Noninvasive Prenatal Screening Results Research Articles

Identification of copy number variations among fetuses with isolated ultrasound soft markers in pregnant women not of advanced maternal age

BackgroundPathogenic (P) copy number variants (CNVs) may be associated with second-trimester ultrasound soft markers (USMs), and noninvasive prenatal screening (NIPS) can enable interrogate the entire fetal genome to screening of fetal CNVs. This study evaluated the clinical application of NIPS for detecting CNVs among fetuses with USMs in pregnant women not of advanced maternal age (AMA).ResultsFetal aneuploidies and CNVs were identified in 6647 pregnant women using the Berry Genomics NIPS algorithm.Those with positive NIPS results underwent amniocentesis for prenatal diagnosis. The NIPS and prenatal diagnosis results were analyzed and compared among different USMs. A total of 96 pregnancies were scored positive for fetal chromosome anomalies, comprising 37 aneuploidies and 59 CNVs. Positive predictive values (PPVs) for trisomy 21, trisomy 18, trisomy 13, and sex chromosome aneuploidies were 66.67%, 80.00%, 0%, and 30.43%, respectively. NIPS sensitivity for aneuploidies was 100%. For CNVs, the PPVs were calculated as 35.59% and false positive rate of 0.57%. There were six P CNVs, two successfully identified by NIPS and four missed, of which three were below the NIPS resolution limit and one false negative. The incidence of aneuploidies was significantly higher in fetuses with absent or hypoplastic nasal bone, while that of P CNVs was significantly higher in fetuses with aberrant right subclavian artery (ARSA), compared with other groups.ConclusionsNIPS yielded a moderate PPV for CNVs in non-AMA pregnant women with fetal USM. However, NIPS showed limited ability in identifying P CNVs. Positive NIPS results for CNVs emphasize the need for further prenatal diagnosis. We do not recommend the use of NIPS for CNVs screening in non-AMA pregnant women with fetal USM, especially in fetuses with ARSA.

Prevalence of high-penetrant copy number variants in 7734 low-risk pregnancies

The rate of clinically significant copy number variants in chromosomal microarray analysis in low-risk pregnancies is approximately 1%. However, these results include copy number variants with low and variable penetrance, although some patients might be interested only in the detection of high-penetrant variants. This study aimed to calculate the prevalence of high-penetrant copy number variants in a large cohort of low-risk pregnancies. This retrospective study was performed using microarray results of pregnancies with normal ultrasound and maternal serum screening. All clinically significant (pathogenic and likely pathogenic) copy number variants were recorded. Of these, only high-penetrant findings were selected. Findings with low and medium penetrance and copy number variants with unknown clinical penetrance, including uniparental disomy of segments not related to known imprinted syndromes, mosaic aneuploidy of <50%, and segmental mosaicism, were excluded. The calculation was performed for the overall cohort, for women aged >35 years and women aged <35 years, and after omission of noninvasive prenatal screening theoretically detectable findings (trisomies 13, 18, and 21). Clinically significant copy number variants were detected in 118 of 7734 cases (1.50% or 1:65), and high-penetrant copy number variants were detected in 33 of 7734 cases (0.43% or 1:234). In women aged ≥35 years, the rates of high-penetrant copy number variants were 29 of 5734 cases (0.51% or 1:198) and 4 of 2000 cases (0.20% or 1:500) in women aged <35 years (P=.0747). Following the omission of 12 theoretically noninvasive prenatal screening-detectable findings, the rates of high-penetrant copy number variants declined to 21 of 7722 cases (0.27% or 1:368) in the whole cohort-18 of 5723 cases (0.31% or 1:318) in woman aged ≥35 years and 3 of 1999 cases (0.15% or 1:666) in younger women (P=.319). The risk of high-penetrant copy number variants in low-risk pregnancies exceeds the risk of miscarriage after invasive testing, even after normal noninvasive prenatal screening results. These results are of importance to genetic counselors and obstetricians, to facilitate maternal informed decision-making when considering invasive prenatal testing in low-risk pregnancies.

SAT337 Maternal Cell free DNA Testing Reveals Incidental Finding Of Adrenocortical Carcinoma

Abstract Disclosure: F. Akanbi: None. S. Raja: None. T. Else: None. Maternal Cell-free DNA Testing Reveals Incidental Adrenocortical Carcinoma IntroductionAdrenocortical carcinoma (ACC) is rare; with 1 to 2 cases per million. It is unclear if ACC in pregnancy represents a specific association though 150 cases have been reported. We report a case of ACC detected during fetal sex determination using cell free DNA (cfDNA). Case Report: A 30 year old G1P0 woman presented at GA of 25 weeks with results of non-invasive prenatal screening (NIPS) done for fetal sex determination, which noted atypical findings concerning for possible maternal neoplasm. Pregnancy had been uncomplicated; she had no significant past medical history or features of hypercortisolism. Family history was positive for lung and prostate cancer. Physical examination revealed healthy looking female with no Cushingoid facies, abdomen matched stated GA. Full body MRI revealed 5.5 cm right adrenal mass with lymph nodes metastases. CT-guided retroperitoneal lymph node biopsy showed ACC.She was asymptomatic with significantly elevated urine free cortisol 3648 (3.5-45 mcg/24 hour), serum cortisol 67.5 (5-25 ug/dl), 11-deoxycortisol 3910 (10-79 ng/dl), and suppressed ACTH &amp;lt;5 (5-52 pg/ml). Electrolytes were normal, DHEAS 342 (35-430 ug/dl), aldosterone &amp;lt; 3 (4-31 ng/dl), renin mass 5 (4-44pg/ml), urinary free normetanephrine 0.23 (&amp;lt; 0.9 nmol/l), urinary free metanephrine &amp;lt; 0.2 (&amp;lt; 0.5 nmol/l). MRI of the chest and brain did not show metastases. She developed at GA 29 weeks, hypertension, proteinuria, and transaminitis. Cesarean section was done at GA 30 weeks followed the next day by right adrenalectomy, IVC repair and retroperitoneal lymph node resection. Pathology showed high-grade adrenal cortical carcinoma (12 cm size) with negative margins, vascular invasion and lymph node involvement (T3, N1, M0), no caval involvement, stage III ACC. During chemotherapy planning, metastases were noted, mitotane and pembrolizumab were initiated, but discontinued after 2 cycles on account of generalized rash and elevated liver enzymes. The tumor progressed on etoposide, doxorubicin and cisplatin (EDP), and second line therapy (gemcitabine and capecitabine) was initiated. Conclusion: Physiologic changes of pregnancy mimic clinical features of ACC and pregnancy associated changes in the HPA axis also make ACC diagnosis challenging. Short fragments of DNA (cfDNA) released into the maternal bloodstream can be detected after 7 weeks of gestation. Approximately 2-20% of total cfDNA is placental, it is used for sex determination and detection of congenital genetic abnormalities, cfDNA can also originate from maternal neoplasms and has been shown to detect lung, breast and colon while case series in patients with ACC showed detection of only 1 out of 3 cases. Surgery remains first line therapy for ACC, but adjuvant therapy, surveillance and hormone replacement are also vital in ACC management. Presentation: Saturday, June 17, 2023

Clinical Experience with Genome-Wide Noninvasive Prenatal Screening in a Large Cohort of Twin Pregnancies

Non-invasive prenatal screening (NIPS) in twin gestations has been shown to have high detection rates and low false-positive rates for trisomy 21, as seen in singleton pregnancies, although there have been few large cohort twin studies, genome-wide studies in particular, to date. In this study, we looked at the performance of genome-wide NIPT in a large cohort consisting of 1244 twin pregnancy samples collected over a two-year period in a single laboratory in Italy. All samples underwent an NIPS for common trisomies, with 61.5% of study participants choosing to undergo genome-wide NIPS for additional fetal anomalies (namely, rare autosomal aneuploidies and CNVs). There were nine initial no-call results, all of which were resolved upon retest. Based on our NIPS results, 17 samples were at high risk for trisomy 21, one for trisomy 18, six for a rare autosomal aneuploidy, and four for a CNV. Clinical follow-up was available for 27 out of 29 high-risk cases; a sensitivity of 100%, a specificity of 99.9%, and a PPV of 94.4% were noted for trisomy 21. Clinical follow-up was also available for 1110 (96.6%) of the low-risk cases, all of which were true negatives. In conclusion, we found that NIPS was a reliable screening approach for trisomy 21 in twin pregnancies.

High rates of "atypical" single nucleotide polymorphism-based noninvasive prenatal screening results among consanguineous Arab American patients: A single center retrospective study.

Noninvasive prenatal screening (NIPS), using placental cell-free DNA from a maternal blood sample, is currently the most sensitive and specific screening tool for detecting common fetal aneuploidies. The aim of this study was to compare the rates of "atypical" single nucleotide polymorphism (SNP)-based NIPS results and subsequent pregnancy outcomes between Arab American and non-Arab American patients. We conducted a retrospective cohort study of pregnant Arab and non-Arab American patients who had SNP-based NIPS performed between September 2018 and January 2021 at an urban health system in Michigan. The rate of "atypical" results and other perinatal outcomes were compared between groups using descriptive statistics. "Atypical" results due to multifetal gestations, either undisclosed or unknown at time of ordering, were excluded. Five thousand eight hundred and seventy-three patients underwent SNP-based NIPS: 771 (13.1%) were identified as Arab American, 5102 (86.9%) were non-Arab American, and 49 (0.8%) patients received "atypical" results. Arab patients represented only 13.1% of patients screened (771/5873) but had a significantly higher rate of "atypical" results than non-Arab American patients (17/771 [2.2%] vs. 32/5102 [0.6%]; p < 0.001). Of the 17 Arab patients with "atypical" results, 9 (52.9%) were in known consanguineous relationships. No major congenital anomalies or chromosomal aberrations were identified for any patients who had "atypical" results, and no significant differences in other perinatal outcomes were observed between Arab and non-Arab American patients. A better understanding of the association between consanguinity and "atypical" SNP-based NIPS results would aid in appropriate test selection and interpretation and may help physicians and genetic counselors provide better perinatal counseling and follow-up care for patients in consanguineous relationships.

Maternal and fetal factors influencing fetal fraction: A retrospective analysis of 153,306 pregnant women undergoing noninvasive prenatal screening.

Genetic factors are important causes of birth defects. Noninvasive prenatal screening (NIPS) is widely used for prenatal screening of trisomy 21, trisomy 18, and trisomy 13, which are the three most common fetal aneuploidies. Fetal fraction refers to the proportion of cell-free fetal DNA in maternal plasma, which can influence the accuracy of NIPS. Elucidating the factors that influence fetal fraction can provide guidance for the interpretation of NIPS results and genetic counseling. However, there is currently no broad consensus on the known factors that influence fetal fraction. The study aimed to explore the maternal and fetal factors influencing fetal fraction. A total of 153,306 singleton pregnant women who underwent NIPS were included. Data on gestational age; maternal age; body mass index (BMI); z-scores for chromosomes 21, 18, and 13; and fetal fraction in NIPS were collected from the study population, and the relationships between fetal fraction and these factors were examined. The relationship between fetal fraction and different fetal trisomy types was also analyzed. The results showed that the median gestational age, maternal age, and BMI of the pregnant women were 18 (16, 20) weeks, 29 (25, 32) years, and 22.19 (20.40, 24.24) kg/m2, respectively. The median fetal fraction was 11.62 (8.96, 14.7)%. Fetal fraction increased with gestational age and decreased with maternal age and BMI (P < 0.001). Fetal fraction of fetuses with trisomies 21, 18, and 13 was similar to that of the NIPS-negative group. The z-scores of pregnant women with trisomy 21 and 18 fetuses were positively correlated with fetal fraction, but not with that of the trisomy 13 cases. The factors that influence fetal fraction need to be taken into consideration before NIPS for quality control and after NIPS for result interpretation.

A retrospective single-center analysis of prenatal diagnosis and follow-up of 626 chinese patients with positive non-invasive prenatal screening results.

This study explored the diagnostic efficiency of different prenatal diagnostic approaches for women with positive non-invasive prenatal screening (NIPS) results by analyzing their clinical information and pregnancy outcomes. We collected data on 626 NIPS-positive pregnant women from January 2017 to June 2021 and arranged subsequent prenatal diagnostic operations for them after genetic counseling, along with long-term intensive follow-up. A total of 567 women accepted invasive prenatal diagnosis (IPD) (90.58%), and 262 cases were confirmed as true positives for NIPS. The positive predictive values for trisomies 21 (T21), 18 (T18), and 13 (T13); sex chromosome aneuploidies (SCAs); rare autosomal trisomies (RATs); and microdeletion and microduplication syndromes (MMS) were 81.13%, 37.93%, 18.42%, 48.83%, 18.37%, and 41.67%, respectively. Discordant results between NIPS and IPD were observed in 48 cases, with the discordance rate being 8.47%. Additionally, there were 43 cases with discordant results between karyotyping and chromosomal microarray analysis (CMA)/copy number variation sequencing. Additional reporting of RATs and MMS with routine NIPS that only detects T21/T18/T13 and SCAs can yield more accurate diagnoses. However, NIPS cannot be used as a substitute for IPD owing to its high false positive rate and discordance with other diagnostic methods. Therefore, we recommend CMA combined with karyotyping as the preferred method for accurately diagnosing NIPS-positive women.

O59 - Psychological benefits and harms of Non-Invasive Prenatal Screening (NIPS): Women’s perspectives

Non-invasive prenatal screening (NIPS) is being increasingly used by expectant parents. Much provision of this test in Australia is occurring in clinical settings where specialised genetic counselling is unavailable. Potential psychosocial consequences of NIPS remain largely unexplored. This study aimed to understand potential psychosocial consequences from prenatal genetic screening tests. We conducted a thematic analysis of semi-structured qualitative interviews with 16 women who received an increased-chance prenatal screening (NIPS, combined first trimester screening, or morphology scan) result. All participants had NIPS as a first line screening test (n=12) or contingent screening test after receiving an increased chance results from another screening test (n=4). Women held positive opinions of NIPS and discussed the need for it to be covered by Medicare. However, some received inadequate pre-test counselling which potentially contributed to negative psychosocial consequences, including increased self-reported anxiety and distress. Several women were unaware of the conditions that NIPS screened for, particularly SCA and microdeletions and were subsequently surprised when they received increased-chance results. False positive results caused some women to feel that bonding with their baby had been significantly disrupted in the period between receiving an increased chance screening result and receiving their contingent NIPS and/or diagnostic testing results. Women discussed several strategies that would have made their experience receiving an increased-chance screening result easier, including better information provision about the conditions tested for, and the possible consequences of an increased-chance screening result, particularly for conditions beyond the three common trisomies. Our results indicate that some expectant parents are not fully informed of the scope and implications of NIPS prior to testing. This may prevent them from making fully considered choices that reflect their personal values and aspirations for parenthood. Better pre-test counselling may facilitate informed decision-making and improve prospective parents’ experiences.

Analysis of the impact of noninvasive prenatal testing for trisomies 21 and 18 in twin pregnancies undergoing artificial reproductive technology.

Purpose:The purpose of this study was to evaluate the performance and impact of noninvasive prenatal screening (NIPS) on twin pregnancies.Patients and methods:Twin pregnancies after artificial reproductive technology(ART) were tested by NIPS for screening trisomy 21, 18, and 13 in a single medical center in Hangzhou. Positive NIPS results were confirmed by karyotyping, while negative results were interviewed after delivery.Results:From January 2019 to December 2020, 474 twin pregnancies were tested by NIPS for screening trisomy 21, 18, and 13 in a single medical center in Hangzhou. The performance of NIPS had been evaluated compared to the invasive diagnostic results. The positive predictive value (PPV) of NIPS for chromosome 21 and 18 aneuploidies is 80% (95CI, 36.09–96.59) and 100%, respectively. The incidence of trisomy 21, and 18 chromosome aneuploidies among the twin pregnancies undergoing ART was 0.84% and 0.21%, respectively.Conclusion:The performance of NIPS was substantially accurate among the twin pregnancies after ART in this study, and NIPS potentially avoided a considerable part of aneuploidies liveborn in twin pregnancies in Hangzhou.

EP466: The use of next generation prenatal screening in a low resource setting among Non-Hispanic Black and Hispanic patients

Just under half of all births in the U.S. are covered under Medicaid insurance. Increasingly, many state public health programs offer noninvasive prenatal screening (NIPS) as first-tier prenatal screening covered under Medicaid insurance or through contracts with private companies. Yet considerable questions remain regarding the cost-effectiveness of NIPS vs. maternal serum screening and its use in a low-health literacy, low-resource population. In order to explore pregnant patient’s views and understanding of prenatal screening, we conducted a qualitative interview study with patients at a federally qualified health center. We recruited from prenatal and maternal-fetal medicine clinics at the University of Florida Jacksonville (UF Health). UF Health offers NIPS to their prenatal patients upon provider recommendation. Patients were included if they were age 18 or older, identified as Black or African American and/or Hispanic or Latina, were currently pregnant, or were pregnant within the past 12 months, and spoke English or Spanish. Interviews were conducted using a semi-structured interview guide and were audio recorded and transcribed verbatim. NVivo12 was used to analyze interview transcripts according to standard qualitative methodology using a grounded theory framework. Eighty-seven patients completed an interview, including 54 (62.1%) non-Hispanic Black, 30 (31.3%) Hispanic, and 3 (3.4%) Hispanic/Black patients. The majority were covered under Medicaid insurance (n=65, 74.7%) followed by private insurance (n=8, 9.2%), financial assistance program (n=2, 2.3%), Tricare/VA Healthcare (n=2, 2.3%), and uninsured/self-pay (n=2, 2.3%). Most participants stated that they had received NIPS and understood its primary utility as determining fetal sex, however, some understood that they were also being tested for Trisomy 21. Some participants indicated that they had NIPS, but their responses reflected that they received quad screening only or vice versa. Pre-test counseling was described as brief, with a few women expressing that the test was mandatory requirement for their prenatal care. Few participants were counseled that a positive screening result would need to be confirmed by chorionic villus sampling, amniocentesis, or umbilical cord blood sampling. No participants were able to recall a chromosomal condition other than Trisomy 21 included in the NIPS panel, but most expressed a perception that they were being tested to rule out fetal anomaly. Many indicated a belief that they were being tested for multifactorial conditions, such as autism, or for developmental delay more broadly. Most participants felt that NIPS was useful for prenatal preparation, such as learning more information about the condition and future medical needs of their child. Only a couple participants indicated they would use NIPS results for a pregnancy continuation decision, with most stating that they intended to continue with the pregnancy regardless of the screening result. Some stated that they were not intimidated by the prospect of having a child with a genetic condition or disability since they worked with children with special needs or had a family member with a similar condition. To the best of our knowledge, this is the largest qualitative study on NIPS in an underserved Black and Hispanic population. Our findings suggest that many underserved patients are unable to make a meaningful distinction between NIPS and maternal serum screening and are not adequately counseled on its scope, limitations as a screening vs. diagnostic test, and implications in the event of a positive result, in accordance with professional guidelines. In contrast to arguments stating that cost-effectiveness of NIPS is supported through elective termination of affected pregnancies, most women stated that they did not intend to use their result for this purpose. These findings indicate that the use of NIPS as a first-tier prenatal screen for fetal aneuploidy may not be appropriate without additional public health investment. Additional resources are also needed to ensure that providers are able to adequately educate and counsel patients with low health literacy on NIPS to meet shared decision-making standards.

Pregnancy outcomes of rare autosomal trisomies results in non-invasive prenatal screening: clinical follow-up data from a single tertiary centre.

This study was performed to assess the association between detection of rare autosomal trisomies (RATs) by non‐invasive prenatal screening (NIPS) and adverse pregnancy outcomes. We retrospectively analyzed women with high‐risk RATs results from January 2014 to December 2020. The women's clinical information was collected, and their pregnancy outcomes were compared with those of women with low‐risk results. In total, 151 (0.24%) RATs results were reported among 62,752 NIPS examinations. Sixty‐five women chose to undergo amniocentesis for confirmation, which revealed 3 cases of true fetal mosaicism for RATs and a positive predictive value of 4.6% (3/65). Among the 139 women with available outcomes, 26 (18.7%) had a preterm birth, 10 (7.2%) underwent pregnancy termination because of fetal defects and 5 (3.6%) had miscarriages. Interestingly, compared with the control group, pregnancies in which NIPS revealed trisomy 16 (T16), T22, T9 and T2 were at higher risk of adverse outcomes, including preterm birth, miscarriage and ultrasound abnormalities. However, the risk of adverse outcomes was comparable between the control group and pregnancies with positive results of T7, T3, T8 and T20. In summary, the risk of adverse pregnancy outcomes was higher in women with specific RATs‐positive NIPS results. Pregnancies with T16, T22, T9 and T2 results, even if false‐positive, should be considered high‐risk pregnancies.

Clinical Selection of Prenatal Diagnostic Techniques Following Positive Noninvasive Prenatal Screening Results in Southwest China.

Background: This study aims to evaluate prenatal diagnosis methods following positive noninvasive prenatal screening (NIPS) results. Methods: According to the positive noninvasive prenatal screening results, 926 pregnant women were divided into three groups: main target disease group (high risk for trisomy 21, trisomy 18, or trisomy 13), sex chromosome aneuploidy (SCA) group, and other chromosomal abnormalities group [abnormal Z-scores for chromosomes other than trisomy (T)21/T18/T13 or SCAs]. The verification methods and results were then retrospectively analysed. Results: In the main target disease group, the positive rate of chromosomal abnormalities confirmed by quantitative fluorescence polymerase chain reaction (QF-PCR) was 75.18% (212/282), which was not significantly different from that by karyotyping (79.36%, 173/218) and copy number variation (CNV) detection methods (71.43%, 65/91). The positive rate of additional findings confirmed by karyotyping and copy number variation detection methods in main target disease group was 0.46% (1/218) and 8.79% (8/91), respectively. The positive rate of chromosomal abnormalities confirmed by karyotyping and CNV detection methods were 27.11% (45/166) and 38.46% (95/247) in the SCA group and 4.17% (1/24) and 20% (36/180) in the other chromosomal abnormalities group, respectively. Fetal sex chromosome mosaicism was detected in 16.13% (20/124) of the confirmed SCA cases. There were no significant differences in the detection rates of chromosomal microarray analysis (CMA) and CNV sequencing (CNVseq) among the three groups (p > 0.05). Conclusion: QF-PCR can quickly and accurately identify aneuploidies following NIPS-positive results for common aneuploidy, and in combination with karyotyping and CNV detection techniques can provide more comprehensive results. With the NIPS-positive results for SCA or other abnormalities, CMA and CNVseq may have the same effect on increasing the detection rate. The addition of fluorescence in situ hybridization assay may help to identify true fetal mosaicism.

Factors Affecting the Fetal Fraction in Noninvasive Prenatal Screening: A Review.

A paradigm shift in noninvasive prenatal screening has been made with the discovery of cell-free fetal DNA in maternal plasma. Noninvasive prenatal screening is primarily used to screen for fetal aneuploidies, and has been used globally. Fetal fraction, an important parameter in the analysis of noninvasive prenatal screening results, is the proportion of fetal cell-free DNA present in the total maternal plasma cell-free DNA. It combines biological factors and bioinformatics algorithms to interpret noninvasive prenatal screening results and is an integral part of quality control. Maternal and fetal factors may influence fetal fraction. To date, there is no broad consensus on the factors that affect fetal fraction. There are many different approaches to evaluate this parameter, each with its advantages and disadvantages. Different fetal fraction calculation methods may be used in different testing platforms or laboratories. This review includes numerous publications that focused on the understanding of the significance, influencing factors, and interpretation of fetal fraction to provide a deeper understanding of this parameter.

Clinical evaluation of non-invasive prenatal screening in 32,394 pregnancies from Changzhi maternal and child health care hospital of Shanxi China.

BackgroundNon-invasive prenatal screening (NIPS) is a highly sensitive and specific screening test to detect fetal chromosomal abnormalities. The primary objective of this study was to evaluate the NIPS as an effective method for prenatal detection of aneuploidies in both high-risk and low-risk pregnancies.MethodsIn current study, we performed NIPS in 32,394 pregnancies, out of which results were available in 32,361 (99.9%) of them. Illumina sequencing was performed for NIPS screening. Hypothesis Z test was used to classify fetal autosomal aneuploidy of T21, T18, and T13. Karyotyping was performed to determine the true negative and true positive NIPS results.ResultsAmong the 32,361 confirmed samples, 164 cases had positive results and 32197 cases had negative results. Of these positive cases, 116 cases were trisomy 21, 34 cases were trisomy 18 and 14 cases were trisomy 13. No false negative results were found in this cohort. The overall sensitivity and specificity were 100% and 99.91%, respectively. There was no significant difference in test performance between the 7,316 high-risk and 25,045 low-risk pregnancies, (sensitivity, 100% vs 100% (P>0.05); specificity, 99.96% vs 99.95% (P > 0.05)). Factors contributing to false-positive results included fetal copy number variants (CNVs), fetal mosaicism and typically producing Z scores between 3 and 4. Moreover, we analyzed NIPS wholegenome sequencing to investigate the Single Nucleotide Polymorphisms (SNPs) associations with drug response or risk of disease. As compare to the 1000g East Asian genome data, the results revealed a significant difference in 7,285,418 SNPs variants of Shanxi pregnant women including 19,293 clinvar recorded variants and 7,266,125 non-clinvar recorded.ConclusionsOur findings showed that NIPS was an effective assay that may be applied as routine screening for fetal trisomies in the prenatal setting. In addition, this study also provides an accurate assessment of significant differences in 7,285,418 SNPs variants in Shanxi pregnant women that were previously unavailable to clinicians in Shanxi population.

Noninvasive Prenatal Screening Based on Second-Trimester Ultrasonographic Soft Markers in Low-Risk Pregnant Women.

Background: We aimed to assess the clinical application of noninvasive prenatal screening (NIPS) based on second-trimester ultrasonographic soft markers (USMs) in low-risk pregnant women. Methods: Data of pregnant women between April 2015 and December 2019 were retrospectively analyzed. Pregnant women [age at expected date of confinement (EDC) of <35 years; low risks for trisomy 21 (T21) and trisomy 18 (T18) based on maternal serum screening; presenting second-trimester USMs (7 types)] who successfully underwent NIPS and had available follow-up information were included in our study. Cases with positive NIPS results were prenatally diagnosed. All patients were followed up for 6 months to 2 years after NIPS, and their clinical outcomes were obtained. Subgroup analyses were performed according to the different USMs. Results: NIPS suggested that among a total of 10,023 cases, 37 (0.37%) were at high risk of aneuploidy, including 4 T21, 6 trisomy 13 (T13), and 27 sex chromosome abnormalities (SCA). Ten cases with aneuploidy (0.10%) were confirmed by prenatal diagnosis, consisting of two T21 and eight SCA. The eight fetuses with SCA consisted of one monosomy X, two XXY, one XXXY, one XXX, one XYY, and two mosaicisms. T21 was detected in one fetus with absent or hypoplastic nasal bone and one fetus with echogenic intracardiac focus (EICF). SCA was detected in five fetuses with EICF, two fetuses with multiple soft markers, and one fetus with echogenic bowel. The positive rate of chromosomal aneuploidy was significantly higher in fetuses with absent or hypoplastic nasal bone (6.25 vs. 0.10%, p = 0.017), echogenic bowel (3.7 vs. 0.10%, p = 0.029), and multiple soft markers (0.678 vs. 0.10%, p = 0.045) than in the total fetuses. The positive predictive values (PPVs) of NIPS in these three groups were 100%, 50%, and 100%, respectively. EICF accounted for 93.25% (9,346/10,023) of the study population, whereas the PPV of NIPS was only 20%. Conclusion: NIPS is an advanced screening test for low-risk pregnant women. In the 10,023 pregnant women sampled, SCA were more common than autosomal trisomy, and EICF was the most frequent USM but the least predictive aneuploidy. Further aneuploidy evaluation is suggested for low-risk pregnant women whose ultrasound indicates absent or hypoplastic nasal bone, echogenic bowel, or multiple soft markers. NIPS can serve as a second-line complementary screening for these women.

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

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

Utility of noninvasive genome-wide screening: a prospective cohort of obstetric patients undergoing diagnostic testing

PurposeCopy-number variant (CNV) assessment is recommended for patients undergoing prenatal diagnostic testing. Noninvasive screening tests have not been extensively validated for CNV detection. The objective of this study was to compare the ability of genome-wide noninvasive prenatal screening (NIPS) to chromosomal microarray to detect clinically significant findings. MethodsWe prospectively enrolled 198 subjects at the time of consent for diagnostic prenatal testing. Genome-wide NIPS results were compared with diagnostic testing results to assess NIPS test performance (n = 160, 38 subjects without microarray results excluded). Cohen’s kappa statistic was used to assess test agreement. ResultsGenome-wide NIPS did not detect clinically significant chromosomal abnormalities at the same rate as diagnostic testing, κ = 0.75 (95% confidence interval [CI], 0.62–0.87). When excluding CNVs <7 Mb and findings outside the limits of genome-wide NIPS, test agreement improved, κ = 0.88 (0.79–0.97) driven by agreement for common aneuploidies (κ = 1.0). However, among patients with an abnormal fetal survey, agreement was only fair, κ = 0.38 (0.08–0.67). ConclusionWhile NIPS is an excellent screening test for common aneuploidies, genome-wide NIPS misses clinically significant findings detected on routine diagnostic testing. False positive and false negative cases highlight the importance of pretest counseling regarding NIPS limitations, especially in the setting of fetal anomalies.

Two factors affecting the success rate of the second non-invasive prenatal screening after initial no-call result: experience from a single tertiary center in China

Background:One inevitable shortcoming of non-invasive prenatal screening (NIPS)/cell-free DNA (cfDNA) sequencing is the uninterpretable (“no-call”) result, which is mainly caused by an insufficient fetal fraction. This study was performed to investigate the factors associated with a successful second NIPS in these cases and determine the optimal management for women with initial no-call results.Methods:We retrospectively analyzed the data of women who underwent NIPS with initial no-call results due to an insufficient fetal fraction from 2017 to 2019 in our center. We compared these women's maternal and pregnancy information with the data of women who had attained a successful second NIPS result and women who had received no-call results for a second time.Results:Among the 33,684 women who underwent NIPS, 137 with a no-call result underwent a retest. Comparison between the 87 (63.50%) women with a successful retest and the other 50 (36.50%) women showed a significant difference in both the initial fetal fraction and maternal body mass index (BMI), whereas the other factors showed no significant differences. In addition, with an initial fetal fraction of < 2.00%, the retest success rate was very limited.Conclusions:We identified two major factors associated with a successful NIPS retest: the initial fetal fraction and the maternal BMI. These findings suggest the need for specialized management for this subset of women and would be instructional for the counseling for these women.

Retrospective analysis and mining of data from 10 840 patients undergoing non-invasive prenatal screening

To retrospectively analyze non-invasive prenatal screening (NIPS) data from two centers. The NIPS results of 10 840 samples were analyzed, including 21/18/13 trisomies (T21/T18/T13), sex chromosome and other autosomal aneuploidies, and copy number variants (CNVs). The maternal age, gestational week, body mass index and concentration of free fetal DNA (cffDNA) were also analyzed. The average gestational age of the 10 840 pregnant women was (32.34±5.04) year old, and the average gestational week for NIPS was (17.60±3.55) week. The overall false positive rate for T21/T18/T13 was 0.11%, sensitivity was 100%, specificity was 99.89%, and positive predictive value was 81.5%. The positive predictive values for sex chromosome and other autosomal aneuploidies and CNVs were 56.67%, 11.76% and 83.33%, respectively. The incidence of T21/T18 in the elder women (35 years or elder) was 2.12 times(P<0.01) and 1.81 times (P> 0.05) that of young women. cffDNA was in proportion to gestational week (r = 0.207) and in inverse proportion to body mass index (r = -0.177). It has increased slowly before 15 weeks of gestation and thereafter at a rate of 0.5% per week after the 16th week. The performance of NIPS in this study is by large close to the reported in the literature, and the results can provide a reference for further study.

Polycystic Ovary Syndrome and Incidental Diagnosis of Mosaic Turner Syndrome

Polycystic ovary syndrome (PCOS) is a common condition in women of reproductive age. Mosaic Turner syndrome (TS) is a genetic disorder with significant phenotypic variability. The occurrence of PCOS in women with mosaic TS has been infrequently studied. A 30-year-old nulligravid woman presented with oligomenorrhea, hyperandrogenism, infertility, and ultrasound polycystic ovary morphology. She was diagnosed with PCOS and conceived following ovulation induction. After 2 inconclusive non-invasive prenatal screening results, she was referred to medical genetics. A maternal karyotype resulted in a diagnosis of 45,X/46,XX mosaic TS. She delivered a healthy 46,XY infant at term. PCOS can affect women with mosaic TS. Further studies are needed to better characterize the reproductive profile of women with mosaic TS, including the presentation of concurrent PCOS.