploidy identification is expanding worldwide. The objective of this study was to evaluate the clinical utility of NIPT for the detection of trisomies 21, 18, and 13 of high-risk fetus in a large Korean population. METHODS:This study was performed retrospectively, using stored maternal plasma from 1,055 pregnant women with singleton pregnancies who underwent invasive prenatal diagnosis because of a high-risk indication for chromosomal abnormalities. The NIPT results were confirmed by karyotype analysis. RESULTS:Among 1,055 cases, 108 cases of fetal aneuploidy, including trisomy 21 (n = 57), trisomy 18 (n = 42), and trisomy 13 (n = 9), were identified by NIPT. In this study, NIPT showed 100% sensitivity and 99.9% specificity for trisomy 21, and 92.9% sensitivity and 100% specificity for trisomy 18, and 100% sensitivity and 99.9% specificity for trisomy 13. The overall positive predictive value (PPV) was 98.1%. PPVs for trisomies 21, 18, and 13 ranged from 90.0% to 100%. CONCLUSION:This study demonstrates that our NIPT technology is reliable and accurate when applied to maternal DNA samples collected from pregnant women. Further large prospective studies are needed to adequately assess the performance of NIPT.
10.3346/jkms.2019.34.e172
Detection of trisomies 13, 18 and 21 using non-invasive prenatal testing.
Experimental and therapeutic medicine
The clinical performance of non-invasive prenatal testing (NIPT) in the Down's syndrome screening based on 1,901 pregnant women in a Chinese hospital was investigated. This was a retrospective analysis of NIPT study in singleton pregnancy (n=1,901). The NIPT test is offered routinely as a prenatal screening test for common fetal aneuploidies, including trisomy 13 (T13), T18 and T21 to pregnant women with risk factors of one or more anomalies. Maternal peripheral blood (5 ml) was collected in an ethylenediaminetetraacetic acid (EDTA) tube at a gestational age of 12+0 to 32+6 weeks. The samples were delivered at -80°C to the certified Shenzhen BGI Clinical Laboratory Center. Sequencing data were analyzed using a proprietary algorithm. Women with positive NIPT results were recommended to receive karyotype analysis and amniotic fluid puncture for further validation. The cases were followed up for 56 days after delivery. All the patients underwent ultrasound examination, and the majority of patients (91.16%) showed normal findings. In contrast, 136 (7.15%) showed ultrasound anomalies. The most common anomaly was echogenic heart focus (n=80), accounting for 4.21% of the patients. Twenty-two cases were classified by the NIPT to be positive for the T21 (n=15), T18 (n=5) and T13 (n=2), respectively, while the others (n=1,879) were classified to be NIPT negative cases. Among these cases, the fetal outcome data were obtained in 1,483 cases, while 396 were lost to follow-up. The majority of cases (75.47%) were normal at birth. Neonatal death was observed in 1 case. Five pregnant women decided termination of pregnancy despite the presence of NIPT negativity. In conclusion, NIPT technique is feasible for the prenatal screening of T18 and T21 with higher sensitivity and specificity compared with conventional methods.
10.3892/etm.2017.4272
Application values of prenatal screening and non-invasive gene sequencing in fetal birth defects.
Pakistan journal of medical sciences
OBJECTIVE:To investigate effects of prenatal screening and non-invasive gene sequencing on the clinical diagnosis of fetal birth defects and the outcome of pregnancy. METHODS:Totally 2520 pregnant women who received prenatal screening in our hospital were selected as the research subjects. The high-risk pregnant women were further tested by the non-invasive gene sequencing technology. Pregnant women with positive results were diagnosed by amniocentesis and fetal chromosome karyotype analysis, and the pregnancy outcome was followed up for one year. RESULTS:870 out of the 2520 pregnant women was tested by non-invasive gene sequencing technology; 26 of the 870 women was 13-trisomy-positive and was diagnosed by amniocentesis and fetal chromosome karyotype analysis, 22 of which was diagnosed as 47, XN, +13 and four of which was normal; the diagnosis accuracy of non-invasive prenatal testing (NIPT) was 84.6%. 18 out of the 22 confirmed cases underwent abortion, three cases had termination of embryonic development, and one case had postnatal anomaly. Thirty four out of the 2520 pregnant women was 18-trisomy-positive and was diagnosed by amniocentesis and fetal chromosome karyotype analysis, 31 of which was diagnosed as 47, XN, +18 and three cases were normal; the diagnosis accuracy of NIPT was 91.2%. 29 out of the 31 confirmed cases underwent abortion and two cases had termination of embryonic development. Forty out of the 2520 pregnant women was 21-trisomy-positive and was diagnosed by amniocentesis and fetal chromosome karyotype analysis, 39 of which was diagnosed as 47, XN, +21 and one case was normal; the diagnosis accuracy of NIPT was 97.5%. Thirty four out of the 39 confirmed cases underwent abortion, three cases had termination of embryonic development, and two cases had postnatal anomaly. Twenty eight cases were tested as sex chromosome-positive and were diagnosed by amniocentesis and fetal chromosome karyotype analysis, 25 out of which was diagnosed as abnormal and three cases were normal; the diagnosis accuracy of NIPT was 89.3%. 24 out of the 25 confirmed cases underwent abortion, and one case had termination of embryonic development. CONCLUSION:Prenatal screening and non-invasive gene sequencing technology have a high accuracy in the diagnosis of fetal birth defects, which can reduce the maternal abortion injury as much as possible and relieve the psychological pressure. The promotion of the mode can be strengthened in clinics.
10.12669/pjms.36.7.2290
[Retrospective analysis of 44 578 pregnancies undergoing non-invasive prenatal testing in Weifang].
Xu Hong
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics
OBJECTIVE:To review the results of non-invasive prenatal testing (NIPT) for trisomy 21 (T21), trisomy 18 (T18), trisomy 13 (T13), numerical aberration of sex and other autosomes and copy number variations with a size of >5 Mb. METHODS:NIPT was carried out for 44 578 pregnant women. For those with a high-risk by NIPT, amniotic fluid or cord blood samples were collected for G-banding karyotype analysis, and the pregnancy outcome was followed up. RESULTS:Among the 44 578 pregnant women, 466 (1.05%) were diagnosed as high risk of T21 (n = 1359), T18 (n = 178) or T13 (n = 129). Among these, 301, 53 and 20 were subjected to prenatal diagnosis by amniocyte or umbilical blood karyotyping analysis, among which 289 were diagnosed as T21, 40 (75.47%) as T18, and 4 (20.00%) as T13. Among the high-risk pregnant women, 2 cases were diagnosed as Down syndrome after birth, while no trisomy 18 and trisomy 13 were recorded. The sensitivity and specificity of NIPT were T21 (99.31%, 99.97%), T18 (100%, 99.97%), T13 (100%, 99.96%), respectively. The positive predictive values for T21, T18 and T13 by NIPT were 96.01%, 75.47% and 20.00%, respectively. CONCLUSION:Compared with conventional serological screening and invasive prenatal diagnosis, NIPT has a high sensitivity and specificity for T21, T18 and T13, and has provided an ideal method to screen fetal chromosomal abnormalities.
10.3760/cma.j.cn511374-20191230-00672
[Analysis of non-invasive prenatal testing in 14 047 cases of advanced age pregnant women].
Lu Zhaie,Tian Liyun,Ying Hongjun,Huang Fang
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics
OBJECTIVE:To assess the value of non-invasive prenatal testing (NIPT) for the diagnosis of fetal chromosomal aneuploidies among women with advanced gestational age. METHODS:14 047 pregnant women have voluntarily accepted the NIPT test. The results of NIPT and amniocytic karyotyping analysis were compared, and the outcome of pregnancy was followed up. RESULTS:NIPT has identified 104 cases with a high risk for trisomies 21, 18 and 13, and 44 cases with a high risk for sex chromosome abnormalities. After genetic consultation, 87 of 104 cases have accepted amniocyte chromosomal karyotyping. 63 cases of fetal chromosome abnormality were confirmed, including 46 cases of 21 trisomy, 11 cases of 18 trisomy and 6 cases of 13 trisomy. The positive predictive value was 83.64% (46/55), 61.11% (11/18), and 42.86% (6/14), the specificity was 99.93%, 99.95%, 99.94%, and the sensitivity was 100%. Among the 44 cases, 34 received amniocytic chromosomal karyotyping analysis, 11 cases were confirmed, the positive predictive value was only 32.35%. No aneuploidy was found in the low-risk cases. The negative predictive value was 100%. CONCLUSION:As a prenatal screening method for women with advanced gestational age, NIPT has the highest positive predictive value for trisomy 21 and trisomy 18, but a lower positive predictive value for sex chromosome abnormalities. NIPT has a very low rate of missed diagnosis of trisomies 21, 18 and 13, which can significantly reduce the number of women undergoing invasive prenatal diagnosis.
10.3760/cma.j.issn.1003-9406.2020.06.004
Analysis of 17,428 pregnant women undergoing non-invasive prenatal testing for fetal chromosome in Northeast China.
Medicine
ABSTRACT:Non-invasive prenatal testing (NIPT) is an incomparable prenatal screening technology, but we should undergo amniocentesis to confirm fetal chromosome when pregnancies receive a positive result via NIPT. We aimed to investigate the detection rate and positive predictive value of NIPT results in pregnancies from Northeast China, and to determine the reasons for false positive and false negative NIPT results.This study evaluates 17,428 singleton pregnancies had undergone NIPT detection. 202 samples were NIPT positive with the detection rate was 1.16% (202/17,428). Among all the positive samples, 160 samples (79.21%) were referred for an amniocentesis procedure to investigate the fetal chromosome. The positive predictive value of T21, T18, and T13 was found to be 75% with a 0.07% false positive rate. Positive predictive value from high to low was as follows: trisomy 21 (84.38%), followed by trisomy 18 (61.54%), autosomal abnormalities (52.94%), sex chromosomal abnormalities (38.46%), and trisomy 13 (33.33%). The positive predictive values for sex chromosome abnormalities turned out to be mosaic sex chromosome aneuploidies (83.33%), followed by XYY (57.14%), XXY (37.50%), XXX (36.36%), and Monosomy X (28.95%). Out of the 160 samples had amniocentesis, the true positive cases in trisomy 21 had a higher percentage of Z-scores compared with the false positive cases in trisomy 21 (P < .05). And the true positive cases in trisomy 18 had a significantly higher percentage of Z-scores compared with the false positive cases in trisomy 18 (P < .01).These findings indicate that the positive predictive value of T21, T18, and T13 was found to be 75% with a 0.07% false positive rate. It is worth noting that the positive predictive value of NIPT for autosomes and sex chromosomes. Moreover, if women receive a positive result via NIPT, they should pay attention to the results with undergoing further prenatal diagnosis.
10.1097/MD.0000000000024740
Non-invasive prenatal paternity testing using cell-free fetal DNA from maternal plasma: DNA isolation and genetic marker studies.
Zhang Shanshan,Han Shuyi,Zhang Maoxiu,Wang Yunshan
Legal medicine (Tokyo, Japan)
Invasive prenatal paternity tests can result in miscarriage and congenital malformations; therefore, a non-invasive method of testing is preferable. However, little progress could be made in this field until the introduction of cell-free fetal DNA (cffDNA) in 2009. In this review, two aspects regarding the history and development of non-invasive prenatal paternity testing (NIPAT) are summarized: (1) extraction and enrichment of cffDNA and (2) genetic marker-based studies. Although column-based kits are used widely for NIPAT, some researchers have suggested that an automated method, such as magnetic extraction, generally has a higher cffDNA yield than that of manual column-based extraction; therefore, its popularity might increase in the near future. In addition, size- and methylation-based enrichment methods are expected to perform better than formaldehyde-based methods. On the other hand, single nucleotide polymorphism-based techniques have contributed to NIPAT, whereas the application of short tandem repeat testing has so far been restricted to pregnant women bearing male fetuses only. Additional methods and techniques are expected to be innovated to facilitate the forensic practice of NIPAT.
10.1016/j.legalmed.2018.03.009
[Results of non-invasive prenatal testing for 2473 women with twin pregnancy].
Chen Shaoning,Dai Peng,Zhao Ganye,Zhang Fengmin,Guo Wanying,Gao Shanshan,Kong Xiangdong
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics
OBJECTIVE:To assess the value of non-invasive prenatal testing (NIPT) for the detection of fetal chromosomal aneuploidies in women with twin pregnancy. METHODS:A total of 2473 women with twin pregnancy underwent the NIPT test to assess the risk for fetal chromosomal aneuploidies from January 2016 to September 2019. Those with a high risk by NIPT were confirmed by amniocentesis or chorionic villus sampling. All cases were followed up to evaluate the positive prediction value of NIPT for twin pregnancies. RESULTS:Among the 2473 women, the NIPT test has identified 31 cases (1.25%) with a high risk for fetal chromosomal aneuploidies, which included 5 cases of trisomy 21, 1 case of chromosome 21 deletion, 4 cases of trisomy 18, 7 cases of sex chromosome abnormality and 14 cases of microdeletion and microduplication. By invasive prenatal diagnosis or chromosomal karyotyping analysis of neonates, 5 cases of trisomy 21, 3 cases of trisomy 18, 1 case of sex chromosome abnormality, and 2 cases of microdeletion and microduplication were confirmed, which yielded a positive predictive value of 100%, 75%, 25% and 25%, respectively. CONCLUSION:NIPT can be used for the screening of fetal chromosomal aneuploidies in women with twin pregnancy with high accuracy. The method is non-invasive, safe and effective for the screening of fetal chromosomal aneuploidies, in particular trisomy 21.
10.3760/cma.j.cn511374-20200521-00368
Non-invasive prenatal aneuploidy testing: Critical diagnostic performance parameters predict sample z-score values.
Blais Jonatan,Giroux Sylvie,Caron André,Clément Valérie,Dionne-Laporte Alexandre,Jouan Loubna,Gauthier Julie,MacLeod Tina,Moore Richard,Parker Jeremy,Swanson Lucas,Zhao Yongjun,Rouleau Guy,Karsan Aly,Langlois Sylvie,Rousseau François
Clinical biochemistry
OBJECTIVES:Non-invasive prenatal aneuploidy testing (NIPT) by next-generation sequencing of circulating cell-free DNA in maternal plasma relies on chromosomal ratio (chr) measurements to detect aneuploid values that depart from euploid ratios. Diagnostic performances are known to depend on the fraction of fetal DNA (FF) present in maternal plasma, although how this translates into specific quantitative changes in specificity/positive predictive values and which other variables might also be important is not well understood. DESIGN & METHODS:To explore this issue, theoretical relationships between FF and various measures of diagnostic performances were assessed for a range of parameter values. Empirical data from three NIPT assays were then used to validate theoretical calculations. RESULTS:For a given positivity threshold, dramatic changes in specificity and positive predictive values (PPV) as a function of both FF and the coefficient of variation (CV) of the chr measurement were observed. Theoretically predicted and observed chr z-scores agreed closely, confirming the determinant impact of small changes in both FF and chr CV. CONCLUSIONS:Evaluation of NIPT assay performances therefore requires knowledge of the FF distribution in the population in which the test is intended to be used and, in particular, of the precise value of the assay chr CV for each chromosome or genomic region of interest. Laboratories offering NIPT testing should carefully measure these parameters to ensure test reliability and clinical usefulness in interpreting individual patients' results.
10.1016/j.clinbiochem.2018.06.015
Non-invasive prenatal testing for the prenatal screening of sex chromosome aneuploidies: A systematic review and meta-analysis of diagnostic test accuracy studies.
Soukkhaphone Bounhome,Lindsay Carmen,Langlois Sylvie,Little Julian,Rousseau Francois,Reinharz Daniel
Molecular genetics & genomic medicine
BACKGROUND:There is little evidence on the performance of non-invasive prenatal testing (NIPT) for the detection of fetal sex chromosomal imbalances. In this review, we aimed to appraise and synthesize the literature on the performance of NIPT for the prenatal detection of fetal sex chromosome aneuploidies. METHODS:We performed our literature search in PubMed, Embase, Cochrane Library, Web of Science, and CADTH. Study selection and data extraction were performed by two reviewers independently. There were no restrictions on the study population. Meta-analyses were performed with "R" software. Pooled sensitivities and specificities with their 95% CI were estimated using a random-effects model. Heterogeneity between studies was assessed by a Q test. RESULTS:Based on 11 studies in high prior risk pregnancies, including 116 affected fetuses in aggregate, Massively Parallel Shotgun Sequencing (MPSS) had a sensitivity of 93.9% (95% CI 84.1%, 97.8%) and a specificity of 99.6% (95% CI 98.7%, 99.9%) for the detection of 45,X. Based on four studies in high-risk pregnancies, with 83 affected fetuses in aggregate, Targeted Massively Parallel Sequencing (TMPS) had a sensitivity of 83.2% (95% CI 49.6%, 96.2%) and specificity was 99.8% (95% CI 98.3%, 100%) for the detection of 45,X. In mixed-risk pregnancies, the sensitivity of TMPS for the detection of 45,X was 90.9% (2 studies; 95% CI 70%, 97.7%) and specificity 99.9% (2 studies; 95% CI 99.4%, 100%); MPSS data were not available in such pregnancies. Based on smaller numbers of studies, and small numbers of affected fetuses in either high-risk or mixed-risk pregnancies (using either MPSS or TMPS), the sensitivities and specificities were equal to or greater than 76.2% for 47,XXX, 47,XXY and 47, XYY. The test failures for SCAs were 0.2% (95% CI 0%, 13.6%) for MPSS and 5.6% (95% CI 3.7%, 8.4%) for TMPS. CONCLUSION:High-quality studies are still desirable in order to estimate the performance of NIPT for the detection of sex chromosome imbalances.
10.1002/mgg3.1654
Performance of cell-free DNA sequencing-based non-invasive prenatal testing: experience on 36,456 singleton and multiple pregnancies.
La Verde Marco,De Falco Luigia,Torella Annalaura,Savarese Giovanni,Savarese Pasquale,Ruggiero Raffaella,Conte Anna,Fico Vera,Torella Marco,Fico Antonio
BMC medical genomics
BACKGROUND:This 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. METHODS:The 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. RESULTS:A 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. CONCLUSION:This 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.
10.1186/s12920-021-00941-y
Expanding the Scope of Non-invasive Prenatal Testing to Detect Fetal Chromosomal Copy Number Variations.
Chen Songchang,Zhang Lanlan,Gao Jiong,Li Shuyuan,Chang Chunxin,Chen Yiyao,Fei Hongjun,Zhang Junyu,Wang Yanlin,Huang Hefeng,Xu Chenming,Lu Daru
Frontiers in molecular biosciences
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.
10.3389/fmolb.2021.649169
Non-invasive prenatal testing in detecting sex chromosome aneuploidy: A large-scale study in Xuzhou area of China.
Suo Feng,Wang Chuangxia,Liu Tianya,Fang Yuan,Wu Qin,Gu Maosheng,Gou Lingshan
Clinica chimica acta; international journal of clinical chemistry
BACKGROUND:Cell-free fetal DNA are widely used in the prenatal genetic testing during recent years. In the present study, we tried to investigate the clinical practical feasibility of non-invasive prenatal testing (NIPT) for prenatal sex chromosome aneuploidy (SCA) analysis among pregnancies in Xuzhou area of China. METHODS:Among a cohort of 8384 pregnancies, maternal plasma samples from our prenatal diagnosis center was subject to the analysis for SCA using NIPT detection. The cases with positive screening results by NIPT detection were validated on karyotyping analysis. RESULTS:From 8384 clinical pregnancies, 64 cases exhibited abnormal results detected by NIPT, in which 34 cases were false positive verified by amniotic fluid puncture and chromosome karyotyping analysis. Twelve positive Turner syndrome (monosomy X) cases in NIPT was confirmed to be sex chromosome abnormal by karyotyping analysis, in which included 9 cases of monosomy X, 1 case of mosaic (45X/47XXX), and 2 cases of mosaic with 45X/45XY karyotype. Of those 9 cases with 47XXX, 5 cases were found to be true positive. Among the ten cases of Klinefelter's syndrome (47XXY) indicated by NIPT, 6 cases (60%) were true positive. Lastly, NIPT indicated 47XYY in 9 cases. Karyotyping analysis found six cases were 47XYY, and one case was mosaic (46XY/47XYY). CONCLUSION:Our findings showed that the true positive rate for monosomy X was lower by NIPT detection, while prediction of other SCA was relatively accurate. Therefore, NIPT could be a potential method for SCA screening, while this technique needed to be further investigated.
10.1016/j.cca.2018.03.007
Clinical performance of non-invasive prenatal testing for trisomies 21, 18 and 13 in twin pregnancies: A cohort study and a systematic meta-analysis.
He Yuting,Wang Yichong,Li Zhuyu,Chen Haitian,Deng Jiankai,Huang Hao,He Xiaohong,Zeng Wentao,Liu Min,Huang Bin,Chen Peisong
Acta obstetricia et gynecologica Scandinavica
INTRODUCTION:The objective of this study was to report on the clinical performance of non-invasive prenatal testing (NIPT) for trisomies 21, 18 and 13 in twin pregnancies and to define the performance of NIPT by combining our cohort study results with published studies in a systematic meta-analysis. MATERIAL AND METHODS:A cohort study was carried out in the First Affiliated Hospital of Sun Yat-sen University and Kanghua Hospital. Meanwhile, searches of PubMed, EMBASE, The Cochrane Library and Web of Science for all relevant peer-reviewed articles were performed with a restriction to English language publication before 15 June 2019. Quality assessments were conducted with the Quality Assessment Tool for Diagnostic Accuracy Studies-2 checklist. Data analysis, heterogeneity, subgroup analysis and publication bias were carried out using META-DISC 1.4 and STATA 12.0. RESULTS:In all, 141 twin pregnancies included in our cohort study; confirmation revealed one true-positive case for trisomy 21 and 140 true-negative cases. The sensitivity and specificity for trisomy 21 by NIPT were both 100%. Twenty-two eligible studies were enrolled in this meta-analysis together with our study. There were 199 cases of trisomy 21, 58 cases of trisomy 18, 14 cases of trisomy 13 and 6347 cases of euploids in total. For trisomy 21, NIPT showed the pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio and diagnostic odds ratio were 0.99, 1.00, 145.81, 0.06 and 1714.09, respectively. For trisomy 18, the pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio and diagnostic odds ratio were 0.88, 1.00, 200.98, 0.19 and 483.68, respectively. CONCLUSIONS:The performance of NIPT for trisomy 21 in twin pregnancy was excellent and it was similar to that reported in singleton pregnancy. However, due to publication bias (trisomy 18) and small number of cases (trisomy 13), accurate assessment of the predictive performance of NIPT for trisomies 18 and 13 could not be achieved.
10.1111/aogs.13842
Non-Invasive Prenatal Testing for Sex Chromosome Aneuploidy in Routine Clinical Practice.
Kornman Louise,Palma-Dias Ricardo,Nisbet Debbie,Scott Fergus,Menezes Melody,da Silva Costa Fabricio,McLennan Andrew
Fetal diagnosis and therapy
OBJECTIVES:To assess the accuracy of non-invasive prenatal testing (NIPT) for sex chromosome aneuploidy (SCA) in routine clinical practice and to review counselling and sonographic issues arising in SCA cases. METHODS:Three specialist Australian obstetric ultrasound and prenatal diagnosis practices offering NIPT after 10 weeks' gestation participated in this study. NIPT was reported for chromosomes 21, 18, 13, X, and Y. RESULTS:NIPT screening was performed in 5,267 singleton pregnancies. The odds of being affected given a positive screening result (OAPR) was lowest for SCAs, most notably for monosomy X (20%). Fewer women underwent invasive prenatal testing when counselled regarding a high risk for SCA (65.5%) compared with those who had a high risk for another aneuploidy (85%). The positive screening rate of NIPT including SCA was 2.3%, but 1.2% if only the autosomal trisomies were included in the panel. CONCLUSION:The addition of SCA testing to NIPT doubles the positive screening rate. The OAPR for SCAs (most notably for monosomy X) is reduced compared with the autosomal trisomies. Clinicians need a more extensive discussion with women prior to the inclusion of the X and Y chromosomes in the NIPT panel, given the complexity in counselling regarding further management and the additional anxiety that these abnormal results may cause. A benefit of sex chromosome analysis is an improvement in antenatal diagnosis of some disorders of sexual development.
10.1159/000479460
[Clinical value of routine non-invasive prenatal testing for the screening of non-target chromosomal abnormalities].
Zhang Yuxin,Yan Lulu,Liu Yingwen,Li Haibo
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics
OBJECTIVE:To assess the value of non-invasive prenatal testing (NIPT) for the identification of sex chromosome aneuploidies (SCAs), copy number variants (CNVs) and rare autosomal trisomies (RATs). METHODS:A total of 11 429 women with singleton pregnancy in Ningbo area were screened by NIPT. 106 women were subjected to invasive prenatal diagnosis due to high risk of chromosomal abnormalities other than 21, 18 and 13 aneuploidies. All cases were followed up for pregnancy outcome and postnatal status. RESULTS:Sixty-six women were signaled by NIPT for fetal SCAs, among whom 54 were willing to undergo prenatal diagnosis. Eighteen cases of fetal SCAs were verified as true positives and 4 were suspected positives, which yielded a positive predictive value (PPV) of 33.3%. Half of the women decided to continue their pregnancy. Forty women were signaled by NIPT for fetal CNVs, among which 32 underwent prenatal diagnosis. 19 cases of fetal CNVs were verified as true positives and 3 cases were suspected positives, which yielded a PPV of 46.8%. All women with pathological or possibly pathological CNVs decided to terminate their pregnancies. Thirty-one women were signaled for with fetal RATs. Two fetuses were confirmed to harbor mosaicism trisomies by prenatal diagnosis, and 1 case was suspected to be positive, which yielded a PPV of 9.7%. All of the three women have decided to terminate their pregnancy. CONCLUSION:In addition to aneuploidies of target chromosomes, NIPT also has important value for the detection of SCAs and CNVs. The results can help to further reduce birth defects. Nevertheless, in view of its low PPV, pregnant women with positive result still need appropriate genetic counseling and prenatal diagnosis to avoid unnecessary induced labor.
10.3760/cma.j.issn.1003-9406.2020.06.006
Genome-wide non-invasive prenatal testing in single- and multiple-pregnancies at any risk: Identification of maternal polymorphisms to reduce the number of unnecessary invasive confirmation testing.
Oneda Beatrice,Sirleto Pietro,Baldinger Rosa,Taralczak Malgorzata,Joset Pascal,Zweier Markus,Niedrist Dunja,Azzarello-Burri Silvia,Britschgi Christian,Breymann Christian,Ochsenbein-Kölble Nicole,Burkhardt Tilo,Wisser Josef,Zimmermann Roland,Steindl Katharina,Rauch Anita
European journal of obstetrics, gynecology, and reproductive biology
OBJECTIVE:Non-invasive prenatal testing by targeted or genome-wide copy number profiling (cnNIPT) has the potential to outperform standard NIPT targeting the common trisomies 13, 18, and 21, only. Nevertheless, prospective results and outcome data on cnNIPT are still scarce and there is increasing evidence for maternal copy number variants (CNVs) interfering with results of both, standard and cnNIPT. STUDY DESIGN:We assessed the performance of cnNIPT in 3053 prospective and 116 retrospective cases with special consideration of maternal CNVs in singleton and multiple gestational pregnancies at any risk, as well as comprehensive follow-up. RESULTS:A result was achieved in 2998 (98.2%) of total prospective cases (89.2% analyzed genome-wide). Confirmed fetal chromosomal abnormalities were detected in 45 (1.5%) cases, of which five (11%) would have remained undetected in standard NIPTs. Additionally, we observed 4 likely fetal trisomies without follow-up and a likely phenotype associated placental partial trisomy 16. Moreover, we observed clinically relevant confirmed maternal CNVs in 9 (0.3%) cases and likely maternal clonal hematopoiesis in 3 (0.1%). For common fetal trisomies we prospectively observed a very high sensitivity (100% [95% CI: 91.96-100%]) and specificity (>99.9% [95% CI: 99.8-100%]), and positive predictive value (PPV) (97.8% [95% CI: 86.1-99.7%]), but our retrospective control cases demonstrated that due to cases of fetal restricted mosaicism the true sensitivity of NIPT is lower. After showing that 97.3% of small CNVs prospectively observed in 8.3% of genome-wide tests were mostly benign maternal variants, sensitivity (75.0% [95% CI: 19.4%-99.4%]), specificity (99.7% [99.5%-99.9%]) and PPV (30.0% [14.5%-52.1%]) for relevant fetal CNVs were relatively high, too. Maternal autoimmune disorders and medication, such as dalteparin, seem to impair assay quality. CONCLUSION:When maternal CNVs are recognized as such, cnNIPT showed a very high sensitivity, specificity and PPV for common trisomies in single and multiple pregnancies at any risk and very good values genome-wide. We found that the resolution for segmental aberrations is generally comparable to standard karyotyping, and exceeds the latter if the fetal fraction is above 10%, which allows detection of the 2.5 Mb 22q11.2 microdeletion associated with the velocardiofacial syndrome, even if the mother is not a carrier.
10.1016/j.ejogrb.2020.05.070
[Value of non-invasive prenatal testing for the detection of fetal chromosomal copy number variations].
Jin Keqin,Luo Jianfeng,Zhang Liping,Shen Shuangshuang,Hu Yuan
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics
OBJECTIVE:To explore the value of non-invasive prenatal testing (NIPT) for the detection of fetal chromosome copy number variations (CNVs). METHODS:Clinical data of 18 661 pregnant women who underwent NIPT were collected. For fetuses suspected for carrying CNVs, amniotic fluid samples were collected for chromosomal karyotyping and/or chromosomal microarray analysis (CMA). RESULTS:Among all samples, NIPT suggested that 58 fetuses carried trisomy 21, 18 carried trisomy 18, 19 carried trisomy 13, 1 carried trisomies 18 and 21. Eighty eight women accepted invasive prenatal diagnosis. The results of CMA in 59 cases were consistent with those of NIPT, which yielded a consistency rate of 67.05%. In addition, 37 cases of fetal CNVs were detected by NIPT, of which 19 (15 microdeletions and 4 microduplications) have accepted invasive prenatal diagnosis. In 14 cases, the results were consistency with those of NIPT, with a consistent rate of 73.68%. CONCLUSION:NIPT features high sensitivity and accuracy. Invasive prenatal diagnosis should be considered for CNVs detected by NIPT, and by tracing its parental origin, it can provide guidance for clinical practice.
10.3760/cma.j.cn511374-20200331-00221
A retrospective analysis the clinic data and follow-up of non-invasive prenatal test in detection of fetal chromosomal aneuploidy in more than 40,000 cases in a single prenatal diagnosis center.
Luo Yanmei,Hu Huamei,Jiang Luping,Ma Yongyi,Zhang Rong,Xu Juchun,Pan Yan,Long Yang,Yao Hong,Liang Zhiqing
European journal of medical genetics
OBJECTIVE:To evaluate the efficacy of non-invasive prenatal test (NIPT) in the detection of chromosomal aneuploidy according to the follow-up information from a single prenatal diagnosis center. METHODS:A total of 40,311 cases were retrospectively reviewed. The screening was performed using a BGI protocol, pre-test and post-test genetic counseling was provided, and the pregnancy outcomes were recorded. The results of NIPT and clinical follow-up data were analyzed together with the pregnancy outcomes, confirmatory testing results, and ultrasound findings. RESULTS:Of the 40,311cases were includes in the study, successful follow-up was conducted in 468 (1.16%) cases with high risk, 225 (0.56%) cases with rare autosomal trisomy (RAT) and copy number variation (CNV). 39,572 (98.17%) cases with low risk and 623 (1.57%) cases of which were confirmed with adverse pregnancy outcomes. 46 (0.1%) cases with failed tests. Among them, 398 (84.7%) cases with high-risk results chose invasive testing, revealing 198 true positive cases. In cases with RAT and CNV results, 189 cases underwent invasive testing, revealing 5 cases RAT and 4 pathogenic CNVs. CONCLUSIONS:NIPT appears to be effective in detecting the fetal chromosomal aneuploidies T21, T18 and SCAs, but it exist false positive/negative cases, unconfirmed high-risk cfDNA results, and the high false positive rate in cases with RAT and CNV results implied the limitations of this screening method. Our study showed the importance to associate cfDNA screening results with clinical follow-up data and provided information that may help with result interpretation, genetic counseling and the decision making in clinic.
10.1016/j.ejmg.2020.104001
Women's preference for non-invasive prenatal DNA testing versus chromosomal microarray after screening for Down syndrome: a prospective study.
Cheng Yky,Leung W C,Leung T Y,Choy K W,Chiu Rwk,Lo T-K,Kwok K Y,Sahota D S
BJOG : an international journal of obstetrics and gynaecology
OBJECTIVE:To examine preferences for follow-up testing in women screened with high or intermediate risk for Down syndrome in the first or second trimester. DESIGN:Prospective cohort study. SETTING:Three public hospitals in Hong Kong, China. SAMPLE:Women with pregnancies termed as high risk (≥1:250; HR) or intermediate risk (1:251-1200; IR) for Down syndrome. METHODS:Women with pregnancies screened as HR were offered the choices of: (1) an invasive test plus chromosomal microarray (CMA) to obtain more detailed fetal genetic information; (2) non-invasive cell-free prenatal DNA screening (NIPT) to detect trisomies 13, 18 and 21, and to avoid procedure-related miscarriage; and (3) to decline any further testing. Women received standardised counselling informing them that the reporting times were identical, the procedure miscarriage risk was 0.1-0.2% and that there was no charge for screening. Women with IR pregnancies (1:251-1200) were offered NIPT as a secondary screening test. MAIN OUTCOME MEASURES:Uptake rate for NIPT. RESULTS:Three hundred and forty-seven women had pregnancies deemed as HR; 344 (99.1%) women opted for follow-up testing, 216 (62.2%) of whom chose NIPT. Five hundred and seven of 614 women (82.6%) with IR risk chose NIPT. Seven (21%) of 34 women with nuchal translucency ≥3.5 mm opted for NIPT. CONCLUSION:In a setting where reporting times are similar and there is no cost difference between options, approximately 60% of women with pregnancies classed as HR would opt for NIPT, offering simple but limited aneuploidy assessment, over a diagnostic procedure with comprehensive and more detailed assessment. TWEETABLE ABSTRACT:60% of pregnant Chinese women prefer NIPT over CMA when screened as high risk for Down syndrome.
10.1111/1471-0528.15022
Clinical utility of non-invasive prenatal testing in pregnancies with ultrasound anomalies.
Beulen L,Faas B H W,Feenstra I,van Vugt J M G,Bekker M N
Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology
OBJECTIVE:To evaluate the application of non-invasive prenatal testing (NIPT) as an alternative to invasive diagnostic prenatal testing in pregnancies with abnormal ultrasound findings. METHODS:This was a retrospective analysis of 251 singleton and multiple pregnancies at high risk for fetal chromosomal abnormality based on findings at sonographic examination, in which NIPT was performed as a first-tier genetic test. NIPT was performed by massively parallel sequencing of cell-free DNA in maternal plasma, allowing genome-wide detection of whole-chromosome, as well as partial, autosomal aneuploidy. Sex chromosomes were not analyzed, according to the current protocol in Dutch laboratories. RESULTS:NIPT was performed at a median gestational age of 20 weeks, indicated by the presence of multiple congenital anomalies (n = 13), isolated structural anomalies (n = 57), increased nuchal translucency ≥ 3.5 mm (n = 58), soft markers (n = 73), growth restriction (n = 40) and other anomalies (n = 10). NIPT results were normal in 224 (89.2%) pregnancies, inconclusive in one (0.4%) and abnormal in 26 (10.4%). Most genetic aberrations detected by NIPT were common whole-chromosome aneuploidies: trisomy 21 (n = 13), trisomy 18 (n = 6) and trisomy 13 (n = 3). Four further NIPT results were abnormal; one was suspected of being confined placental mosaicism and one was of maternal origin. In those with normal NIPT results, sonographic follow-up or examination of the newborn indicated the need for diagnostic genetic testing in 33/224 (14.7%) pregnancies. Clinically relevant genetic aberrations were revealed in 7/224 (3.1%) cases, two of which were whole-chromosome aneuploidies: trisomy 13 and monosomy X. As sex chromosomal aberrations are not included in NIPT analysis, the latter cannot be considered a false-negative result. Other discordant findings were subchromosomal aberrations (< 20 megabases, n = 2) and monogenic aberrations (n = 3). CONCLUSIONS:NIPT should not be recommended for genetic evaluation of the etiology of ultrasound anomalies, as both resolution and sensitivity, or negative predictive value, are inferior to those of conventional karyotyping and microarray analysis. Nonetheless, some pregnant women consider NIPT to be an acceptable alternative to invasive diagnostic testing. © 2016 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of the International Society of Ultrasound in Obstetrics and Gynecology.
10.1002/uog.17228
[Factors affecting the failure of non-invasive prenatal testing and the feasibility analysis of retesting].
Luo Yanmei,Hu Huamei,Zhang Rong,Pan Yan,Ma Yongyi,Long Yang,Xu Juchun,Xu Liang,Hu Bin,Yao Hong,Chang Qing
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics
OBJECTIVE:To explore the cause for the failure of non-invasive prenatal testing (NIPT) and feasibility of repeated testing. METHODS:Clinical data, test results and pregnancy outcomes of 40 311 pregnant women who received NIPT test from January 2011 to December 2018 were reviewed. RESULTS:Among all the pregnant women, 1116 cases failed in the first test, 9 cases (0.81%) had fetal free DNA concentration lower than 4%, 663 cases (59.41%) were retested after the establishment of Z value gray area, and the remainder 444 cases (39.78%) needed to be retested after the blood collection due to the fetal free DNA concentration lower than 4%. After retesting, 1069 cases (95.78%) obtained effective NIPT results. The results showed that 53 cases were at high risk (6 cases for trisomy 21, 6 cases for trisomy 18, 13 cases for trisomy 13, 16 cases for sex chromosomal abnormality, 12 cases for chromosomal copy number variation). Forty-eight cases were selected for invasive prenatal diagnosis, and 2 cases of 47, XXY and 2 CNV were confirmed. A total of 47 cases (0.12%) did not obtain results because the concentration of fetal free DNA was lower than 4%. Only 16 cases (34%) chose invasive prenatal diagnosis. CONCLUSION:Repeated detection of the gray area of Z value can reduce the false positive rate of NIPT and invasive prenatal diagnosis, and the feasibility of repeated detection is high. In the case of fetal free DNA concentration lower than 4%, the success rate of obtaining effective NIPT results by re-sampling and re-detection increases with the increase of gestational age, but may delay the diagnosis for fetal aneuploidies. Therefore, personalized estimation should be made according to gestational age and clinical indications. It is suggested that pregnant women should choose invasive prenatal diagnosis when they have failed in the retest.
10.3760/cma.j.issn.1003-9406.2020.06.002
Non-invasive prenatal testing: impact on invasive prenatal diagnosis at a mainland Chinese tertiary medical center.
Li Dong-Zhi,Zhen Li,Pan Min,Han Jin,Yang Xin,Ou Yan-Mei
The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians
OBJECTIVE:We describe the changes over a 4-year period in the number of diagnostic testing after the introduction of non-invasive prenatal testing (NIPT). METHODS:The rate of NIPT as an indication in women who received amniocentesis, and the number of amniocentesis required for detection of one case with major aneuploidy were compared between a 1-year baseline period before the introduction of NIPT, and the 3 years following NIPT introduction. RESULTS:A total of 7536 amniocentesis procedures were performed over the 4-year study period. During the baseline period of the year 2011, the number of invasive testing required for detection of one common trisomy was 57. During the first 2 years that NIPT was offered, NIPT averaged 1.7 percent of the total indications for amniocentesis, and the required number of invasive testing decreased to 30. With the increase of the percentage of NIPT during the 3rd year, the required number of invasive testing further decreased to 26. CONCLUSION:After the clinical introduction of NIPT, invasive prenatal diagnostic testing had not decreased at a Chinese prenatal diagnostic unit, but a remarkably improved detection rate of major aneuploidies in diagnostic procedures was observed.
10.3109/14767058.2016.1138464
Lower detectability of non-invasive prenatal testing compared to prenatal diagnosis in high-risk pregnant women.
Annals of translational medicine
BACKGROUND:To investigate the detectability of non-invasive prenatal testing (NIPT) after prenatal screening to detect foetal chromosomal abnormalities in pregnant women at high risk, and the number of foetal abnormalities could be missed by NIPT. METHODS:From January 2009 to March 2018, 3,099 pregnant women at high risk for trisomy 21 and 18 according to the results of prenatal serological screening were enrolled in this study. The women underwent amniocentesis at 18-23 weeks, as well as karyotype testing and/or chromosomal microarray analyses (CMA). We assessed the ability of NIPT to detect chromosomal abnormalities. RESULTS:In all, 177 (5.7%, 177/3,099) chromosomal abnormalities were identified. These included 129 (72.9%) abnormal numbers of chromosomes, 6 (3.4%) chromosome structural abnormalities, and 42 (23.7%) other abnormalities, including copy number variation, inversions, and chromosome additions/deletions. Of the 177 (70.0%) chromosomal abnormalities, 124 were detected and 53 were missed by NIPT. CONCLUSIONS:NIPT could miss 30.0% of the chromosomal abnormalities detected by amniocentesis and cytogenetic testing. This proportion will likely decrease in the future due to further development of NIPT.
10.21037/atm.2019.06.70
Evaluation of non-invasive prenatal testing to detect chromosomal aberrations in a Chinese cohort.
Cui Wanting,Liu Xiaoliang,Zhang Yuanyuan,Wang Yueping,Chu Guoming,He Rong,Zhao Yanyan
Journal of cellular and molecular medicine
The aim of this study was to evaluate the clinical feasibility of non-invasive prenatal testing (NIPT) to detect foetal copy number variations (CNVs). Next-generation sequencing for detecting foetal copy number variations (CNVs) was performed on the collected samples from 161 pregnancies with ultrasound anomalies and negative NIPT results for aneuploidy. The performance of NIPT for detecting chromosome aberrations was calculated. The sensitivity and specificity of NIPT for detecting CNVs > 1 Mb were 83.33% and 99.34%; the PPV and negative predictive rate (NPV) were 90.91% and 98.68%. Non-invasive prenatal testing can be performed to detect chromosomal aberrations in first trimester with high performance for CNVs, and occasional discordant cases are unavoidable.
10.1111/jcmm.14614
Analysis of the accuracy of Z-scores of non-invasive prenatal testing for fetal Trisomies 13, 18, and 21 that employs the ion proton semiconductor sequencing platform.
Tian Yuan,Zhang Linlin,Tian Weifang,Gao Jinshuang,Jia Liting,Cui Shihong
Molecular cytogenetics
BACKGROUND:Non-invasive prenatal testing (NIPT) is frequently being used to screen for trisomies 13, 18 and 21 for prenatal diagnosis. However, NIPT performs poorly when compared with invasive testing and thus should not be used to diagnose trisomies. The result of NIPT for an individual woman in most genome-wide methods is calculated as a Z-score. The aim of this study was to assess the correlation between Z-scores of NIPT results and the accuracy of non-invasive prenatal testing. RESULTS:We evaluated 108 pregnant women with positive NIPT results, which were validated through karyotype analysis of amniotic fluid puncture by means of sequencing, bioinformatics analysis, and follow-up. Utilizing the ion proton semiconductor sequencing platform, we report a performance evaluation of NIPT-positive results at Third Affiliated Hospital of Zhengzhou University of Henan Province, China, by classifying Z-scores as 3 ≤ Z<5, 5 ≤ Z < 9 and Z ≥ 9. The findings indicate that positive NIPT results at Z ≥ 9 have a higher accuracy compared with positive NIPT results at 5 ≤ Z < 9 and 3 ≤ Z<5. CONCLUSIONS:The findings show that Z-scores of NIPT results are closely related to the accuracy of non-invasive prenatal testing. However, false-positive NIPT results at 3 ≤ Z<5 may occur due to confined placental mosaicism (CPM).
10.1186/s13039-018-0397-x
A two-year experience of non-invasive prenatal testing (NIPT) at an urban tertiary medical center in South Korea.
Noh Joseph J,Ryu Hyun Mee,Oh Soo-Young,Choi Suk-Joo,Roh Cheong-Rae,Kim Jong-Hwa
Taiwanese journal of obstetrics & gynecology
OBJECTIVE:To report our experience of implementing non-invasive prenatal testing (NIPT) in a tertiary urban academic medical center in South Korea. MATERIALS AND METHODS:An observational retrospective study of singleton and twin pregnancies that underwent prenatal screening for fetal aneuploidy from July 2016 to April 2018 was conducted. Demographics of the study population electing NIPT versus those opting the integrated test were compared. We also assessed clinical significant factors influencing cfDNA fetal fraction in NIPT. RESULTS:Among the 817 women who underwent serum screening tests during the study period, 490 women (60.0%) chose the integrated test while 327 women (40.0%) chose NIPT. Compared to the integrated test group, women in the NIPT group were older (mean age 34.7 ± 3.7 vs. 32.6 ± 3.4; p-value < 0.01), multiparous (47.1% vs. 39.8%; p-value = 0.046), and had higher rate of previous abortion history (28.4% vs. 21.6%; p-value = 0.033). A significant decrease in the number of invasive diagnostic tests was observed since the adoption of NIPT. The screen negative and positive rates of the integrated test group for fetal aneuploidy were 95.3% and 4.7%, respectively while those of the NIPT group were 95.9% and 1.2%, respectively. The rate of inadequate cfDNA fetal fraction was 3.0%. Low fetal fraction was associated with higher maternal age, body weight and BMI. CONCLUSIONS:The implementation of NIPT has significantly affected the practice pattern of prenatal aneuploidy screening by replacing the integrated test and decreasing invasive diagnostic tests.
10.1016/j.tjog.2019.05.021
Current genetic counseling practice in the United States following positive non-invasive prenatal testing for sex chromosome abnormalities.
Fleddermann Lauren,Hashmi Syed Shahrukh,Stevens Blair,Murphy Lauren,Rodriguez-Buritica David,Friel Lara A,Singletary Claire
Journal of genetic counseling
The purpose of this study was to describe current genetic counseling practice in the United States following a non-invasive prenatal testing (NIPT) result positive for a sex chromosome abnormality (SCA). Screening for SCAs can be confounded by confined placental mosaicism, natural loss of the X chromosome from maternal cells during aging, and undiagnosed maternal SCA or copy number variant (CNV). Furthermore, with the exception of 45,X, individuals with SCAs usually have no ultrasound or postnatal findings. This makes follow-up for unresolved positive NIPT necessary; however, there are currently no clinical guidelines. This study used a cross-sectional design with an anonymous questionnaire to survey 176 genetic counselors. The majority of prenatal respondents always offered diagnostic testing (>88%) and anatomy ultrasound (~90%), but the percent consistently offering maternal karyotype (22%-52%) and postnatal evaluation (28%-87%) varied. Maternal karyotype was offered more often when NIPT was positive for 45,X or 47,XXX and patients had normal prenatal diagnostic testing (p < 0.02) or declined testing (p < 0.02). Offer of postnatal evaluation was more likely when diagnostic testing was declined (p < 0.001). The majority of pediatric providers always offered a postnatal karyotype for the newborn (>72%) but the percent offering maternal karyotype (6%-46%) varied widely. With the current inconsistencies, many newborns with undiagnosed SCAs who could benefit from growth hormone therapy, early intervention, and/or targeted surveillance may be missed. Therefore, there is a need for professional guidelines to help improve the consistency of clinical care for patients with NIPT results positive for SCAs.
10.1002/jgc4.1122
An assessment of the analytical performance of non-invasive prenatal testing (NIPT) in detecting sex chromosome aneuploidies: 34,717-patient sample in a single prenatal diagnosis Centre in China.
Luo Yanmei,Hu Huamei,Zhang Rong,Ma Yongyi,Pan Yan,Long Yang,Hu Bin,Yao Hong,Liang Zhiqing
The journal of gene medicine
OBJECTIVE:The present study aimed to evaluate the efficacy of a non-invasive prenatal test (NIPT) in the detection of the sex chromosome aneuploidies (SCAs) at our prenatal diagnosis centre. METHODS:Among a cohort of 34,717 pregnancies, maternal plasma samples from our prenatal diagnosis centre were subject to analysis of SCAs using NIPT detection. Pregnant women with NIPT positive results of SCAs were recommended to undergo an invasive prenatal diagnosis (i.e. karyotyping and fluorescence in situ hybridization) to validate the prediction value of NIPT. RESULTS:From 34,717 clinical pregnancies, 229 (0.66%) pregnancies were identified with SCAs. Of these, 78 (34.1%) cases were positive for 45,X and 151 (65.9%) cases comprised a sex chromosome trisomy. Of the 229 positive NIPT results, 193 (84.3%) cases had accepted an invasive diagnosis involving karyotyping analysis of the amniotic fluid, which confirmed 67 cases (34.7%) as true positive, as well as 126 cases (65.3%) as false positive. The positive predictive values were 23.07%, 50%, 36% and 27.27% respectively. The remaining 36 (15.7%) cases declined a prenatal diagnosis. The termination rates of 45,X, 47,XXY, 47,XXX and 47,XYY were 20.5%,46%,12.9% and 11.5% respectively. CONCLUSIONS:NIPT demonstrated a lower accuracy in predicting monosomy X than sex chromosome trisomies. After invasive testing, the fetal chromosome with 45,X and 47,XXY were terminated more often than those with 47,XXX, 47,XYY. Because NIPT is a screening test, false positive/negative cases exist, and pre- and post-test counselling is essential for informing patients about the benefits and limitations of the test. Confirmatory testing of abnormal results is recommended prenatally or after birth, and the importance of confirmatory testing and benefits of early diagnosis should be addressed.
10.1002/jgm.3362
National data on the early clinical use of non-invasive prenatal testing in public and private healthcare in Denmark 2013-2017.
Lund Ida C B,Petersen Olav B,Becher Naja H,Lildballe Dorte L,Jørgensen Finn S,Ambye Louise,Skibsted Lillian,Ernst Anja,Jensen Ann N,Fagerberg Christina,Brasch-Andersen Charlotte,Tabor Ann,Zingenberg Helle J,Nørgaard Pernille,Almind Gitte J,Vestergaard Else Marie,Vogel Ida
Acta obstetricia et gynecologica Scandinavica
INTRODUCTION:In Denmark, non-invasive prenatal testing (NIPT) has been used since 2013. We aimed to evaluate the early clinical use of NIPT in Danish public and private healthcare settings before NIPT became an integrated part of the national guidelines on prenatal screening and diagnosis in 2017. MATERIAL AND METHODS:NIPT data were collected between March 2013 and June 2017 from national public registries and private providers. Results from follow-up samples (chorionic villi, amniotic fluid, postnatal blood or fetal tissue) were included from The Danish Cytogenetics Central Registry and indications and outcome from The Danish Fetal Medicine Database. RESULTS:A total of 3936 NIPT results were included in the study from public hospitals (n = 3463, 88.0%) and private clinics (n = 473, 12.0%). The total number of prenatal tests was 19 713 during the study period: 20% were NIPT analyses (n = 3936) and 80% invasive procedures (n = 15 777). Twenty-five percent of NIPTs in the private clinics were performed before gestational week 11 , whereas NIPT in public settings was used only after combined first trimester screening (P < .001). Regardless of indication, the national public sensitivity was 96.9% (95% CI 82.0%-99.8%) for trisomy 21, 100% (95% CI 46.3%-100%) for trisomy 18, 100% (95% CI 5.5%-100%) for trisomy 13, and 87.0% (95% CI 74.5%-92.4%) for any fetal chromosomal aberration. Forty-seven true-positive NIPT results included cases of common aneuplodies (trisomy 21, n = 31; trisomy 18, n = 5; and trisomy 13, n = 1), sex chromosomal aberrations (n = 7) and atypical chromosomal aberrations (n = 3). One false-negative NIPT result occurred (trisomy 21). Of 47 cases, 21 (45%) cases with a true-positive NIPT result resulted in live births by choice; 11 of these children had Down and 4 had Edwards syndrome. CONCLUSIONS:The total number of NIPT analyses was low compared with the number of invasive procedures in the implementation period. In contrast to the generally high termination rate after a positive result following invasive testing in Denmark, a high proportion of true-positive NIPT results from the public setting resulted in live births. NIPT may be an important risk-free alternative to invasive testing for a minority of women in the public setting who wish to use prenatal genetic testing for information only and not for reproductive decision-making.
10.1111/aogs.14052
Clinical application of noninvasive prenatal testing in the detection of fetal chromosomal diseases.
Pang Yu,Wang Chaohong,Tang Junxiang,Zhu Jiansheng
Molecular cytogenetics
OBJECTIVE:To assess the detection efficiency of noninvasive prenatal testing (NIPT) for fetal autosomal aneuploidy, sex chromosome aneuploidy (SCA), other chromosome aneuploidy, copy number variation (CNV), and to provide further data for clinical application of NIPT. MATERIALS AND METHODS:25,517 pregnant women who underwent NIPT testing in Anhui Province Maternity and Child Health Hospital from September 2019 to September 2020 were selected, and samples with high-risk test results were subjected to karyotype analysis for comparison by using amniotic fluid, with some samples subjected to further validation by chromosomal microarray analysis, and followed up for pregnancy outcome. RESULTS:A total of 25,517 pregnant women who received NIPT, 25,502 cases were tested successfully, and 294 high-risk samples (1.15%) were detected, there were 96 true positive samples, 117 false positive samples and 81 cases were refused further diagnosis. Samples with high risk of autosomal aneuploidy were detected in 71 cases (0.28%), and 51 cases were confirmed, including: trisomy 21 (T21) in 44 cases, trisomy 18 (T18) in 5 cases, and trisomy 13 (T13) in 2 cases; the positive predictive value (PPV) was 91.67%, 45.45%, and 33.33%, respectively, and the negative predictive value was 100%, the false positive rate (FPR) was 0.02%, 0.02%, and 0.02%, respectively.13 samples with high risk of mosaic trisomies 21, 18, and 13 were detected, and 1 case of T21mos was confirmed with a PPV of 8.33%. Samples with high risk of SCA were detected in 72 cases (0.28%), and the diagnosis was confirmed in 23 cases, with a PPV of 41.07% and a FPR of 0.13%. These included 3 cases of 45,X, 6 cases of 47,XXY, 8 cases of 47,XXX and 6 cases of 47,XYY, with PPVs of 12.00%, 50.00%, 72.73%, and 75.00%, respectively, and false-positive rates of 0.09%, 0.02%, 0.01% and 0.01% respectively. Samples with high risk of CNV were detected in 104 cases (0.41%) and confirmed in 18 cases, with a PPV of 32.14% and a FPR of 0.15%. Samples with high risk of other chromosomal aneuploidy were detected in 34 cases (0.13%), and the diagnosis was confirmed in 3 cases, which were T2, T9, and T16 respectively. The overall PPV for other chromosome aneuploidy was 12.50%, with a FPR of 0.08%. CONCLUSION:NIPT is indicated for trisomies 21, 18 and 13 screening, especially for T21. It also has some certain reference value for SCA and CNV, but is not recommended for screening of other chromosomal aneuploidy.
10.1186/s13039-021-00550-5
Non-invasive prenatal testing in the management of twin pregnancies.
Benn Peter,Rebarber Andrei
Prenatal diagnosis
Twin pregnancies are common and associated with pregnancy complications and adverse outcomes. Prenatal clinical management is intensive and has been hampered by inferior screening and less acceptable invasive testing. For aneuploidy screening, meta-analyses show that non-invasive prenatal testing (NIPT) through analysis of cell-free DNA (cf-DNA) is superior to serum and ultrasound-based tests. The positive predictive value for NIPT is driven strongly by the discriminatory power of the assay and only secondarily by the prior risk. Uncertainties in a priori risks for aneuploidies in twin pregnancies are therefore of lesser importance with NIPT. Additional information on zygosity can be obtained using NIPT. Establishing zygosity can be helpful when chorionicity was not reliably established early in pregnancy or where the there is a concern for one versus two affected fetuses. In dizygotic twin pregnancies, individual fetal fractions can be measured to ensure that both values are satisfactory. Vanishing twins can be identified by NIPT. Although clinical utility of routinely detecting vanishing twins has not yet been demonstrated, there are individual cases where cf-DNA analysis could be helpful in explaining unusual clinical or laboratory observations. We conclude that cf-DNA analysis and ultrasound have synergistic roles in the management of multiple gestational pregnancies.
10.1002/pd.5989