Accuracy of fetal fraction measurements in a single-nucleotide polymorphism-based noninvasive prenatal test.

BACKGROUND: Noninvasive prenatal testing (NIPT) for fetal aneuploidy relies on the analysis of fetoplacental cell-free DNA (cfDNA) found in maternal plasma. A minimum cfDNA fetal fraction (FF) is required for reliable test performance, but some methods may have suboptimal accuracy for FF measurement. This study investigated the accuracy of a single-nucleotide polymorphism- (SNP-) based NIPT method to assess FF. METHODS: FF measurements using SNP-based NIPT in consecutive samples from singleton male pregnancies were compared with FF measured using a "gold standard" Y-chromosome method. RESULTS: In a cohort of 106,846 samples, the SNP-based FF method showed a standard deviation (SD) of 0.42%. Compared to the Y chromosome FF method, a correlation coefficient, r, of 0.995, and bias of 0.17% were observed. The SD was not substantially different across specific FF ranges or for samples with high-risk NIPT results. CONCLUSIONS: The SNP-based NIPT method estimates FF with good accuracy, with a SD three to eight times better than other NIPT methods (0.42% vs. 1.3%-3.4%). FF is an important quality control parameter and should be routinely reported as part of NIPT.

Reproductive Carrier Screening: Identifying Families at Risk for Familial Hypercholesterolemia in the United States.

BACKGROUND: Familial hypercholesterolemia is a treatable genetic condition but remains underdiagnosed. We reviewed the frequency of pathogenic or likely pathogenic (P/LP) variants in the LDLR gene in female individuals receiving reproductive carrier screening. METHODS: This retrospective observational study included samples from female patients (aged 18-55 years) receiving a 274-gene carrier screening panel from January 2020 to September 2022. LDLR exons and their 10 base pair flanking regions were sequenced. Carrier frequency for P/LP variants was calculated for the entire population and by race/ethnicity. The most common variants and their likely functional effects were evaluated. RESULTS: A total of 91 637 tests were performed on women with race/ethnicity reported as Asian (8.8%), Black (6.1%), Hispanic (8.5%), White (29.0%), multiple or other (15.0%), and missing (33.0%). Median age was 32.8 years with 83 728 (91%) <40 years. P/LP LDLR variants were identified in 283 samples (1 in 324). No patients were identified with >1 P/LP variant. LDLR carrier frequency was higher in Asian (1 in 191 [95% CI, 1 in 142-258]) compared with White (1 in 417 [95% CI, 1 in 326-533]; P<0.001) or Black groups (1 in 508 [95% CI, 1 in 284-910]; P=0.004). The most common variants differed between populations. Of all variants, at least 25.0% were predicted as null variants. CONCLUSIONS: P/LP variants in LDLR are common. Expanding the use of reproductive carrier screening to include genes associated with FH presents another opportunity to identify people predisposed to cardiovascular disease.

Overview of Noninvasive Prenatal Testing (NIPT) for the Detection of Fetal Chromosome Abnormalities; Differences in Laboratory Methods and Scope of Testing.

Although nearly all noninvasive prenatal testing is currently based on analyzing circulating maternal cell-free DNA, the technical methods usedvary considerably. We review the different methods. Based on validation trials and clinical experience, there are mostly relatively small differences in screening performance for trisomies 21, 18, and 13 in singleton pregnancies. Recent reports show low no-call rates for all methods, diminishing its importance when choosing a laboratory. However, method can be an important consideration for twin pregnancies, screening for sex chromosome abnormalities, microdeletion syndromes, triploidy, molar pregnancies, rare autosomal trisomies, and segmental imbalances, and detecting maternal chromosome abnormalities.

Reproductive Carrier Screening Results With Maternal Health Implications During Pregnancy.

OBJECTIVE: To identify conditions on a reproductive carrier screening panel with the potential for carrier manifestations during pregnancy and review the implications for obstetric care. METHODS: This was a retrospective cross-sectional study of consecutive samples from female patients aged 18-55 years submitted to a commercial laboratory for a 274-gene carrier screening panel (January 2020 to September 2022). A literature review was performed to identify genes on the panel with potential for pregnancy complications in carriers. Carrier expression and published recommendations for clinical management were reviewed. RESULTS: We identified 12 genes with potential for carrier manifestations during pregnancy based on reports in the literature: nine with manifestations irrespective of the fetal genetic status ( ABCB11 , COL4A3 , COL4A4 , COL4A5 , DMD , F9 , F11 , GLA , and OTC ) and three ( CPT1A , CYP19A1 , and HADHA ) with manifestations only if the fetus is affected by the condition. Manifestations included cardiomyopathy, hemorrhage, gestational hypertensive disorders, cholestasis of pregnancy, acute fatty liver, hyperammonemic crisis, and maternal virilization. Published recommendations for carrier management were identified for 11 of the 12 genes. Of 91,637 tests performed during the study period, a pathogenic or likely pathogenic variant was identified in 2,139 (2.3%), giving a carrier frequency for any of the 12 genes of 1 in 43 (95% CI 1/41-45) 1,826 (2.0%) of the study population were identified as carriers for one of the nine genes with the potential for carrier manifestations irrespective of an affected or unaffected fetus. CONCLUSION: Approximately 1 in 40 female patients were identified as carriers for a condition with potential for maternal manifestations in pregnancy, including some serious or even life-threatening complications. Obstetric care professionals should be aware of the possibility of pregnancy complications among carriers and the available recommendations for management. FUNDING SOURCE: This study was funded by Natera, Inc.

Assessment of an automated approach for variant interpretation in screening for monogenic disorders: A single-center study.

BACKGROUND: Automation has been introduced into variant interpretation, but it is not known how automated variant interpretation performs on a stand-alone basis. The purpose of this study was to evaluate a fully automated computerized approach. METHOD: We reviewed all variants encountered in a set of carrier screening panels over a 1-year interval. Observed variants with high-confidence ClinVar interpretations were included in the analysis; those without high-confidence ClinVar entries were excluded. RESULTS: Discrepancy rates between automated interpretations and high-confidence ClinVar entries were analyzed. Of the variants interpreted as positive (likely pathogenic or pathogenic) based on ClinVar information, 22.6% were classified as negative (variants of uncertain significance, likely benign or benign) variants by the automated method. Of the ClinVar negative variants, 1.7% were classified as positive by the automated software. On a per-case basis, which accounts for variant frequency, 63.4% of cases with a ClinVar high-confidence positive variant were classified as negative by the automated method. CONCLUSION: While automation in genetic variant interpretation holds promise, there is still a need for manual review of the output. Additional validation of automated variant interpretation methods should be conducted.

A Critical Evaluation of Validation and Clinical Experience Studies in Non-Invasive Prenatal Testing for Trisomies 21, 18, and 13 and Monosomy X.

Non-invasive prenatal testing (NIPT) for trisomies 21, 18, 13 and monosomy X is widely utilized with massively parallel shotgun sequencing (MPSS), digital analysis of selected regions (DANSR), and single nucleotide polymorphism (SNP) analyses being the most widely reported methods. We searched the literature to find all NIPT clinical validation and clinical experience studies between January 2011 and January 2022. Meta-analyses were performed using bivariate random-effects and univariate regression models for estimating summary performance measures across studies. Bivariate meta-regression was performed to explore the influence of testing method and study design. Subgroup and sensitivity analyses evaluated factors that may have led to heterogeneity. Based on 55 validation studies, the detection rate (DR) was significantly higher for retrospective studies, while the false positive rate (FPR) was significantly lower for prospective studies. Comparing the performance of NIPT methods for trisomies 21, 18, and 13 combined, the SNP method had a higher DR and lower FPR than other methods, significantly so for MPSS, though not for DANSR. The performance of the different methods in the 84 clinical experience studies was consistent with validation studies. Clinical positive predictive values of all NIPT methods improved over the last decade. We conclude that all NIPT methods are highly effective for fetal aneuploidy screening, with performance differences across methodologies.

Non-invasive prenatal screening for fetal triploidy using single nucleotide polymorphism-based testing: Differential diagnosis and clinical management in cases showing an extra haplotype.

OBJECTIVE: An extra haplotype is infrequently encountered in single nucleotide polymorphism(SNP)-based non-invasive prenatal testing (NIPT) and is usually attributed to an undetected twin or triploidy. We reviewed a large series to establish relative frequencies of these outcomes and identify alternative causes. METHODS: In 515,804 women receiving NIPT from September 2017 through March 2019, all results with an extra haplotype were reviewed. Known viable and vanished twin pregnancies were excluded. For positive cases, pregnancy outcome information was sought. RESULTS: Of 1005 results with an extra haplotype (1 in 513), pregnancy outcome was available for 773 cases: 11% were confirmed or suspected triploidy; 65% to vanished twin; 10% with pregnancy loss. Rare explanations included complete mole, chimera, undisclosed donor egg pregnancy, maternal organ transplant and one instance of maternal neoplasm. Among triploid cases that were detected and independently confirmed, 23/27 (85%) were diandric. CONCLUSION: SNP-based NIPT, with detection of an extra haplotype, is 11% predictive of triploidy. For results with an extra haplotype, ultrasound is recommended to establish viability, evaluate for twins (viable or vanished), and detect findings consistent with triploidy. Review of patient history, serum screening, and ultrasound will reduce the number of CVS or amniocenteses necessary to confirm a diagnosis of triploidy.

Non-invasive prenatal testing in the management of twin pregnancies.

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.

Performance of conventional cytogenetic analysis on chorionic villi when only one cell layer, cytotrophoblast or mesenchyme alone, is analyzed.

OBJECTIVE: To provide an estimation of the probability of error when chorionic villi (CV) cytogenetic analysis is limited to a single placental layer; either a direct preparation (Dir) or long-term culture (LTC). METHODS: We retrospectively reviewed cytogenetic studies on 81,593 consecutive CV samples in which both Dir and LTC were analyzed. All mosaic cases received amniocentesis. The false omission and false discovery rates were calculated by assessing the results that would have been reported when analysis was limited to either Dir or LTC. RESULTS: For all abnormalities combined, the proportion of normal Dir or LTC only reports that would have been inconsistent with a subsequent amniocentesis was 0.09% and 0.03%, respectively (false omissions). Among abnormal reports based on Dir or LTC alone, 8.01% and 3.17%, respectively, would be inconsistent with a subsequent amniocentesis result (false discoveries). Differences are present for individual abnormalities. CONCLUSIONS: From the perspective of identifying all abnormalities of potential clinical significance, the analysis of both placental layers is optimal. LTC alone is the preferred approach if only one layer of placenta is to be analyzed. Although rare, it is important to acknowledge that one cell layer analysis alone can cause misdiagnosis due to undetected mosaicism.

The origins of aneuploidy research consortium.

The presence of high levels of aneuploidy in oocytes and early embryos and their fate is of considerable scientific and clinical importance. The Origins of Aneuploidy Research Consortium (OARC) was established to promote interdisciplinary communication and collaborative research into this topic. Under the umbrella of OARC, a series of papers has now been published in this Special Issue of Prenatal Diagnosis. Recent studies have transformed the view that aneuploidy is usually attributable to meiotic non-disjunction. The molecular basis for the association between meiotic error and maternal age is becoming understood. The clinical significance of mitotic instability in the earliest cells divisions of the embryo is also becoming clearer. An error in the segregation of one or more whole chromosomes from a parent does not invariably result in a non-viable pregnancy or an abnormal outcome. Epidemiologic data allows an assessment of in utero viability, the effect of maternal age, and secondary factors that may affect aneuploidy prevalence. We advocate careful use of nomenclature and revision of educational materials to more accurately explain the complex and often nuanced mechanisms. OARC plans to hold additional workshops, promote additional publications and offer educational resources.

Review of epidemiological factors (other than maternal age) that determine the prevalence of common autosomal trisomies.

The birth prevalence of each common autosomal trisomy (21, 18 and 13) increases with advancing maternal age and this is the most important epidemiological risk factor. Prevalence during pregnancy is also dependent on gestational age. Other factors claimed to influence prevalence include paternal age, ethnicity, family history, premature reproductive aging, parity, twinning, smoking, environmental exposures, maternal medical conditions, and predispositions. We review the evidence for these associations since they may provide insights into causal mechanisms. When investigating potential co-factors it is important to adequately allow for maternal age and minimize its confounding contribution. This is well illustrated by reports of an inverse paternal age effect where there is strong correlation between parental ages. Gestational age at diagnosis, availability of prenatal screening, diagnostic testing, and elective termination of affected pregnancies and healthcare disparities also confound the studies on ethnicity, medical conditions, and predispositions or environmental factors. Data from twin zygosity studies demonstrate the importance of differences in fetal viability for affected pregnancies. We conclude that existing epidemiological evidence for most of the co-factors discussed should currently be considered tenuous; history of Down syndrome, albeit biased, may be an exception. The co-factors may yet provide clues to hitherto poorly understood causal pathways.

Aneuploidy in first trimester chorionic villi and spontaneous abortions: Windows into the origin and fate of aneuploidy through embryonic and fetal development.

OBJECTIVE: To review the mosaic autosomal trisomies in chorionic villi sample (CVS) trophoblasts, mesenchyme, and both cell lineages and to compare them with trisomies in spontaneous abortions. METHODS: Mosaic autosomal trisomies from 76 102 diagnostic CVS tests were classified as involving trophoblasts, involving mesenchyme, or present in both. Autosomal trisomies in products of conception were based on 18 published studies. We evaluated correlates between trisomy frequency with chromosome size or number of protein coding genes in the imbalance. RESULTS: Distinctly different patterns of trisomy were found in trophoblasts, mesenchyme, or both. In trisomic spontaneous abortions, there was a weak, borderline significant, inverse association between frequency and trisomic chromosome size and also with the number of protein coding genes involved (r = 0.43, P = 0.04 and r = 0.39, P = 0.07, respectively). These associations became stronger after excluding trisomy 16 (r = 0.52, P = 0.01 and r = 0.64, P = 0.001, respectively). Only CVS trisomies in both trophoblasts and mesenchyme resembled the trisomies found in spontaneous abortions and these were also associated with chromosome size and protein coding genes (r = 0.42, P = 0.05 and r = 0.57, P = 0.006, respectively). CONCLUSION: The abnormalities seen in CVS differ from those reported in early embryos. From conception through birth, there are lineage-specific, evolving spectrums of aneuploidy in trophoblasts, mesenchyme, and fetus.

Uniparental disomy: Origin, frequency, and clinical significance.

Uniparental disomy (UPD) is defined as two copies of a whole chromosome derived from the same parent. There can be multiple mechanisms that lead to UPD; these are reviewed in the context of contemporary views on the mechanism leading to aneuploidy. Recent studies indicate that UPD is rare in an apparently healthy population and also rare in spontaneous abortion tissues. The most common type of UPD is a maternal heterodisomy (both maternal allele sets present). Isodisomy (a duplicated single set of alleles) or segmental loss of heterozygosity is sometimes encountered in SNP-based microarray referrals. Decisions regarding the most appropriate follow-up testing should consider the possibility of consanguinity (that will generally involve multiple regions), an imprinted gene disorder (chromosomes 6, 7, 11, 14, 15, 20), expression of an autosomal recessive disorder, and an occult aneuploid cell line that may be confined to the placenta. Upd(16)mat, per se, does not appear to be associated with an abnormal phenotype. UPD provides an insight into the history of early chromosome segregation error and understanding the rates and fate of these events are of key importance in the provision of fertility management and prenatal healthcare.

Correction: Clinical experience with carrier screening in a general population: support for a comprehensive pan-ethnic approach.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Clinical experience with carrier screening in a general population: support for a comprehensive pan-ethnic approach.

PURPOSE: To present results from a large cohort of individuals receiving expanded carrier screening (CS) in the United States. METHODS: Single-gene disorder carrier status for 381,014 individuals was determined using next-generation sequencing (NGS) based CS for up to 274 genes. Detection rates were compared with literature-reported values derived from disease prevalence and carrier frequencies. Combined theoretical affected pregnancy rates for the 274 screened disorders were calculated. RESULTS: For Ashkenazi Jewish (AJ) diseases, 81.6% (4434/5435) of carriers identified did not report AJ ancestry. For cystic fibrosis, 44.0% (6260/14,229) of carriers identified had a variant not on the standard genotyping panel. Individuals at risk of being a silent spinal muscular atrophy carrier, not detectable by standard screening, comprised 1/39 (8763/344,407) individuals. For fragile X syndrome, compared with standard premutation screening, AGG interruption analysis modified risk in 83.2% (1128/1356) premutation carriers. Assuming random pairing across the study population, approximately 1/175 pregnancies would be affected by a disorder in the 274-gene screening panel. CONCLUSION: Compared with standard screening, NGS-based CS provides additional information that may impact reproductive choices. Pan-ethnic CS leads to substantially increased identification of at-risk couples. These data support offering NGS-based CS to all reproductive-aged women.