A Novel Graphic-Aided Algorithm (gNIPT) Improves the Accuracy of Noninvasive Prenatal Testing

Noninvasive Prenatal Testing (NIPT) has advanced the detection of fetal chromosomal aneuploidy by analyzing cell-free DNA in peripheral maternal blood. The statistic Z-test that it utilizes, which measures the deviation of each chromosome dosage from its negative control, is now widely accepted in clinical practice. However, when a chromosome has loss and gain regions which offset each other in the z-score calculation, merely using the Z-test for the result tends to be erroneous. To improve the performance of NIPT in this aspect, a novel graphic-aided algorithm (gNIPT) that requires no extra experiment procedures is reported in this study. In addition to the Z-test, this method provides a detailed analysis of each chromosome by dividing each chromosome into multiple 2 Mb size windows, calculating the z-score and copy number variation of each window, and visualizing the z-scores for each chromosome in a line chart. Data from 13537 singleton pregnancy women were analyzed and compared using both the normal NIPT (nNIPT) analysis and the gNIPT method. The gNIPT method had significantly improved the overall positive predictive value (PPV) of nNIPT (88.14% vs. 68.00%, p=0.0041) and the PPV for trisomy 21 (T21) detection (93.02% vs. 71.43%, p=0.0037). There were no significant differences between gNIPT and nNIPT in PPV for trisomy 18 (T18) detection (88.89% vs. 63.64%, p=0.1974) and in PPV for trisomy 13 (T13) detection (57.14% vs. 50.00%, p=0.8004). One false-negative T18 case in nNIPT was detected by gNIPT, which demonstrates the potency of gNIPT in discerning chromosomes that have variation in multiple regions with an offsetting effect in z-score calculation. The gNIPT was also able to detect copy number variation (CNV) in chromosomes, and one case with pathogenic CNV was detected during the study. With no additional test requirement, gNIPT presents a reasonable solution in improving the accuracy of normal NIPT.

Download Full-text

Copy number variation profile in noninvasive prenatal testing (NIPT) can identify co-existing maternal malignancies: Case reports and a literature review

Taiwanese Journal of Obstetrics and Gynecology ◽

10.1016/j.tjog.2018.10.032 ◽

2018 ◽

Vol 57 (6) ◽

pp. 871-877 ◽

Cited By ~ 1

Author(s):

Xing Ji ◽

Fang Chen ◽

Yafeng Zhou ◽

Jia Li ◽

Yuying Yuan ◽

...

Keyword(s):

Literature Review ◽

Copy Number Variation ◽

Copy Number ◽

Case Reports ◽

Prenatal Testing ◽

Noninvasive Prenatal Testing ◽

Number Variation

Download Full-text

Investigation on combined copy number variation sequencing and cytogenetic karyotyping for prenatal diagnosis

BMC Pregnancy and Childbirth ◽

10.1186/s12884-021-03918-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Jinman Zhang ◽

Xinhua Tang ◽

Jilin Hu ◽

Guilin He ◽

Jian Wang ◽

...

Keyword(s):

Copy Number Variation ◽

Copy Number ◽

Prenatal Testing ◽

Maternal Serum ◽

Ultrasound Scanning ◽

Maternal Serum Screening ◽

Fetal Ultrasound ◽

Noninvasive Prenatal Testing ◽

Screening Performance ◽

Number Variation

Abstract Background We aimed to evaluate the clinical value of copy number variation-sequencing (CNV-Seq) in combination with cytogenetic karyotyping in prenatal diagnosis. Methods CNV-Seq and cytogenetic karyotyping were performed in parallel for 9452 prenatal samples for comparison of the diagnostic performance of the two methods, and to evaluate the screening performance of maternal age, maternal serum screening, fetal ultrasound scanning and noninvasive prenatal testing (NIPT) for fetal pathogenic copy number variation (CNV). Results Among the 9452 prenatal samples, traditional karyotyping detected 704 cases (7.5%) of abnormal cytogenetic karyotypes, 171 (1.8%) chromosome polymorphism, 20 (0.2%) subtle structural variations, 74 (0.7%) mutual translocation (possibly balanced), 52 (0.6%) without karyotyping results, and 8431 (89.2%) normal cytogenetic karyotypes. Among the 8705 cases with normal karyotype, polymorphism, mutual translocation, or marker chromosome, CNV-Seq detected 63 cases (0.7%) of pathogenic chromosome microdeletion/duplication. Retrospectively, noninvasive prenatal testing (NIPT) had high sensitivity and specificity for the screening of fetal pathogenic CNV, and NIPT combining with maternal age, maternal serum screening or fetal ultrasound scanning, which improved the screening performance. Conclusion The combined application of cytogenetic karyotyping and CNV-Seq significantly improved the detection rate of fetal pathogenic chromosome microdeletion/duplication. NIPT was recommended for the screening of pathogenic chromosome microdeletion/duplication, and NIPT combining with other screening methods further improved the screening performance for pathogenic fetal CNV.

Download Full-text

Expanded noninvasive prenatal testing for fetal aneuploidy and copy number variations and parental willingness for invasive diagnosis in a cohort of 18,516 cases

BMC Medical Genomics ◽

10.1186/s12920-021-00955-6 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Yunsheng Ge ◽

Jia Li ◽

Jianlong Zhuang ◽

Jian Zhang ◽

Yanru Huang ◽

...

Keyword(s):

Prenatal Diagnosis ◽

High Risk ◽

Pregnant Women ◽

Copy Number ◽

Prenatal Testing ◽

Copy Number Variations ◽

Trisomy 13 ◽

Noninvasive Prenatal Testing ◽

Predictive Values ◽

Parental Willingness

Abstract Background Noninvasive prenatal testing (NIPT) has been wildly used to screen for common aneuplodies. In recent years, the test has been expanded to detect rare autosomal aneuploidies (RATs) and copy number variations (CNVs). This study was performed to investigate the performance of expanded noninvasive prenatal testing (expanded NIPT) in screening for common trisomies, sex chromosomal aneuploidies (SCAs), rare autosomal aneuploidies (RATs), and copy number variations (CNVs) and parental willingness for invasive prenatal diagnosis in a Chinese prenatal diagnosis center. Methods A total of 24,702 pregnant women were retrospectively analyzed at the Women and Children’s Hospital from January 2013 to April 2019, among which expanded NIPT had been successfully conducted in 24,702 pregnant women. The high-risk expanded NIPT results were validated by karyotype analysis and chromosomal microarray analysis. All the tested pregnant women were followed up for pregnancy outcomes. Results Of the 24,702 cases, successful follow-up was conducted in 98.77% (401/446) of cases with common trisomies and SCAs, 91.95% (80/87) of RAT and CNV cases, and 76.25% (18,429/24,169) of cases with low-risk screening results. The sensitivity of expanded NIPT was 100% (95% confidence interval[CI], 97.38–100%), 96.67%(95%CI, 82.78–99.92%), and 100%(95%CI, 66.37–100.00%), and the specificity was 99.92%(95%CI, 99.87–99.96%), 99.96%(95%CI, 99.91–99.98%), and 99.88% (95%CI, 99.82–99.93%) for the detection of trisomies 21, 18, and 13, respectively. Expanded NIPT detected 45,X, 47,XXX, 47,XXY, XYY syndrome, RATs, and CNVs with positive predictive values of 25.49%, 75%, 94.12%, 76.19%, 6.45%, and 50%, respectively. The women carrying fetuses with Trisomy 21/Trisomy 18/Trisomy 13 underwent invasive prenatal diagnosis and terminated their pregnancies at higher rates than those at high risk for SCAs, RATs, and CNVs. Conclusions Our study demonstrates that the expanded NIPT detects fetal trisomies 21, 18, and 13 with high sensitivity and specificity. The accuracy of detecting SCAs, RATs, and CNVs is still relatively poor and needs to be improved. With a high-risk expanded NIPT result, the women at high risk for common trisomies are more likely to undergo invasive prenatal diagnosis procedures and terminate their pregnancies than those with unusual chromosome abnormalities.

Download Full-text

Unexplained False Negative Results in Noninvasive Prenatal Testing: Two Cases Involving Trisomies 13 and 18

Case Reports in Genetics ◽

10.1155/2015/926545 ◽

2015 ◽

Vol 2015 ◽

pp. 1-7 ◽

Cited By ~ 4

Author(s):

R. Hochstenbach ◽

G. C. M. L. Page-Christiaens ◽

A. C. C. van Oppen ◽

K. D. Lichtenbelt ◽

J. J. T. van Harssel ◽

...

Keyword(s):

False Negative ◽

Prenatal Testing ◽

High Sensitivity ◽

Trisomy 13 ◽

Maternal Weight ◽

Noninvasive Prenatal Testing ◽

Root Cause ◽

Negative Results ◽

False Negative Results ◽

Negative Case

Noninvasive prenatal testing (NIPT) validation studies show high sensitivity and specificity for detection of trisomies 13, 18, and 21. False negative cases have rarely been reported. We describe a false negative case of trisomy 13 and another of trisomy 18 in which NIPT was commercially marketed directly to the clinician. Both cases came to our attention because a fetal anatomy scan at 20 weeks of gestation revealed multiple anomalies. Karyotyping of cultured amniocytes showed nonmosaic trisomies 13 and 18, respectively. Cytogenetic investigation of cytotrophoblast cells from multiple placental biopsies showed a low proportion of nontrisomic cells in each case, but this was considered too small for explaining the false negative NIPT result. The discordant results also could not be explained by early gestational age, elevated maternal weight, a vanishing twin, or suboptimal storage or transport of samples. The root cause of the discrepancies could, therefore, not be identified. The couples involved experienced difficulties in accepting the unexpected and late-adverse outcome of their pregnancy. We recommend that all parties involved in caring for couples who choose NIPT should collaborate to clarify false negative results in order to unravel possible biological causes and to improve the process of patient care from initial counseling to communication of the result.

Download Full-text

A retrospective study of noninvasive prenatal testing for chromosome aneuploidies and subchromosomal copy number variations in 24359 single pregnancies

10.21203/rs.3.rs-33798/v1 ◽

2020 ◽

Author(s):

yuefang Liu ◽

Longfei Cheng ◽

Yuan Peng ◽

Zhe Liang ◽

Xin Jin ◽

...

Keyword(s):

Prenatal Diagnosis ◽

Copy Number ◽

False Negative ◽

Prenatal Testing ◽

Clinical Information ◽

Copy Number Variations ◽

Trisomy 13 ◽

Chromosomal Microarray ◽

Chromosomal Microarray Analysis

Abstract Background: With the development of whole-genome sequencing, small subchromosomal deletions and duplications could be found by non-invasive prenatal testing(NIPT). Our study is aimed to review the efficacy of NIPT as a screening test for aneuploidies and subchromosomal copy number variations (CNVs) in 24359 single pregnancies.Methods: A total of 24359 single pregnancies with different clinical features were retrospectively analyzed. Pathogenicity of abnormal NIPT results were assessed according to American College of Medical Genetics and Genomics(ACMG). Chromosome aneuploidies and subchromosomal CNVs were confirmed by karyotyping and chromosomal microarray analysis(CMA). Results: A total of 442 pregnancies (442/24359,1.9%) were with abnormal NIPT results. The positive predictive value (PPV) for trisomy 21(T21), trisomy 18 (T18), trisomy 13 (T13), and sex chromosome aneuploidies (SCAs) was 84.8%, 54.2%, 11.1% an 40.5% respectively. The PPV for subchromosomal CNVs was 59.0% (46/78). The clinical information, prenatal diagnosis results and follow-up results of 46 true positive cases, 6 cases with subchromosomal CNVs inconsistent with NIPT and 1 case of false negative were also demonstrated in detail.Conclusion: Our data have potential significance in demonstrating the significance of NIPT not only for common whole chromosome aneuploidies but also for subchromosomal CNV. Besides, the clinical information, prenatal diagnosis results and follow-up results of 52 cases with subchromosomal CNV and 1 case of false negative would provide important guidance for genetic counseling.

Download Full-text

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

10.1101/002006 ◽

2014 ◽

Author(s):

Guoqiang Yi ◽

Lujiang Qu ◽

Jianfeng Liu ◽

Yiyuan Yan ◽

Guiyun Xu ◽

...

Keyword(s):

Copy Number Variation ◽

Copy Number ◽

Association Studies ◽

False Negative ◽

Gene Copy ◽

Comparative Genomic ◽

Mineral Density ◽

Validation Rate ◽

Genome Wide ◽

Number Variation

Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform genome-wide CNV analysis in 12 diversified chicken genomes based on whole genome sequencing. A total of 9,025 CNV regions (CNVRs) covering 100.1 Mb and representing 9.6% of the chicken genome are identified, ranging in size from 1.1 to 268.8 kb with an average of 11.1 kb. Sequencing-based predictions are confirmed at high validation rate by two independent approaches, including array comparative genomic hybridization (aCGH) and quantitative PCR (qPCR). The Pearson?s correlation values between sequencing and aCGH results range from 0.395 to 0.740, and qPCR experiments reveal a positive validation rate of 91.71% and a false negative rate of 22.43%. In total, 2,188 predicted CNVRs (24.2%) span 2,182 RefSeq genes (36.8%) associated with specific biological functions. Besides two previously accepted copy number variable genesEDN3andPRLR, we also find some promising genes with potential in phenotypic variants.FZD6andLIMS1, two genes related to diseases susceptibility and resistance are covered by CNVRs. Highly duplicatedSOCS2may lead to higher bone mineral density. Entire or partial duplication of some genes likePOPDC3andLBFABPmay have great economic importance in poultry breeding. Our results based on extensive genetic diversity provide the first individualized chicken CNV map and genome-wide gene copy number estimates and warrant future CNV association studies for important traits of chickens.

Download Full-text

Noninvasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield

BioMed Research International ◽

10.1155/2018/9498140 ◽

2018 ◽

Vol 2018 ◽

pp. 1-6

Author(s):

Irene Gómez-Manjón ◽

Ana Moreno-Izquierdo ◽

Sonia Mayo ◽

Marta Moreno-García ◽

Aitor Delmiro ◽

...

Keyword(s):

Peripheral Blood ◽

Trisomy 21 ◽

Diagnostic Yield ◽

False Negative ◽

Prenatal Testing ◽

False Positives ◽

Trisomy 18 ◽

Trisomy 13 ◽

Noninvasive Prenatal Testing ◽

Semiconductor Sequencing

Objective. The aim of this study was to determine if the use of different mappers for NIPT may vary the results considerably. Methods. Peripheral blood was collected from 217 pregnant women, 58 pathological (34 pregnancies with trisomy 21, 18 with trisomy 18, and 6 with trisomy 13) and 159 euploid. MPS was performed following a manufacturer’s modified protocol of semiconductor sequencing. Obtained reads were mapped with two different software programs: TMAP and HPG-Aligner, comparing the results. Results. Using TMAP, 57 pathological samples were correctly detected (sensitivity 98.28%, specificity 93.08%): 33 samples as trisomy 21 (sensitivity 97.06%, specificity 99.45%), 16 as trisomy 18 (sensibility 88.89%, specificity 93.97%), and 6 as trisomy 13 (sensibility 100%, specificity 100%). 11 false positives, 1 false negative, and 2 samples incorrectly identified were obtained. Using HPG-Aligner, all the 58 pathological samples were correctly identified (sensibility 100%, specificity 96.86%): 34 as trisomy 21 (sensibility 100%, specificity 98.91%), 18 as trisomy 18 (sensibility 100%, specificity 98.99%), and 6 as trisomy 13 (sensibility 100%, specificity 99.53%). 5 false positives were obtained. Conclusion. Different mappers use slightly different algorithms, so the use of one mapper or another with the same batch file can provide different results.

Download Full-text

Prenatal Diagnosis of Microduplication of Fetal Chromosome 17 Following Noninvasive Prenatal Testing

10.21203/rs.3.rs-557915/v1 ◽

2021 ◽

Author(s):

Ye Shi ◽

Fang-xiu Zheng ◽

Jing Wang ◽

Qin Zhou ◽

Ying-ping Chen ◽

...

Keyword(s):

Prenatal Diagnosis ◽

Copy Number ◽

Prenatal Testing ◽

Copy Number Variant ◽

Chromosome 17 ◽

Noninvasive Prenatal Testing ◽

Number Variation ◽

Case Presentations ◽

Chromosome Microarray ◽

Duplication Syndrome

Abstract Background Chromosome 17q12 duplication syndrome is a disease caused by the complete or partial duplication of q12 in the long arm of chromosome 17, there were no cases reported about the prenatal diagnosis of the syndrome. Most of the fetal phenotype of the syndrome may not be evident during the pregnancy, which means the syndrome was only be discovered accidentally or missed during the prenatal examination. Objective Noninvasive prenatal testing (NIPT) is widely used in the screening of common fetal chromosome aneuploidy. However, reports on chromosomal microduplication and microdeletion are rare. The aim of the study was to investigate the application value of NIPT for the detection of chromosomal microduplication. Case presentations: We found two cases of microduplication in the long arm of chromosome 17(17q12), they were first detected by NIPT and then were further diagnosed by copy number variation (CNV) analysis based on chromosome microarray analysis (CMA). The CMA results of prenatal diagnosis showed that the microduplications in 17q12 (one was 1.5Mb, the other was 1.9Mb) were consistent with the NIPT results. The amniotic fluid karyotype analysis showed no abnormalities. Finally, because it was pathogenic copy number variant, both of the parents chose to terminate the pregnancy. Conclusion In the study, two cases of microduplication fragment in the long arm of chromosome 17 were detected by NIPT and were confirmed by CMA. To our knowledge, this is the first report of prenatal diagnosis of chromosome 17q12 duplication syndrome following NIPT. This suggests that NIPT is an effective method to screen chromosome microduplications in prenatal diagnosis, especially for the chromosome 17q12 duplication syndrome.

Download Full-text

Performance of Cell-Free DNA Sequencing-Based Non-invasive Prenatal Testing: Our Experience on 36456 both Singleton and Multiple Pregnancies.

10.21203/rs.3.rs-144192/v1 ◽

2021 ◽

Author(s):

Marco La Verde ◽

Luigia De Falco ◽

Annalaura Torella ◽

Giovanni Savarese ◽

Pasquale Saverese ◽

...

Keyword(s):

Dna Sequencing ◽

Retrospective Analysis ◽

False Negative ◽

Screening Method ◽

Prenatal Testing ◽

Maternal Blood ◽

Noninvasive Prenatal Testing ◽

Cell Free Dna ◽

Detection Rates ◽

Free Dna

Abstract Background: To describe the clinical practice and performance of cell-free DNA sequencing-based noninvasive prenatal testing as a screening method for detecting trisomy 21, 18, and 13 (T21, T18, and T13, respectively), as well as sex chromosome aneuploidy (SCA), in a general Italian pregnancy population.Methods: The AMES-accredited laboratory offers noninvasive prenatal testing in maternal blood as a clinical screening test for foetal 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 a cohort of 36456 consecutive maternal blood samples, including 35650 singleton pregnancies, 800 twin pregnancies, and 6 triplet pregnancies, which were tested between April 2017 and September 2019. The cohort included 46% elevated-risk and 54% low-risk patients. Genetic and/or clinical outcomes were available in 36000 cases (98.7%). In the overall cohort, 356 (1%) results were indicative of classic trisomy: 254 T21, 69 T18, and 33 T13. In addition, 145 results (0.4%) were indicative of SCA. Of the combined 501 screen-positive cases, 484 had confirmatory diagnostic testing results available: 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 were confirmed. Follow-up data were available for 98.8% of the 35955 cases reported as unaffected by trisomy or SCA. No false negative cases were reported. The sensitivity of NIPT was 100.00% for T21 (95% Cl 98.47-100.0), T18 (95% Cl 94.17-100.0), T13 (95% Cl 87.54-100.0) and SCA (95% Cl 96.62-100.0). 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 showed excellent detection rates and low false positive rates.

Download Full-text