Combining count- and length-based z-scores leads to improved predictions in non-invasive prenatal testing

Comparison of the performance of NIPT and NIPT-plus for fetal chromosomal aneuploidy and high Z-score increases the positive predictive value

OBJECTIVE

To evaluate non-invasive prenatal testing (NIPT) and expanded non-invasive prenatal testing (NIPT-plus) for detecting aneuploidies at different sequencing depths and assess Z-score accuracy in predicting trisomies 21, 18, 13, 45X, and 47XXX.

METHODS

Pregnancies with positive NIPT or NIPT-plus results detected at the prenatal diagnosis center of Nanfang Hospital were included in this retrospective study, between January 2017 and December 2022. Invasive prenatal diagnostic results were collected. Logistic regression analyses were used to study the relationship between Z-score and positive predictive value (PPV). Optimal cut-off values were obtained based on receiver operating characteristic analysis, and PPVs were calculated in different groups.

RESULTS

We evaluated 1348 pregnant women with positive results, including 930 reported by NIPT and 418 reported by NIPT-plus. NIPT reported significantly more rare chromosomal aneuploidies (RCAs), and NIPT-plus had a significantly higher PPV for trisomy 21 (T21). Logistic regression analyses showed a significant association (P < 0.001) between Z-score and PPVs for T21 and trisomy 18 (T18). A linear relationship was observed between fetal fraction (FF) and Z-values in the true positive cases of T21 and T18.The high Z-score group had significantly higher PPVs than the low Z-score group for T21, T18, trisomy 13, and 47XXX, but not for 45X.

CONCLUSION

The Z-score is helpful in assessing NIPT or NIPT-plus results. Therefore, we suggest including the Z-score and FF in the results. By combining the Z-score, FF, and maternal age, clinicians can interpret NIPT results more accurately and improve personal counsel to reduce patients' anxiety.

SnakeLines: integrated set of computational pipelines for sequencing reads

With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilising sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on bioinformatics processing, which is often too demanding for clinicians and researchers without a computational background. Another problem represents the reproducibility of computational analyses across separated computational centres with inconsistent versions of installed libraries and bioinformatics tools. We propose an easily extensible set of computational pipelines, called SnakeLines, for processing sequencing reads; including mapping, assembly, variant calling, viral identification, transcriptomics, and metagenomics analysis. Individual steps of an analysis, along with methods and their parameters can be readily modified in a single configuration file. Provided pipelines are embedded in virtual environments that ensure isolation of required resources from the host operating system, rapid deployment, and reproducibility of analysis across different Unix-based platforms. SnakeLines is a powerful framework for the automation of bioinformatics analyses, with emphasis on a simple set-up, modifications, extensibility, and reproducibility. The framework is already routinely used in various research projects and their applications, especially in the Slovak national surveillance of SARS-CoV-2.

Noninvasive Prenatal Screening for Common Fetal Aneuploidies Using Single-Molecule Sequencing

Amplification biases caused by next-generation sequencing (NGS) for noninvasive prenatal screening (NIPS) may be reduced using single-molecule sequencing (SMS), during which PCR is omitted. Therefore, the performance of SMS-based NIPS was evaluated. We used SMS-based NIPS to screen for common fetal aneuploidies in 477 pregnant women. The sensitivity, specificity, positive predictive value, and negative predictive value were estimated. The GC-induced bias was compared between the SMS- and NGS-based NIPS methods. Notably, a sensitivity of 100% was achieved for fetal trisomy 13 (T13), trisomy 18 (T18), and trisomy 21 (T21). The positive predictive value was 46.15% for T13, 96.77% for T18, and 99.07% for T21. The overall specificity was 100% (334/334). Compared with NGS, SMS (without PCR) had less GC bias, a better distinction between T21 or T18 and euploidies, and better diagnostic performance. Overall, our results suggest that SMS improves the performance of NIPS for common fetal aneuploidies by reducing the GC bias introduced during library preparation and sequencing.

Noninvasive prenatal screening in southeast China: clinical application and accuracy evaluation

OBJECTIVE

To assess the clinical performance of noninvasive prenatal screening (NIPS) for both common trisomy and sex chromosome aneuploidy (SCA).

METHODS

We recruited 71,888 pregnant women to undergo NIPS testing from December 2015 to June 2021. Demographic characteristics, diagnostic results, and follow-up outcomes were collected.

RESULTS

There were a total of 381 high-risk cases for common trisomy and 343 positive screens for SCA. Invasive prenatal diagnosis (IPD) was performed in 507 (70.0%) participants. The positive predictive value (PPV) was 83.7% for T21, 72.5% for T18, 14.3% for T13, 31.9% for 45,X, 72.0% for 47,XXX, 89.8% for 47,XXY, and 72.2% for 47,XYY, respectively. Logistic regression analysis presented a significant association between Z-score and PPV in common trisomy (P < 0.05) while not in SCA (P > 0.05). PPV in the high-risk group (Z-score ≥ cutoff) was superior to that in the intermediate risk group (3 ≤ Z-score < cutoff) for T21/T18/T13. PPV for 45,X, 47,XXY, and 47,XYY tended to be higher with the increasing Z-score, except for 47,XXX.

CONCLUSIONS

NIPS would be a valuable strategy in prenatal screening, while cautions should be kept in mind for subsequent genetic consulting about the risk of Z-score.

The Optimal Cutoff Value of Z-scores Enhances the Judgment Accuracy of Noninvasive Prenatal Screening

Objective

To evaluate the accuracy of Z-scores of noninvasive prenatal screening (NIPS) in predicting 21, 18 trisomy, and X chromosome aneuploidy.

Methods

A total of 39,310 prenatal women were recruited for NIPS from September 2015 to September 2020. Interventional prenatal diagnosis was applied to verify the diagnosis of NIPS-positive results. Logistic regression analysis was employed to relate the Z-scores to the positive predictive value (PPV) of NIPS-positive results. Using receiver operating characteristic (ROC) curves, we calculated the optimal cutoff value of Z-scores to predict fetal chromosome aneuploidy. According to the cutoff value, NIPS-positive results were divided into the medium Z-value (MZ) and high Z-value (HZ) groups, and PPV was calculated to access the accuracy of Z-scores.

Results

A total of 288 effective values of Z-scores were used as the final data set. The logistics regression analysis revealed that Z-scores were significantly associated with true-positive results for 21 trisomy (T21) and 18 trisomy (T18) (P < 0.05), whereas the same was not observed for X chromosome aneuploids (P > 0.05). The optimal cutoff value of the Z-score for T21, T18, XO, XXX, and XXY indicated by ROC curve analysis were 5.79, 6.05, −9.56, 5.89, and 4.47, and the area under the curve (AUC) were 0.89, 0.80, 0.48, 0.42, and 0.45, respectively. PPV in the HZ group was higher than that in the MZ group, and the application of the cutoff value reduced the false discovery rate (FDR), which was only 2.9% in the HZ group compared with 61.1% in the MZ group for T21 and T18. The difference in total PPV between the MZ and HZ groups for X chromosome aneuploids was statistically significant. Moreover, the PPV for XXX and XXY seemed to increase with Z-scores but not for XO.

Conclusion

The Z-score is helpful for the accurate judgment of NIPS results and for clinical prenatal counseling. Especially for T21 and T18, Z-scores have an excellent clinical association, which is superior to that seen with X chromosome aneuploids. In addition, using Z-scores to judge NIPS results offers a certain reference value for XXX and XXY but not for XO.

Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes

Analyzes of cell-free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes.

Prenatal genetic diagnosis: Fetal therapy as a possible solution to a positive test

BACKGROUND

Fetal abnormalities cause 20% of perinatal deaths. Advances in prenatal genetic and other types of screening offer great opportunities for identifying high risk pregnancies.

METHODS

Through a literature search, here we summarise what are the prenatal diagnostic technique that are being used and how those techniques may allow for prenatal interventions.

RESULTS

Next generation sequencing and non-invasive prenatal testing are fundamental for clinical diagnostics because of their sensitivity and accuracy in identifying point mutations, aneuploidies, and microdeletions, respectively. Timely identification of genetic disorders and other fetal abnormalities enables early intervention, such as in-utero gene therapy, fetal drug therapy and prenatal surgery.

CONCLUSION

Prenatal intervention is mainly focused on conditions that may cause death or lifelong disabilities, like spina bifida, congenital diaphragm hernia and sacrococcygeal teratoma; and may be an alternative therapeutic option to termination of pregnancy. However, it is not yet widely available, due to lack of specialized centers.

Size profile of cell-free DNA: A beacon guiding the practice and innovation of clinical testing

Cell-free DNA (cfDNA) has pioneered the development of noninvasive prenatal testing and liquid biopsy, its emerging applications include organ transplantation, autoimmune diseases, and many other disorders; size profile of cfDNA is a crucial biological property and is essential for its clinical applications. Therefore, a thorough mastery of the characteristic and potential applications of cfDNA size profile is needed. Methods: Based on the recent researches, we summarized the size profile of cfDNA in pregnant women, tumor patients, transplant recipients and systemic lupus erythematosus (SLE) patients to explore the common features. We also concluded the applications of size profile in pre-analytical phases, analytical phases for novel assays, and preparation of quality control materials (QCMs). Results: The size profile of cfDNA shared common features in different populations, and was distributed as a "ladder" pattern with a dominant peak at ~166 bp. However, cfDNA entailed slightly discrepant characteristics due to specific tissues of origin. The dominant peaks of fetal and maternal cfDNA fragments in pregnant women were at 143 bp and 166 bp, respectively. The plasma cfDNA in tumor patients, transplant recipients, and SLE patients had a peak of around 166 bp. In pre-analytical phases, size profile served as a vital indicator to judge the eligibility of specimens, thus ensuring the successful implementation of assays. More importantly, the size profile had the potential to enrich short fragments, calculate fetal fraction, detect fetal abnormalities, predict tumor progress in analytical phase and to guide the preparation of QCMs. Conclusions: Our finding summarized the characteristics and potential applications of cfDNA size profile, providing clinical researchers with novel assays by the extensive application of cfDNA.

Identification of Structural Variation from NGS-Based Non-Invasive Prenatal Testing

Copy number variants (CNVs) are an important type of human genome variation, which play a significant role in evolution contribute to population diversity and human genetic diseases. In recent years, next generation sequencing has become a valuable tool for clinical diagnostics and to provide sensitive and accurate approaches for detecting CNVs. In our previous work, we described a non-invasive prenatal test (NIPT) based on low-coverage massively parallel whole-genome sequencing of total plasma DNA for detection of CNV aberrations ≥600 kbp. We reanalyzed NIPT genomic data from 5018 patients to evaluate CNV aberrations in the Slovak population. Our analysis of autosomal chromosomes identified 225 maternal CNVs (47 deletions; 178 duplications) ranging from 600 to 7820 kbp. According to the ClinVar database, 137 CNVs (60.89%) were fully overlapping with previously annotated variants, 66 CNVs (29.33%) were in partial overlap, and 22 CNVs (9.78%) did not overlap with any previously described variant. Identified variants were further classified with the AnnotSV method. In summary, we identified 129 likely benign variants, 13 variants of uncertain significance, and 83 likely pathogenic variants. In this study, we use NIPT as a valuable source of population specific data. Our results suggest the utility of genomic data from commercial CNV analysis test as background for a population study.

Adaptable Model Parameters in Non-Invasive Prenatal Testing Lead to More Stable Predictions

Recent advances in massively parallel shotgun sequencing opened up new options for affordable non-invasive prenatal testing (NIPT) for fetus aneuploidy from DNA material extracted from maternal plasma. Tests typically compare chromosomal distributions of a tested sample with a control set of healthy samples with unaffected fetuses. Deviations above certain threshold levels are concluded as positive findings. The main problem with this approach is that the variance of the control set is dependent on the number of sequenced fragments. The higher the amount, the more precise the estimation of actual chromosomal proportions is. Testing a sample with a highly different number of sequenced reads as used in training may thus lead to over- or under-estimation of their variance, and so lead to false predictions. We propose the calculation of a variance for each tested sample adaptively, based on the actual number of its sequenced fragments. We demonstrate how it leads to more stable predictions, mainly in real-world diagnostics with the highly divergent inter-sample coverage.

Recent trends in prenatal genetic screening and testing

Prenatal testing in recent years has been moving toward non-invasive methods to determine the fetal risk for genetic disorders without incurring the risk of miscarriage. Rapid progress of modern high-throughput molecular technologies along with the discovery of cell-free fetal DNA in maternal plasma led to novel screening methods for fetal chromosomal aneuploidies. Such tests are referred to as non-invasive prenatal tests (NIPTs), non-invasive prenatal screening, or prenatal cell-free DNA screening. Owing to many advantages, the adoption of NIPT in routine clinical practice was very rapid and global. As an example, NIPT has recently become a standard screening procedure for all pregnant women in the Netherlands. On the other hand, invasive sampling procedures remain important, especially for their diagnostic value in the confirmation of NIPT-positive findings and the detection of Mendelian disorders. In this review, we focus on current trends in the field of NIPT and discuss their benefits, drawbacks, and consequences in regard to routine diagnostics.