Reference-Based Versus Reference-Free Cell Type Estimation In DNA Methylation Studies Using Human Placental Tissue

The placenta is a central organ during early development, influencing trajectories of health and disease. DNA methylation (DNAm) studies of human placenta improve our understanding of how its function relates to disease risk. However, DNAm studies can be biased by cell type heterogeneity, so it is essential to control for this in order to reduce confounding and increase precision. Computational cell type deconvolution approaches have proven to be very useful for this purpose. For human placenta, however, an assessment of the performance of these estimation methods is still lacking. Here, we compare the predictive performance of reference-based versus reference-free estimated proportions of cell types from genome-wide DNAm in placental samples taken at birth and from chorion villus biopsies early in pregnancy using three independent studies comprising over 1,000 samples. We found both reference-free and reference-based estimated cell type proportions to have predictive value for DNAm, however, reference-based cell type estimation outperformed reference-free estimation for the majority of data sets. Reference-based cell type estimations mirror previous histological knowledge on changes in cell type proportions through gestation. Further, CpGs whose variation in DNAm was largely explained by reference-based estimated cell type proportions were in the proximity of genes that are highly tissue-specific for placenta. This was not the case for reference-free estimated cell type proportions. We provide a list of these CpGs as a resource to help researchers to interpret results of existing studies and improve future DNAm studies of human placenta.

Fetal procedures during COVID-19 pandemic: Challenges in a newly developing centre

Prenatal invasive diagnostic and therapeutic procedures have drastically reduced during COVID-19 pandemic. Unlike routine prenatal care, these are time bound and highly skilled procedures available at specialized centres. This adds to the limited accessibility for at-risk women. Major concerns including procedure related risk, exposure of health care personnel and vertical transmission of COVID-19. At newly developing tertiary centre, we had done 36 fetal procedures during pandemic including 25 amniocentesis, three chorion villus sampling and eight intrauterine transfusions. It is advisable to perform life-saving fetal interventions irrespective of COVID-19 status taking full precautions and proper counselling of women.

Genetic counselling for unaffected family members

This chapter focuses on aspects of genetic counselling for those at 50 per cent risk for Huntington’s disease (HD). There are various options including not being tested. Predictive testing for HD is described together with some perspectives from patients. There are four types of results from a predictive test: normal, intermediate allele, reduced penetrance, and abnormal. The implications of these are discussed. Options regarding testing in pregnancy are discussed which include: no testing and accepting a risk, invasive tests such as chorion villus sampling or amniocentesis and preimplantation genetic diagnosis. Finally, the issue of testing someone at 25 per cent risk is discussed.

Prenatal diagnosis of rare form of chromosomal abnormality: double trisomy 48,XXX,+18 in the first trimester in association with spina bifida

The case of prenatal diagnosis of neural tube defect at 11+5 weeks of gestation is presented. Chorion villus sampling performed. Karyotyping revealed double trisomy (48,XXX,+18). Termination of pregnancy was performed at 13 weeks of gestation.

Chromosomal microarray analysis in prenatal diagnosis: ethical considerations of the Belgian approach

Detection of genetic aberrations in prenatal samples, obtained through amniocentesis or chorion villus biopsy, is increasingly performed using chromosomal microarray (CMA), a technique that can uncover both aneuploidies and copy number variants throughout the genome. Despite the obvious benefits of CMA, the decision on implementing the technology is complicated by ethical issues concerning variant interpretation and reporting. In Belgium, uniform guidelines were composed and a shared database for prenatal CMA findings was established. This Belgian approach sparks discussion: it is evidence-based, prevents inconsistencies and avoids parental anxiety, but can be considered paternalistic. Here, we reflect on the cultural and moral bases of the Belgian reporting system of prenatally detected variants.

Cloacal dysgenesis sequence in the first trimester of gestation

The autopsy data in 17 first trimester fetuses with cloacal dysgenesis sequence are presented. The prenatal ultrasound showed dilated bladder. Cytogenetic analysis of 16 cases carried out by chorion villus sampling or obtained from post-abortion tissues demonstrated normal karyotype. The complete autopsy revealed cystic dilated cloaca, smooth perineum, absence of anal opening and a phallus-like structure. There were 12 cases with isolated cloacal dysgenesis sequence and 5 cases with multiple malformations. In the latter group cloacal dysgenesis were associated with VACTERL association and non-classified multiple malformation complex.

Prenatal diagnosis of organic acidemias at a tertiary center

The aim of this study was to share our experience in the prenatal diagnosis (PND) of organic acidemias (OAs) in our clinic. This study consisted of 10 cases in whom an invasive prenatal diagnostic test (IPNDT) was performed by a single physician for the PND of OAs. Median maternal age, parity, gestational week of IPNDT, prenatal test indications, OA types, method of IPNDT, IPNDT results and gestational outcomes were evaluated. Targeted mutation analysis was performed in fetal DNA for the specific mutations by using polymerase chain reaction (PCR) and direct Sanger sequencing. The diagnosis was confirmed by genetic targeted mutation analysis after birth. Median maternal age, parity and gestational week of IPNDT values were 30 (range 21-35), one (range 0-4) and 11.5 (range 11-17), respectively. Indications for IPNDT were mother being a carrier of the disease for one case (10.0%) and at least one child with OA in the family for nine cases (90.0%). Organic acidemia types investigated were maple syrup urine disease (MSUD), methylmalonic acidemia (MMA) and isovaleric acidemia (IVA) in five (50.0%), three (30.0%) and two (20.0%) patients, respectively. Chorion villus sampling (CVS) was done in seven (70.0%) patients and amniocentesis was performed in three (30.0%) patients. Eight fetuses (80.0%) were found to be healthy and two fetuses (20.0%) were found to be affected (one case with IVA and one case with MMA). The two pregnancies (20.0%) with affected fetuses were terminated. Prenatal diagnosis of OAs is critical. Appropriate prenatal counseling should be given to families with known risk factors.

Comparison of adverse perinatal outcomes after single-needle and double-needle CVS techniques

Objective:To determine the impact of the chorion villus sampling (CVS) technique on adverse perinatal outcomes.Methods:In this case-control study, 412 women who underwent CVS at 11–14 weeks of gestation and 231 women who did not undergo any invasive procedure were retrospectively evaluated. The women in the CVS group were further divided into two groups according to the use of single-needle technique (n=148) vs. double-needle technique (n=264). The adverse outcomes were compared between controls and the two CVS groups, and regression analysis was used to determine the significance of independent contribution.Results:The rate of preeclampsia for the control group was 2.2%, for the double-needle group was 3% and for the single-needle group was 8.1%. CVS with single-needle technique was found to be an independent and statistically significant risk factor for preeclampsia [odds ratio (OR)=2.1, 95% confidence interval (CI); 1.4–2.7, P=0.008].Conclusion:The risk of preeclampsia after CVS appears to be increased with single-needle technique compared with double-needle technique.

Recurrent Cystic Hygroma with Normal Karyotype in Two Consecutive Pregnancies

<p>We herein describe a woman with two consecutive pregnancies affected by fetal nuchal cystic hygroma (CH) with a normal karyotype.<br />A 33-year-old woman (gravidity 2, parity 1) was referred to us because of fetal hydrops. No consanguinity or Rh isoimmunization was involved in her current or previous pregnancy. First-trimester ultrasonography revealed nuchal CH, and chorion villus sampling was performed to exclude aneuploidy.<br />In the first pregnancy, the CH had regressed and aortic coarctation was detected by second-trimester fetal echocardiography. In the current pregnancy, the CH had progressed and was complicated by the development of nonimmune hydrops. Termination of the pregnancy was performed at 21 weeks’ gestation.<br />Recurrence of fetal CH in subsequent pregnancies is extremely rare. CH with a normal karyotype can be inherited as an autosomal recessive trait. This report describes a woman with recurrent CH with normal karyotypes and different prognoses</p>