Cell-Free DNA Screening for Sex Chromosome Abnormalities and Pregnancy Outcomes, 2018–2020: A Retrospective Analysis

To evaluate the efficacy of non-invasive prenatal screening (NIPT) for detecting fetal sex chromosome abnormalities, a total of 639 women carrying sex chromosome abnormalities were selected from 222,107 pregnant women who participated in free NIPT from April 2018 to December 2020. The clinical data, prenatal diagnosis results, and follow-up pregnancy outcomes of participants were collected. The positive predictive value (PPV) was used to analyze the performance of NIPT. Around 235 cases were confirmed with sex chromosome abnormalities, including 229 cases with sex chromosome aneuploidy (45, X (n = 37), 47, XXX (n = 37), 47, XXY (n = 110), 47, XYY (n = 42)) and 6 cases with structural abnormalities. The total incidence rate was 0.11% (235/222,107). The PPV of NIPT was 45.37% (235/518). NIPT accuracy for detecting sex chromosome polysomes was higher than that for sex chromosome monomers. The termination of pregnancy rate for fetal diagnosis of 45, X, and 47, XXY was higher than that of 47, XXX, and 47, XYY. The detection rate of fetal sex chromosome abnormalities was higher in 2018–2020 than in 2010–2012 (χ2 = 69.708, P < 2.2 × 10−16), indicating that NIPT is greatly efficient to detect fetal sex chromosome abnormalities.

Large Intra-Age Group Variation in Chromosome Abnormalities in Human Blastocysts

Research Question: Is maternal age only a gross predictor of chromosome abnormalities in human embryos? Design: Here, we evaluated the less-studied variation in chromosome abnormality rates in embryos of patients within the same age group. Patients undergoing IVF and PGD for chromosomal abnormalities in ~127 different IVF clinics were included. PGT-A analysis was performed by a single reference laboratory using array CGH or NGS. To get an estimate of the range of abnormalities observed, the aCGH and NGS data were studied both independently and together. Results: The overall results showed the typical increase in aneuploidy rates with advancing maternal age (AMA) but extensive variability within each age group. Conclusions: Increasing aneuploidy with maternal age has been demonstrated in live births, unborn fetuses, IVF embryos and oocytes. In contrast, post-meiotic and other abnormalities that might lead to mosaicism, polyploidy and haploidy, are commonplace (around 30%), regardless of maternal age. Here we conclude that age is only a gross predictor of chromosome abnormalities in IVF embryos. In contrast to the existing standard of offering PGT-A to AMA patients, the high rate and extreme variation of chromosomal abnormalities in human embryos may warrant PGT-A for further IVF cycles even in younger age groups, especially if a history of increased levels of aneuploidy is evident. Furthermore, better indicators are needed to determine which patients are at a higher risk of producing increased levels of aneuploid embryos.

Proposal of Algorithm for Automated Chromosomal Abnormality Detection

The article considers the problem of automatic chromosome abnormalities recognition, using images of chromosomes as an input. This paper’s scope includes overview of application domain and analysis of existing solutions. A high-level algorithm for chromosome abnormalities recognition automation is proposed, and a proof-of-concept application is built on top of the algorithm.

Haplotype-aware inference of human chromosome abnormalities

Extra or missing chromosomes—a phenomenon termed aneuploidy—frequently arise during human meiosis and embryonic mitosis and are the leading cause of pregnancy loss, including in the context of in vitro fertilization (IVF). While meiotic aneuploidies affect all cells and are deleterious, mitotic errors generate mosaicism, which may be compatible with healthy live birth. Large-scale abnormalities such as triploidy and haploidy also contribute to adverse pregnancy outcomes, but remain hidden from standard sequencing-based approaches to preimplantation genetic testing for aneuploidy (PGT-A). The ability to reliably distinguish meiotic and mitotic aneuploidies, as well as abnormalities in genome-wide ploidy, may thus prove valuable for enhancing IVF outcomes. Here, we describe a statistical method for distinguishing these forms of aneuploidy based on analysis of low-coverage whole-genome sequencing data, which is the current standard in the field. Our approach overcomes the sparse nature of the data by leveraging allele frequencies and linkage disequilibrium (LD) measured in a population reference panel. The method, which we term LD-informed PGT-A (LD-PGTA), retains high accuracy down to coverage as low as 0.05 × and at higher coverage can also distinguish between meiosis I and meiosis II errors based on signatures spanning the centromeres. LD-PGTA provides fundamental insight into the origins of human chromosome abnormalities, as well as a practical tool with the potential to improve genetic testing during IVF.

Clinical Utility of Noninvasive Prenatal Screening for Rare Chromosome Abnormalities in Singleton Pregnancies

Objective: To systematically investigate the clinical utility of noninvasive prenatal screening (NIPS) commercially used for the common fetal aneuploidies as a prenatal screening tool for rare chromosome abnormalities (RCAs). Design: Prospective study. Setting: Hospital-based. Population or Sample: 528 gravidas with positive NIPS results for RCAs. Methods: Gravidas with positive NIPS results for RCAs subsequently underwent amniocentesis for single nucleotide polymorphism array (SNP-array) were recruit. The degrees of concordance between NIPS and SNP-array were classified into full concordance, partial concordance, discordance related and discordance. Main Outcome Measures: The positive predictive values (PPVs) for rare aneuploidies and segmental imbalances, while incidental findings for regions of homozygosity/uniparental disomy (ROH/UPD), were used to evaluate the performance of NIPS. Results: Of the 528 gravidas with positive NIPS results, 29.2% were confirmed with positive prenatal SNP-array results (154/528). The PPVs for rare aneuploidies and segmental imbalances were 6.1% (7/115) and 21.1% (87/413), respectively. ROH/UPDs, as incidental findings, have been identified in 9.5% (50/528) of gravidas with positive NIPS results. The PPV for clinical significant findings was 8.9% (47/528), including 7 cases with mosaic rare aneuploidies, 35 with pathogenic/likely pathogenic copy number variants, and 5 with imprinting disorders. Conclusions: NIPS commercially used for the common fetal aneuploidies yielded low PPV for rare aneuploidies, moderate PPV for segmental imbalances, and incidental findings for ROH/UPD. For the low PPV for clinical significant findings, NIPS has limited clinical utility for RCAs. Prenatal SNP-array should be regarded as the first-tier test for positive NIPS, particularly for those involved imprinted chromosomes.

Efficiency of Noninvasive Prenatal Testing for Sex Chromosome Aneuploidies

<b><i>Objective:</i></b> This study was designed to investigate the efficiency of noninvasive prenatal testing (NIPT) for screening fetal sex chromosome aneuploidies (SCAs) through sequencing of cell-free DNA in maternal plasma. <b><i>Methods:</i></b> This is a retrospective study on the positive NIPT results for SCAs collected from our hospital between January 2012 and December 2018. Samples with positive NIPT results for SCAs were then confirmed by prenatal or postnatal karyotyping analysis. <b><i>Results:</i></b> After cytogenetic analysis, abnormal karyotypes were confirmed in 104 cases and the overall positive predictive value (PPV) of NIPT for SCAs was 43.40% (102/235). The most frequently detected karyotypes included 47,XXY (<i>n</i> = 42), 47,XXX (<i>n</i> = 20), 47,XYY (<i>n</i> = 16), and 45,X (<i>n</i> = 2). Meanwhile, 10 cases were confirmed with mosaic karyotype 45,X/46,XX and 14 cases with numerical or structural chromosome abnormalities, including a double trisomy 48,XXX,+18. Cytogenetic results from the other 131 cases showed normal XX or XY, which were discordant with NIPT results. Upon analysis of parental karyotypes, 29 (12.34%) showed false positivity in NIPT results that were caused by maternal sex chromosome abnormalities. <b><i>Conclusion:</i></b> NIPT is an effective screening tool for SCA with a PPV of 43.40%. Maternal karyotype abnormalities occurred in 12.34% of the cases with abnormal NIPT. Diagnostic testing of the fetus and the mother are recommended.

O-020 Aneuploidy and mosaicism in human embryos: How correct detection may improve IVF clinical outcomes

text Study question Can new next-generation sequencing (NGS) based strategies for preimplantation genetic testing of aneuploidy (PGT-A) improve clinical outcomes after assisted reproductive technology (ART)? Summary answer Recent randomised controlled trials (RCTs) suggest that NGS-based PGT-A strategies can improve clinical outcomes for older women. The clinical management of mosaic embryos remains controversial. What is known already There are two types of chromosome abnormalities present in embryos, meiotic arising mostly during oogenesis, and mitotic arising after fertilisation. Meiotic aneuploidies are present in all of the embryonic cells and in their vast majority are lethal. Conversely, mitotic abnormalities are present in only part of the embryonic cells with the remaining cells having a different cytogenetic constitution. This phenomenon is known as mosaicism. The sensitivity of NGS meant that mosaic aneuploidy became readily detectable in trophectoderm (TE) samples during PGT-A. The viability and clinical management of mosaic embryos has led to debates and controversies in the reproductive medicine field. Study design, size, duration The study involved an assessment of the impact of mosaic chromosome abnormalities to embryonic viability and clinical outcomes after ART cycles using PGT-A via NGS. A large number of embryos generated in IVF clinics in Europe and the USA was examined. Participants/materials, setting, methods Embryos were generated by couples referred for PGT-A due to various indications. All embryos were cultured to the blastocyst stage, and underwent a TE biopsy, followed by vitrification. TE samples were shipped to 6 reference PGT laboratories and analysed via the use of the same NGS platform. Mosaic chromosome abnormalities were scored according to validated thresholds set by the reference laboratories. The clinical management of mosaic embryos took place according to published guidelines. Main results and the role of chance Comparison of clinical outcomes seen after the transfer of mosaic embryos with those seen after the transfer of euploid embryos led to the following findings: Mosaic embryos with &lt;40% abnormal cells in the TE sample had an OIR of 50% compared to 27% for mosaics with 40–80% abnormal cells in the TE, and 9% for complex mosaic embryos. Karyotyping of ongoing pregnancies resulting after the transfer of mosaic embryos demonstrated a normal chromosome constitution of the resulting foetuses. Limitations, reasons for caution - Cytogenetic classification was based on TE samples removed from blastocysts during PGT-A analysis. As only a fraction of the cells from each embryo are tested, inevitably some mosaic embryos will be incorrectly classified fully euploid or aneuploid. However, this misclassification is expected to have little impact on the results. Wider implications of the findings - The transfer of NGS-classified mosaic embryos was associated with poorer clinical outcomes compared to euploid embryos. However, the ongoing pregnancies resulting from mosaic transfers were euploid. NGS’s ability to identify embryos of reduced viability has the potential to improve IVF clinical outcomes.