Recent advances in the prenatal interrogation of the human fetal genome

Maternal obesity alters methylation level of cytosine in CpG island for epigenetic inheritance in fetal umbilical cord blood

BACKGROUND

Over the past few decades, global maternal obesity prevalence has rapidly increased. This condition may induce long-lasting pathophysiological effects on either fetal or infant health that could be attributable to unknown unique changes in the umbilical blood composition.

METHODS

A total of 34 overweight/obese and 32 normal-weight pregnant women were recruited. Fifteen umbilical blood samples including 8 overweight/obese subjects and 7 normal weight women were sequenced using Targeted Bisulfite Sequencing technology to detect the average methylation level of cytosine and identify the differentially methylated region (DMR). GO and KEGG analyses were then employed to perform pathway enrichment analysis of DMR-related genes and promoters. Moreover, the mRNA levels of methylation-related genes histone deacetylases (HDACs) and DNA methyltransferases (DNMTs) were characterized in the samples obtained from these two groups.

RESULTS

Average methylated cytosine levels in both the CpG islands (CGI) and promoter significantly decreased in overweight/obese groups. A total of 1669 DMRs exhibited differences in their DNA methylation status between the overweight/obese and control groups. GO and KEGG analyses revealed that DMR-related genes and promoters were enriched in the metabolism, cancer and cardiomyopathy signaling pathways. Furthermore, the HDACs and DNMTs mRNA levels trended to decline in overweight/obese groups.

CONCLUSIONS

Decreased methylated cytosine levels in overweight/obese women induce the gene expression activity at a higher level than in the control group. DMRs between these two groups in the fetal blood may contribute to the changes in gene transcription that underlie the increased risk of metabolic disorders, cancers and cardiomyopathy in their offspring.

Fetomaternal microchimerism and genetic diagnosis: On the origins of fetal cells and cell-free fetal DNA in the pregnant woman

During pregnancy several types of fetal cells and fetal stem cells, including pregnancy-associated progenitor cells (PAPCs), traffic into the maternal circulation. Whereas they also migrate to various maternal organs and adopt the phenotype of the target tissues to contribute to regenerative processes, fetal cells also play a role in the pathogenesis of maternal diseases. In addition, cell-free fetal DNA (cffDNA) is detectable in the plasma of pregnant women. Together they constitute the well-known phenomenon of fetomaternal microchimerism, which inspired the concept of non-invasive prenatal testing (NIPT) using maternal blood. An in-depth knowledge concerning the origins of these fetal cells and cffDNA allows a more comprehensive understanding of the biological relevance of fetomaternal microchimerism and has implications for the ongoing expansion of resultant clinical applications.

Genetic analysis of products of conception. Should we abandon classic karyotyping methodology?

OBJECTIVE

To compare the results obtained by the classic and molecular methodology in the analysis of products of conception, the advantages and disadvantages of each method.

METHODS

Retrospective non-randomized analysis of results obtained from product of conception samples submitted to genetic evaluation, from 2012 to 2017. The evaluations were performed using cytogenetics and/or chromosomal microarray analysis or arrays.

RESULTS

Forty samples were analyzed using classic cytogenetics, of which 10% showed no cell growth, 50% had normal results and 40% had abnormalities. Of the 41 cases sent for array analysis it was not possible to obtain results in 7.3%, 39.5% were normal and 60.5% had abnormalities. There was no statistical difference among the results (p=0.89). Most abnormal results were seen till 9 weeks' gestation. The later abnormal miscarriage was seen at 28 weeks' gestation, with karyotype 46,XX,del(15)(q26.2-qter). The results are corroborated by the international literature.

CONCLUSION

Classic cytogenetics and array techniques showed comparable results on the type of alteration observed. Array analysis is preferable to cell culture in delayed abortions, while cytogenetics is more able to show polyploidies. Both have the same growth failure rates when product of conception tissue is not properly collected.

Health behaviors of American pregnant women: a cross-sectional analysis of NHANES 2007-2014

BACKGROUND

This study examined engagement in five health behaviors among pregnant women in the USA.

METHODS

Pregnant women who participated in the National Health and Nutrition Examination Survey 2007-2014 were included in this study. Five health behaviors were examined: adequate fruit and vegetable consumption, prenatal multivitamin use, physical activity, sleep and smoking. Multivariable regressions were used to estimate the odds ratio and 95% confidence interval of characteristics associated with health behaviors.

RESULTS

Among 248 pregnant women, only 10.2% engaged in all five health behaviors and 35.4% consumed adequate fruits and vegetables. For adequate fruit and vegetable consumption, Hispanic and women of 'other' race were more likely to meet the recommendation compared to non-Hispanic white (P = 0.01 and P = 0.03, respectively); high school graduates were less likely to meet the recommendation compared to those with at least some college education or more (P = 0.04).

CONCLUSIONS

Adequate fruit and vegetable consumption among pregnant women was poor and differed by race/ethnicity and education status. Because of the cross-sectional design, we cannot examine engagement in health behaviors continuously throughout pregnancy. Future research with longitudinal data over the course of pregnancy is needed to confirm these results.

Transcriptomic Analysis of Cell-free Fetal RNA in the Amniotic Fluid of Vervet Monkeys (Chlorocebus sabaeus)

NHP are important translational models for understanding the genomic underpinnings of growth, development, fetal programming, and predisposition to disease, with potential for the development of early health biomarkers. Understanding how prenatal gene expression is linked to pre- and postnatal health and development requires methods for assessing the fetal transcriptome. Here we used RNAseq methodology to analyze the expression of cell-free fetal RNA in the amniotic fluid supernatant (AFS) of vervet monkeys. Despite the naturally high level of degradation of free-floating RNA, we detected more than 10,000 gene transcripts in vervet AFS. The most highly expressed genes were H19, IGF2, and TPT1, which are involved in embryonic growth and glycemic health. We noted global similarities in expression profiles between vervets and humans, with genes involved in embryonic growth and glycemic health among the genes most highly expressed in AFS. Our study demonstrates both the feasibility and usefulness of prenatal transcriptomic profiles, by using amniocentesis procedures to obtain AFS and cell-free fetal RNA from pregnant vervets.

Cross-cultural perspectives on decision making regarding noninvasive prenatal testing: A comparative study of Lebanon and Quebec

Noninvasive prenatal testing (NIPT), based on the detection of cell-free fetal DNA in maternal blood, has transformed the landscape of prenatal care by offering clinical benefits (noninvasive, high specificity and sensitivity, early detection of abnormalities) compared to existing prenatal screening tests. NIPT has expanded rapidly and is currently commercially available in most of the world. As NIPT spreads globally, culturally sensitive and ethically sound implementation will require policies that take into consideration the social and cultural context of prenatal testing decisions. In a Western context, the main ethical argument for providing access and public funding of prenatal tests is the promotion of reproductive autonomy (also referred to as "procreative liberty" and "reproductive freedom"), by enabling pregnant women and couples to access information about the fetus in order to choose a certain course of action for pregnancy management (continuation of pregnancy and preparation for birth or termination). So how is the framework of reproductive autonomy operationalized in non-Western cultural contexts? We used Quebec, Canada, and Beirut, Lebanon, for case studies to explore what ethical considerations related to reproductive autonomy should guide the implementation of the test in various cultural contexts. To answer this question, we conducted a qualitative study to (1) explore the perceptions, values, and preferences of pregnant women and their partners about NIPT and (2) examine how these values and perceptions influence reproductive autonomy and decision making in relation to NIPT in these two different cultural settings, Lebanon and Quebec. Our findings may guide health care professionals in providing counseling and in helping women and their partners make better informed prenatal testing decisions. Further, at a policy level, such understanding might inform the development of local guidelines and policies that are appropriate to each context.

Gene overexpression screen for chromosome instability in yeast primarily identifies cell cycle progression genes

Loss of heterozygosity (LOH) in a vegetatively growing diploid cell signals irregularity of mitosis. Therefore, assays of LOH serve to discover pathways critical for proper replication and segregation of chromosomes. We screened for enhanced LOH in a whole-genome collection of diploid yeast strains in which a single gene was strongly overexpressed. We found 39 overexpression strains with substantially increased LOH caused either by recombination or by chromosome instability. Most of them, 32 in total, belonged to the category of "cell division", a broadly defined biological process. Of those, only one, TOP3, coded for an enzyme that uses DNA as a substrate. The rest related to establishment and maintenance of cell polarity, chromosome segregation, and cell cycle checkpoints. Former studies, in which gene deletions were used, showed that an absence of a protein participating in the DNA processing machinery is a potent stimulator of genome instability. As our results suggest, overexpression of such proteins is not comparably damaging as the absence of them. It may mean that the harmful effect of overexpression is more likely to occur in more complex and multistage processes, such as chromosome segregation. We also report a side finding, resulting from the fact that we worked with the yeast strains bearing a 2-micron plasmid. We noted that intense transcription from such a plasmid led to an enhanced rate of an entire chromosome loss (as opposed to LOH produced by recombination). This observation may support models linking segregation of 2-micron plasmids to segregation of chromosomes.

"We want to do everything": how parents represent their experiences with maternal-fetal surgery online

OBJECTIVE

There is little available evidence on how patients make decisions regarding maternal-fetal surgery. We studied online patient narratives for insight on how pregnant women and their partners consider such decisions.

STUDY DESIGN

We used Google search strings and a purposive snowball method to locate patient blogs. We analyzed blog entries using qualitative methods to identify author details, medical information, and common themes.

RESULTS

We located 32 blogs of patients who describe maternal-fetal surgery consultation. Twenty-eight (88%) underwent fetal interventions. Most (91%) explicitly described consultation with maternal-fetal surgery teams; 83% of those depicted making decisions prior to formal consultation. Few expressed regret for decisions made (6%).

CONCLUSIONS AND RELEVANCE

Patients openly share experiences with maternal-fetal surgery online. Women portray their decisions as made outside of formal medical processes and overwhelmingly feel these decisions were "right". As the field of maternal-fetal surgery expands, prospective evaluation of patient decision-making is needed.

Genomic sequencing in clinical practice: applications, challenges, and opportunities

The development of massively parallel sequencing (or next-generation sequencing) has facilitated a rapid implementation of genomic sequencing in clinical medicine. Genomic sequencing (GS) is now an essential tool for evaluating rare disorders, identifying therapeutic targets in neoplasms, and screening for prenatal aneuploidy. Emerging applications, such as GS for preconception carrier screening and predisposition screening in healthy individuals, are being explored in research settings and utilized by members of the public eager to incorporate genomic information into their health management. The rapid pace of adoption has created challenges for all stakeholders in clinical GS, from standardizing variant interpretation approaches in clinical molecular laboratories to ensuring that nongeneticist clinicians are prepared for new types of clinical information. Clinical GS faces a pivotal moment, as the vast potential of new quantities and types of data enable further clinical innovation and complicated implementation questions continue to be resolved.

Moving toward a shared process: The impact of parent experiences on perinatal palliative care

Perinatal palliative care programs seek to support parents expecting a baby diagnosed with a serious medical condition. Clinicians have increasingly recognized the importance of parental perspectives on the medical care mothers and their fetuses and live-born children receive, especially regarding factors influencing individual choices and knowledge of the medical community. We describe, using literature on trisomy 13 and trisomy 18, how information shared between parents and providers can improve perinatal counseling and family support.

First trimester contingent screening for trisomies 21,18,13: is this model cost efficient and feasible in public health system?

PURPOSE

To evaluate the effectiveness of three different first trimester screening models for trisomies 21, 18 and 13, in terms of detection rate, invasive test rate and final costs.

MATERIAL AND METHODS

We analyzed the distribution of risk for trisomies 21, 18 and 13 in a population of 20,831 singleton pregnancies based on maternal age, fetal heart rate, nuchal translucency, free beta human chorionic gonadotropin and pregnancy-associated plasma protein A (Combined test). On the basis of our data, we estimated the performance and cost of screening for trisomies using three different models at specific cutoffs: Combined test; Cell free DNA test and Contingent screening test.

RESULTS

Using Combined test, DR for major trisomies was estimated to be 94.92%, invasive test rate was 6.3%. cfDNA would result in a DR of 97.92%, with an invasive test rate of 3.64%. Contingent screening approach would result in an overall DR of 97.82, with a rate for invasive procedure of 1.36% and a final cost lower than other screening policies (2,338,433 euro vs 5,796,060 of cfDNA and 2,385,473 of Combined test).

CONCLUSIONS

Contingent screening test could be a cost-efficient and feasible first trimester screening test for aneuploidies in public health system.

Recent advances in prenatal genetic screening and testing

The introduction of new technologies has dramatically changed the current practice of prenatal screening and testing for genetic abnormalities in the fetus. Expanded carrier screening panels and non-invasive cell-free fetal DNA-based screening for aneuploidy and single-gene disorders, and more recently for subchromosomal abnormalities, have been introduced into prenatal care. More recently introduced technologies such as chromosomal microarray analysis and whole-exome sequencing can diagnose more genetic conditions on samples obtained through amniocentesis or chorionic villus sampling, including many disorders that cannot be screened for non-invasively. All of these options have benefits and limitations, and genetic counseling has become increasingly complex for providers who are responsible for guiding patients in their decisions about screening and testing before and during pregnancy.

The use of chromosomal microarray for prenatal diagnosis

Chromosomal microarray analysis is a high-resolution, whole-genome technique used to identify chromosomal abnormalities, including those detected by conventional cytogenetic techniques, as well as small submicroscopic deletions and duplications referred to as copy number variants. Because chromosomal microarray analysis has a greater resolution than conventional karyotyping, it can detect deletions and duplications down to a 50- to 100-kb level. The purpose of this document is to discuss the technique, advantages, and disadvantages of chromosomal microarray analysis and its indications and limitations. We recommend the following: (1) that chromosomal microarray analysis be offered when genetic analysis is performed in cases with fetal structural anomalies and/or stillbirth and replaces the need for fetal karyotype in these cases (GRADE 1A); (2) that providers discuss the benefits and limitations of chromosomal microarray analysis and conventional karyotype with patients who are considering amniocentesis and chorionic villus sampling (CVS), and that both options should be available to women who choose to undergo diagnostic testing (GRADE 1B); (3) that pre- and posttest counseling should be performed by trained genetic counselors, geneticists, or other providers with expertise in the complexities of interpreting chromosomal microarray analysis results (Best Practice); (4) that patients be informed that chromosomal microarray analysis does not detect every genetic disease or syndrome and specifically does not detect autosomal-recessive disorders associated with single gene point mutations, as well as that chromosomal microarray analysis can detect consanguinity and nonpaternity in some cases (Best Practice); (5) that patients in whom a fetal variant of uncertain significance is detected by prenatal diagnosis receive counseling from experts who have access to databases that provide updated information concerning genotype-phenotype correlations (Best Practice).

Stillbirth and congenital anomalies in migrants in Europe

The risk of giving birth to a stillborn child or a child with severe congenital anomaly is higher for women who have immigrated to Europe as compared to the majority population in the receiving country. The literature, however, reveals great differences between migrant groups, even within migrants from low-income countries, although there is no clear pattern regarding refugee or non-refugee status. This heterogeneity argues against a particular migration-related explanation. There are social disparities in stillbirth risk worldwide, and it has been suggested that the demonstrated ethnic disparity is a result of the socioeconomic disadvantage most migrants face. Consanguinity has been considered as another cause for the increased stillbirth risk and the high risk of congenital anomaly observed in many migrant groups. Utilization and quality of care during pregnancy and childbirth is the third major aspect. All three factors seem to contribute to stillbirth risk, and they should be considered in clinical practice and public health.

Genome-Wide Sequencing for Prenatal Detection of Fetal Single-Gene Disorders

New sequencing methods capable of rapidly analyzing the genome at increasing resolution have transformed diagnosis of single-gene or oligogenic genetic disorders in pediatric and adult medicine. Targeted tests, consisting of disease-focused multigene panels and diagnostic exome sequencing to interrogate the sequence of the coding regions of nearly all genes, are now clinically offered when there is suspicion for an undiagnosed genetic disorder or cancer in children and adults. Implementation of diagnostic exome and genome sequencing tests on invasively and noninvasively obtained fetal DNA samples for prenatal genetic diagnosis is also being explored. We predict that they will become more widely integrated into prenatal care in the near future. Providers must prepare for the practical, ethical, and societal dilemmas that accompany the capacity to generate and analyze large amounts of genetic information about the fetus during pregnancy.

Population-based trends in prenatal screening and diagnosis for aneuploidy: a retrospective analysis of 38 years of state-wide data

OBJECTIVE

To analyse population-based trends over the entire history of prenatal testing for aneuploidy.

DESIGN

Retrospective analysis of state-wide data sets.

SETTING

Australian state of Victoria with ~70 000 annual births.

POPULATION

All pregnant women undergoing invasive prenatal testing at <25 weeks' gestation from 1976 to 2013.

METHODS

Analysis of three state-wide data sets: (1) Prenatal diagnosis data set of 119 404 amniocenteses and chorionic villus samplings from 1976 to 2013; (2) central serum screening laboratory data set from 1996 to 2013; (3) government birth statistics from 1976 to 2013.

MAIN OUTCOME MEASURES

Annual numbers and uptake rates of invasive prenatal tests and serum screening, indications for invasive prenatal testing, prenatal diagnoses of aneuploidy, diagnostic yield of invasive tests.

RESULTS

Annual numbers of invasive prenatal tests climbed steadily from 1976, then declined from 2000. In 2013, the number of invasive prenatal tests was the lowest in 25 years, while the number of trisomy 21 diagnoses was the highest ever recorded. Annual uptake of serum screening climbed from 1.6 to 83% over 1996-2013. Results from 2013 showed a high diagnostic yield (15.8%) for a low rate of invasive testing (3.4% of births). Over four decades, the number of invasive procedures performed for each diagnosis of major chromosome abnormality declined from 100 to six.

CONCLUSIONS

This study demonstrates historic reductions in the proportion of women undergoing invasive testing and dramatic improvements in diagnostic yield. Monitoring the impact of new prenatal technologies on this progress remains an important research priority.

TWEETABLE ABSTRACT

Invasive prenatal testing has reached historic lows due to dramatic improvements in Down syndrome screening.

Comparing outcomes and costs between contingent and combined first-trimester screening strategies for Down's syndrome

OBJECTIVE

To compare a contingent strategy with a combined strategy for prenatal detection of Down's syndrome (DS) in terms of cost, outcomes and safety.

STUDY DESIGN

The contingent strategy was based on a simulation, removing measurement of the free beta subunit of human chorionic gonadotropin (free βhCG) and calculating the DS risk retrospectively in 32,371 pregnant women who had been screened with the combined strategy in the first trimester. In the contingent strategy, a risk between 1:31 and 1:1000 in the first trimester indicated further testing in the second trimester (alpha-fetoprotein, inhibin A, unconjugated oestriol and free βhCG). The cut-off risk values for the contingent and combined strategies in the first trimester were 1:30 and 1:250, respectively, and the cut-off risk value for integrated screening in the second trimester was 1:250. Costs were compared in terms of avoided DS births, and the ratio of loss of healthy fetuses following invasive procedures per avoided DS birth was calculated.

RESULTS

The combined strategy had sensitivity of 40/44 (90.9%) and a false-positive rate of 2.8%. Corresponding values for the contingent strategy were 39/44 (88.6%) and 1.3%, respectively. Only 11% of pregnant women required tests in the second trimester, and the approximate cost reduction for each avoided DS birth was 5000€. The ratio of lost healthy fetuses following invasive procedures per avoided DS birth improved by up to 0.65.

CONCLUSION

The contingent strategy has similar effectiveness to the combined strategy, but has lower costs and fewer invasive procedures.

Genomic sciences for developmentalists: a merge of science and practice

The etiological forces of development have been a central question for the developmental sciences (however defined) since their crystallization as a distinct branch of scientific inquiry. Although the history of these sciences contains examples of extreme positions capitalizing on either the predominance of the genome (i.e., the accumulation of genetic factors driving development) or the environmentome (i.e., the accumulation of environmental factors driving development), the moderate view of development as the emergence of a person from a particular genome and within a specific context has settled into the driver's seat and is disputed no longer. Yet, although there is a converging theoretical perspective, a gap between this perspective and practice remains. In other words, society needs to translate this position into praxis. This opinion exemplifies the current state of corresponding knowledge in the developmental sciences, with a particular emphasis on the understanding of the role of the genome in child and adolescent development, and offers a set of comments on how this translation is being shaped by the newest technologies in the genomic sciences.

Tay-Sachs disease: current perspectives from Australia

Tay-Sachs disease (TSD) is a fatal, recessively inherited neurodegenerative condition of infancy and early childhood. Although rare in most other populations, the carrier frequency is one in 25 in Ashkenazi Jews. Australian high-school-based TSD preconception genetic screening programs aim to screen, educate, and optimize reproductive choice for participants. These programs have demonstrated high uptake, low psychological morbidity, and have been shown to result in fewer than expected Jewish TSD-affected births over 18 years of operation. The majority of Jewish individuals of reproductive age outside of the high school screening program setting in Australia have not accessed screening. Recent recommendations advocate supplementing the community high school screening programs with general practitioner- and obstetrician-led genetic screening of Ashkenazi Jewish individuals for TSD and other severe recessive diseases for which this group is at risk. Massively parallel DNA sequencing is expected to become the testing modality of choice over the coming years.

Amplification-free sequencing of cell-free DNA for prenatal non-invasive diagnosis of chromosomal aberrations

Cell-free DNA has been used for fetal rhesus factor and sex determination, fetal aneuploidy screening, cancer diagnostics and monitoring, and other applications. However current methods of using cell free DNA require amplification, which leads to allelic dropout and bias especially when starting with small amounts of DNA. Here we describe an amplification-free method for sequencing of cell-free DNA, even from low levels of starting material. We evaluated this method in the context of prenatal diagnosis of fetal aneuploidy and compared it with a PCR-based library preparation method as well as a recently described method using unique molecular identifiers (UMI). All methods performed well, however coverage was increased by the amplification-free method and GC-induced bias was reduced by both the amplification-free method and the UMI method. Future diagnostic applications including whole genome sequencing of cell-free DNA will benefit from amplification-free sequencing.

Counseling Challenges with Variants of Uncertain Significance and Incidental Findings in Prenatal Genetic Screening and Diagnosis

Prenatal genetic screening and testing provides prospective parents information about the health of their fetus. It is offered to find or address an increased risk for chromosomal abnormalities or other genetic conditions in the fetus or to identify the cause of fetal structural abnormalities detected by prenatal imaging. Genome-wide tests, such as the already widely-used chromosomal microarray analysis and emerging diagnostic whole exome and whole genome sequencing, have improved the ability to detect clinically significant findings, but have also increased the chance of detecting incidental findings and variants of uncertain significance. There is an extensive ongoing discussion about optimal strategies for diagnostic laboratories to report such findings and for providers to communicate them with patients. While consensus opinions and guidelines are beginning to appear, they often exclude the prenatal setting, due to its unique set of challenging considerations. These include more limited knowledge of the impact of genetic variants when prospectively detected in an ongoing pregnancy, the absence or limitations of detecting clinically recognizable phenotypes at the time of testing and the different decision-making processes that will ensue from testing. In this review, we examine these challenges within the medical ethical framework unique to prenatal care.

Exome sequencing for gene discovery in lethal fetal disorders--harnessing the value of extreme phenotypes

Massively parallel sequencing has revolutionized our understanding of Mendelian disorders, and many novel genes have been discovered to cause disease phenotypes when mutant. At the same time, next-generation sequencing approaches have enabled non-invasive prenatal testing of free fetal DNA in maternal blood. However, little attention has been paid to using whole exome and genome sequencing strategies for gene identification in fetal disorders that are lethal in utero, because they can appear to be sporadic and Mendelian inheritance may be missed. We present challenges and advantages of applying next-generation sequencing approaches to gene discovery in fetal malformation phenotypes and review recent successful discovery approaches. We discuss the implication and significance of recessive inheritance and cross-species phenotyping in fetal lethal conditions. Whole exome sequencing can be used in individual families with undiagnosed lethal congenital anomaly syndromes to discover causal mutations, provided that prior to data analysis, the fetal phenotype can be correlated to a particular developmental pathway in embryogenesis. Cross-species phenotyping allows providing further evidence for causality of discovered variants in genes involved in those extremely rare phenotypes and will increase our knowledge about normal and abnormal human developmental processes. Ultimately, families will benefit from the option of early prenatal diagnosis.

Hemolytic anemia and progressive neurologic impairment: think about triosephosphate isomerase deficiency

We have reported the first Tunisian case of triosephosphate isomerase (TPI) deficiency in a 2-year-old girl. She was the first child of a nonconsanguineous couple. The disease included a neonatal onset of chronic hemolytic anemia, recurrent low-respiratory infections then progressive neurological involvement. The diagnosis was made after her death from the TPI values of her parents who exhibited intermediate enzyme deficiency. Molecular study of TPI genes showed that the father and the mother are heterozygous for Glu105Asp mutation. Pediatricians must be alert to the differential diagnosis in patients having hemolytic anemia and other concomitant manifestations.

Cell-free nucleic acids as non-invasive biomarkers of gynecological cancers, ovarian, endometrial and obstetric disorders and fetal aneuploidy

BACKGROUND

Proper folliculogenesis is fundamental to obtain a competent oocyte that, once fertilized, can support the acquisition of embryo developmental competence and pregnancy. MicroRNAs (miRNAs) are crucial regulators of folliculogenesis, which are expressed in the cumulus-oocyte complex and in granulosa cells and some can also be found in the bloodstream. These circulating miRNAs are intensively studied and used as diagnostic/prognostic markers of many diseases, including gynecological and pregnancy disorders. In addition, serum contains small amounts of cell-free DNA (cfDNA), presumably resulting from the release of genetic material from apoptotic/necrotic cells. The quantification of nucleic acids in serum samples could be used as a diagnostic tool for female infertility.

METHODS

An overview of the published literature on miRNAs, and particularly on the use of circulating miRNAs and cfDNA as non-invasive biomarkers of gynecological diseases, was performed (up to January 2014).

RESULTS

In the past decade, cell-free nucleic acids have been studied for potential use as biomarkers in many diseases, particularly in gynecological cancers, ovarian and endometrial disorders, as well as in pregnancy-related pathologies and fetal aneuploidy. The data strongly suggest that the concentration of cell-free nucleic acids in serum from IVF patients or in embryo culture medium could be related to the ovarian hormone status and embryo quality, respectively, and be used as a non-invasive biomarker of IVF outcome.

CONCLUSIONS

The profiling of circulating nucleic acids, such as miRNAs and cfDNA, opens new perspectives for the diagnosis/prognosis of ovarian disorders and for the prediction of IVF outcomes, namely (embryo quality and pregnancy).

Noninvasive prenatal screening by next-generation sequencing

Noninvasive prenatal screening (NIPS) has emerged as a highly accurate method of screening for fetal Down syndrome, with a detection rate and specificity approaching 100%. Challenging the widespread use of this technology are cost and the paradigm shift in counseling that accompanies any emerging technology. The expense of the test is expected to decrease with increased utilization, and well beyond the current NIPS technology, its components (fetal genome measurements, sequencing technology, and bioinformatics) will be utilized alone or in combinations to interrogate the fetal genome. The end goal is simple: to offer patients information early in pregnancy about fetal genomes without incurring procedural risks. This will allow patients an opportunity to make informed reproductive and pregnancy management decisions based on precise fetal genomic information.

Placental mosaicism for Trisomy 13: a challenge in providing the cell-free fetal DNA testing

PURPOSE

We investigated the disagreement between the positive cell-free fetal DNA test for trisomy 13 and the standard cytogenetic diagnosis of one case.

METHODS

Cell-free fetal DNA testing was performed by massively parallel sequencing. We used conventional cytogenetic analysis to confirm the commercial cell-free fetal DNA testing. Additionally, postnatal fluorescent in situ hybridization (FISH) testing was performed on placental tissues.

RESULTS

The cell-free fetal DNA testing result was positive for trisomy 13. G-banded analysis of amniotic fluid was normal, 46, XY. FISH testing of tissues from four quadrants of the placenta demonstrated mosaicism for trisomy 13.

CONCLUSIONS

A positive cell-free fetal DNA testing result may not be representative of the fetal karyotype because of placental mosaicism. Cytogenetic analysis should be performed when abnormal cell-free fetal DNA test results are obtained.

Genomic microarrays in prenatal diagnosis

The application of microarray-based techniques for the diagnosis of genomic rearrangements has been steadily growing in popularity since its introduction in 2004. Given the many advantages of these techniques over conventional cytogenetics, there is increasing pressure towards their application in prenatal diagnosis. However, there remain several important issues that must be addressed. For example, microarray-based techniques (comparative genomic hybridization-based arrays and single nucleotide polymorphism-based arrays) allow detection of even very small genomic imbalances that can determine pathological clinical conditions. In addition, there are other copy number variations which represent normal variation, with no detectable effects on phenotype. Given the still incomplete knowledge of the changes in our genome and the associated phenotypes, microarray-based diagnosis is likely to find variants of uncertain and unknown clinical significance. The interpretation of these variants is now a major challenge for the medical geneticist, who often find it difficult to establish precise correlations between genotype and phenotype. There is sufficient available evidence to justify the use of microarray-based diagnostics for a select number of specific conditions, but there is also an inevitable trend towards ever wider application. It is very important that this drift does not progress in an unchecked and uncontrolled manner under the thrust of commercial interests. Therefore, we recommend that scientific societies be vigilant and take an advisory role in the adopting of these technologies as new scientific knowledge becomes available.

Pre-analytical conditions in non-invasive prenatal testing of cell-free fetal RHD

Background

Non-invasive prenatal testing of cell-free fetal DNA (cffDNA) in maternal plasma can predict the fetal RhD type in D negative pregnant women. In Denmark, routine antenatal screening for the fetal RhD gene (RHD) directs the administration of antenatal anti-D prophylaxis only to women who carry an RhD positive fetus. Prophylaxis reduces the risk of immunization that may lead to hemolytic disease of the fetus and the newborn. The reliability of predicting the fetal RhD type depends on pre-analytical factors and assay sensitivity. We evaluated the testing setup in the Capital Region of Denmark, based on data from routine antenatal RHD screening.

Methods

Blood samples were drawn at gestational age 25 weeks. DNA extracted from 1 mL of plasma was analyzed for fetal RHD using a duplex method for exon 7/10. We investigated the effect of blood sample transportation time (n = 110) and ambient outdoor temperatures (n = 1539) on the levels of cffDNA and total DNA. We compared two different quantification methods, the delta Ct method and a universal standard curve. PCR pipetting was compared on two systems (n = 104).

Results

The cffDNA level was unaffected by blood sample transportation for up to 9 days and by ambient outdoor temperatures ranging from -10°C to 28°C during transport. The universal standard curve was applicable for cffDNA quantification. Identical levels of cffDNA were observed using the two automated PCR pipetting systems. We detected a mean of 100 fetal DNA copies/mL at a median gestational age of 25 weeks (range 10–39, n = 1317).

Conclusion

The setup for real-time PCR-based, non-invasive prenatal testing of cffDNA in the Capital Region of Denmark is very robust. Our findings regarding the transportation of blood samples demonstrate the high stability of cffDNA. The applicability of a universal standard curve facilitates easy cffDNA quantification.

Cellular fetal microchimerism in preeclampsia

Previous studies have shown elevated concentrations of free fetal DNA and erythroblasts in maternal circulation in women with preeclampsia compared with those with normal pregnancy. Pluripotent and immunocompetent fetal cells also transfer to the maternal circulation during pregnancy, but whether concentrations of fetal mononuclear cells also differed in preeclampsia was unknown. We sought to quantify cellular fetal microchimerism in maternal circulation in women with preeclampsia and healthy controls. We studied women with preeclampsia and compared them with women with healthy pregnancies at similar gestational age. To identify a targetable polymorphism unique to the fetus to quantify fetal microchimerism, participants and family members were genotyped for the human leukocyte antigen loci DRB1, DQA1, and DQB1, as well as several other polymorphisms. A panel of polymorphism-specific quantitative polymerase chain reaction assays was used to identify and quantify fetal microchimerism in maternal peripheral blood mononuclear cells. Of 53 preeclampsia samples tested for cellular fetal microchimerism, 17 (32%) were positive when compared with 6 of 57 (6%) control samples (unadjusted odds ratio for detection, 4.0; 95% confidence interval, 1.5-11.1; P=0.007). The concentration of cellular fetal microchimerism (expressed as genome equivalents of fetal microchimerism per 100,000 maternal genome equivalents) was also higher among women with preeclampsia: median 0.0, mean 5.7, range 0 to 153.7, compared with those with controls: median 0.0, mean 0.3, range 0 to 9.1, P=0.002. We conclude that women with preeclampsia harbor cellular fetal microchimerism more commonly and at higher concentrations compared with women with uncomplicated pregnancy. The functional capacity and phenotype of these fetal cells are not yet known.