Discordant Noninvasive Prenatal Testing and Cytogenetic Results

Wang, Jia‐Chi; Sahoo, Trilochan; Schonberg, Steven; Kopita, Kimberly A; Ross, Leslie; Patek, Kyla; Strom, Charles M.

doi:10.1097/01.ogx.0000469203.83102.db

Cited by 4 publications

(2 citation statements)

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“…One study shows that the incidence of CPM could be 4.8% [8]. Regarding to this, confirmation using an invasive test remains necessary, at least when the woman is considering an irreversible decision [3,28]. According to this, and taking into account that cffDNA comes from placenta, amniocentesis would be a more appropriate and reliable followup diagnostic test than CVS in case of positive NIPT, especially if there is an absence of sonographic features in the fetus suggestive of trisomy [29][30][31].…”

Section: Discussionmentioning

confidence: 99%

Non-Invasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield

Gómez-Manjón¹,

Moreno-Izquierdo²,

Mayo³

et al. 2021

Prime Archives in Biomedical Sciences

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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 www.videleaf.com 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.

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Section: Discussionmentioning

confidence: 99%

Non-Invasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield

Gómez-Manjón¹,

Moreno-Izquierdo²,

Mayo³

et al. 2021

Prime Archives in Biomedical Sciences

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“…Except those employing deep sequencing or array-based methods, most NIPTs were performed using the low-coverage next-generation sequencing (NGS) platforms such as Verifi [11], Materni21 [12], panorama [13] and NIFTY [14]. Similar to copy number variation analysis, the sequencing reads from a test sample were mapped and counted as depth in bins of a certain size, following by a measurement of deviation from negative control.…”

Section: Introductionmentioning

confidence: 99%

Improving the calling of non-invasive prenatal testing on 13-/18-/21-trisomy by support vector machine discrimination

Yang¹,

Ding

Zhu³

2018

PLoS ONE

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With the advance of next-generation sequencing (NGS) technologies, non-invasive prenatal testing (NIPT) has been developed and employed in fetal aneuploidy screening on 13-/18-/21-trisomies through detecting cell-free fetal DNA (cffDNA) in maternal blood. Although Z-test is widely used in NIPT NGS data analysis, there is still necessity to improve its accuracy for reducing a) false negatives and false positives, and b) the ratio of unclassified data, so as to lower the potential harm to patients as well as the induced cost of retests. Combining the multiple Z-tests with indexes of clinical signs and quality control, features were collected from the known samples and scaled for model training using support vector machine (SVM). We trained SVM models from the qualified NIPT NGS data that Z-test can discriminate and tested the performance on the data that Z-test cannot discriminate. On screenings of 13-/18-/21-trisomies, the trained SVM models achieved 100% accuracies in both internal validations and unknown sample predictions. It is shown that other machine learning (ML) models can also achieve similar high accuracy, and SVM model is most robust in this study. Moreover, four false positives and four false negatives caused by Z-test were corrected by using the SVM models. To our knowledge, this is one of the earliest studies to employ SVM in NIPT NGS data analysis. It is expected to replace Z-test in clinical practice.

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Genomics-based non-invasive prenatal testing for detection of fetal chromosomal aneuploidy in pregnant women

Badeau

Lindsay

Blais

et al. 2017

Cochrane Database of Systematic Reviews

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These results show that MPSS and TMPS perform similarly in terms of clinical sensitivity and specificity for the detection of fetal T31, T18, T13 and sex chromosome aneuploidy (SCA). However, no study compared the two approaches head-to-head in the same cohort of patients. The accuracy of gNIPT as a prenatal screening test has been mainly evaluated as a second-tier screening test to identify pregnancies at very low risk of fetal aneuploidies (T21, T18 and T13), thus avoiding invasive procedures. Genomics-based non-invasive prenatal testing methods appear to be sensitive and highly specific for detection of fetal trisomies 21, 18 and 13 in high-risk populations. There is paucity of data on the accuracy of gNIPT as a first-tier aneuploidy screening test in a population of unselected pregnant women. With respect to the replacement of invasive tests, the performance of gNIPT observed in this review is not sufficient to replace current invasive diagnostic tests.We conclude that given the current data on the performance of gNIPT, invasive fetal karyotyping is still the required diagnostic approach to confirm the presence of a chromosomal abnormality prior to making irreversible decisions relative to the pregnancy outcome. However, most of the gNIPT studies were prone to bias, especially in terms of the selection of participants.

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Discordant Noninvasive Prenatal Testing and Cytogenetic Results

Cited by 4 publications

References 0 publications

Non-Invasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield

Non-Invasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield

Improving the calling of non-invasive prenatal testing on 13-/18-/21-trisomy by support vector machine discrimination

Genomics-based non-invasive prenatal testing for detection of fetal chromosomal aneuploidy in pregnant women

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