Comprehensive evaluation of genetic variants using chromosomal microarray analysis and exome sequencing in fetuses with congenital heart defect

OBJECTIVE

To evaluate comprehensively, using chromosomal microarray analysis (CMA) and exome sequencing (ES), the prevalence of chromosomal abnormalities and sequence variants in unselected fetuses with congenital heart defect (CHD) and to evaluate the potential diagnostic yields of CMA and ES for different CHD subgroups.

METHODS

This was a study of 360 unselected singleton fetuses with CHD detected by echocardiography, referred to our department for genetic testing between February 2018 and December 2019. We performed CMA, as a routine test for aneuploidy and copy number variations (CNV), and then, in cases without aneuploidy or pathogenic CNV on CMA, we performed ES.

RESULTS

Overall, positive genetic diagnoses were made in 84 (23.3%) fetuses: chromosomal abnormalities were detected by CMA in 60 (16.7%) and sequence variants were detected by ES in a further 24 (6.7%) cases. The detection rate of pathogenic and likely pathogenic genetic variants in fetuses with non-isolated CHD (32/83, 38.6%) was significantly higher than that in fetuses with isolated CHD (52/277, 18.8%) (P < 0.001), this difference being due mainly to the difference in frequency of aneuploidy between the two groups. The prevalence of a genetic defect was highest in fetuses with an atrioventricular septal defect (36.8%), ventricular septal defect with or without atrial septal defect (28.4%), conotruncal defect (22.2%) or right ventricular outflow tract obstruction (20.0%). We also identified two novel missense mutations (c.2447G>C, p.Arg816Pro; c.1171C>T, p.Arg391Cys) and a new phenotype caused by variants in PLD1.

CONCLUSIONS

Chromosomal abnormalities were identified in 16.7% and sequence variants in a further 6.7% of fetuses with CHD. ES should be offered to all pregnant women with a CHD fetus without chromosomal abnormality or pathogenic CNV identified by CMA, regardless of whether the CHD is isolated. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.

Complex mosaic blastocysts after preimplantation genetic testing: prevalence and outcomes after re-biopsy and re-vitrification

RESEARCH QUESTION

What is the incidence of complex mosaic in preimplantation genetic testing (PGT) blastocysts and can it be managed in clinical practice?

DESIGN

A retrospective study of PGT cycles conducted between January 2018 and October 2019 at a single centre. Biopsies of blastocysts were collected and analysed by next-generation sequencing (NGS). Complex mosaic blastocysts were defined as those with three or more mosaic chromosomes. The cryopreserved complex mosaic blastocysts underwent a second round of biopsy, NGS analysis and vitrification. The euploid blastocysts identified by the re-biopsy were warmed again for embryo transfer. The main outcomes included the prevalence of the complex mosaic and the ongoing pregnancy rate.

RESULTS

The prevalence of the complex mosaic was 2.4% (437/17,979). The prevalence of the complex mosaic was not associated with maternal age and morphological quality. A total of 89 complex mosaic blastocysts underwent re-biopsy and 96.6% (86/89) survived the first warming. For the re-biopsy samples, 61.6% (53/86) were euploid. The poor-quality blastocysts had higher rates of aneuploidy compared with good-quality blastocysts. The survival rate for blastocysts undergoing the second warming was 100% (18/18) and resulted in an ongoing pregnancy rate of 38.9% (7/18) as well as the birth of six healthy infants.

CONCLUSION

Re-biopsy may rescue blastocysts with development potential for transfer and improve the cumulative pregnancy rate per stimulation cycle in patients containing complex mosaic blastocysts.

Next-Generation Sequencing-Based Pre-Implantation Genetic Testing for Aneuploidy (PGT-A): First Report from Saudi Arabia

Recently, high-throughput next-generation sequencing (NGS)-based preimplantation genetic testing for aneuploidies techniques came into use. This technique is essential for successful embryo transfer and accomplishing pregnancy, thus reducing the time and cost of additional cycles. In this study, we describe our first experience in introducing an NGS-based preimplantation genetic testing for aneuploidy (PGT-A) service using next-generation sequencing in King Abdulaziz Medical City located in Riyadh, Saudi Arabia. Our main goal was to report the successful implementation of this new technology in clinical practice and highlight the factors that may affect the results. In total, 200 blastomere biopsies were obtained from 36 in vitro fertilization (IVF) cycles from Saudi couples suffering from prolonged infertility or recurrent embryo transfer failure. NGS-based PGT-A was performed in all embryos. The results were analyzed in five age groups, showing that aneuploidy rates increased with maternal age. Moreover, the results also showed that complex abnormal embryos with (2-5) aneuploidy are the most common type of embryos. Additionally, our data showed that chromosome 16-related abnormality was the most frequent abnormality detected among all reported abnormalities. In conclusion, our study suggests that NGS-based PGT-A is an applicable and reliable technique for routine-based embryo screening, especially for couples suffering from recurrent miscarriages or multiple embryo transfer failures.

Clinical utility of expanded non-invasive prenatal screening and chromosomal microarray analysis in high-risk pregnancy

OBJECTIVE

To evaluate the utility of expanded non-invasive prenatal screening (NIPS), compared with chromosomal microarray analysis (CMA), for the detection of chromosomal abnormalities in high-risk pregnancies.

METHODS

This was a multicenter retrospective study of singleton pregnancies at high risk for chromosomal abnormality. Patients who underwent expanded NIPS and CMA sequentially during pregnancy from 2015 to 2019 were included in the analysis. Pregnancies with a positive result for sex chromosome aneuploidy were excluded as the full details could not be retrieved. The utility of expanded NIPS and CMA for detection of chromosomal abnormalities in this cohort was compared by assessing the concordance between the results.

RESULTS

Of the 774 included high-risk pregnancies, 550 (71.1%) had a positive NIPS result, while a positive CMA result was detected in 308 (39.8%) cases. The rate of full or partial concordance between NIPS and CMA was 82.2%, 59.6% and 25.0% for trisomies 21, 18 and 13, respectively. For rare aneuploidies and segmental imbalances, NIPS and CMA results were fully or partially concordant in 7.5% and 33.3% of cases, respectively. Copy-number variants < 5 Mb were detected more often by CMA, with an incidence of 7.9% (61/774) compared with 3.1% (24/774) by NIPS. A genetic aberration was detected by CMA in 1 in 17 (5.8%) high-risk pregnancies that had a negative or non-reportable NIPS result.

CONCLUSION

CMA allows for comprehensive detection of genome-wide chromosomal abnormalities in high-risk pregnancies. CMA should be offered instead of expanded NIPS for high-risk pregnancies. Copyright © 2020 ISUOG. Published by John Wiley & Sons Ltd.

Molecular pathogenesis of spontaneous abortions - Whole genome copy number analysis and expression of angiogenic factors

OBJECTIVE

To study two major molecular alterations in spontaneous abortions (SA) with unexplained etiology - fetal genomic anomalies and the endometrial expression of main angiogenic factors VEGFA/VEGFR2 and chemokines SDF-1/CXCR4.

MATERIALS AND METHODS

Whole genome copy number analysis by arrayCGH or Next Generation Sequencing (NGS) was applied for detection of fetal genomic imbalances. The abortive decidua of SA without fetal aneuploidies was further investigated for expression levels of the abovementioned factors using real time PCR analysis. A total of 30 abortive materials were collected from spontaneous abortions after exclusion of known predisposing factors.

RESULTS

In 21 of 30 spontaneous abortions (70%), genomic anomalies were discovered by whole genome copy number analysis. Numerical anomalies were detected in 90% of aberrant cases, and in 10% - structural aberrations were revealed. An increased expression for essential factors of angiogenesis was identified in spontaneous abortions' tissues - 3.44 times for VEGFA and 10.29 times for VEGFR2. We found an average of 14 times increase in the expression levels of SDF-1 and 3.21 times for its receptor CXCR4.

CONCLUSION

We could suggest the occurrence of increased angiogenesis in SA without fetal aneuploidies, compared to the control tissues, which could lead to increased oxidative stress and fetal loss.

State-wide utilization and performance of traditional and cell-free DNA-based prenatal testing pathways: the Victorian Perinatal Record Linkage (PeRL) study

OBJECTIVES

To perform individual record linkage of women undergoing screening with cell-free DNA (cfDNA), combined first-trimester screening (CFTS), second-trimester serum screening (STSS), and/or prenatal and postnatal cytogenetic testing with the aim to (1) obtain population-based estimates of utilization of prenatal screening and invasive diagnosis, (2) analyze the performance of different prenatal screening strategies, and (3) report the residual risk of any major chromosomal abnormality following a low-risk aneuploidy screening result.

METHODS

This was a retrospective study of women residing in the state of Victoria, Australia, who underwent prenatal screening or invasive prenatal diagnosis in 2015. Patient-funded cfDNA referrals from multiple providers were merged with state-wide results for government-subsidized CFTS, STSS and invasive diagnostic procedures. Postnatal cytogenetic results from products of conception and infants up to 12 months of age were obtained to ascertain cases of false-negative screening results and atypical chromosomal abnormalities. Individual record linkage was performed using LinkageWiz^TM .

RESULTS

During the study period, there were 79 140 births and 66 166 (83.6%) women underwent at least one form of aneuploidy screening. Linkage data were complete for 93.5% (n = 61 877) of women who underwent screening, and of these, 73.2% (n = 45 275) had CFTS alone, 20.2% (n = 12 486) had cfDNA alone; 5.3% (n = 3268) had STSS alone, 1.3% (n = 813) had both CFTS and cfDNA, and < 0.1% (n = 35) had both STSS and cfDNA. CFTS had a combined sensitivity for trisomies 21 (T21), 18 (T18) and 13 (T13) of 89.57% (95% CI, 82.64-93.93%) for a screen-positive rate (SPR) of 2.94%. There were 12 false-negative results in the CFTS pathway, comprising 10 cases of T21, one of T18 and one of T13. cfDNA had a combined sensitivity for T21, T18 and T13 of 100% (95% CI, 95.00-100%) for a SPR of 1.21%. When high-risk cfDNA results for any chromosome (including the sex chromosomes) and failed cfDNA tests were treated as screen positives, the SPR for cfDNA increased to 2.42%. The risk of any major chromosomal abnormality (including atypical abnormalities) detected on prenatal or postnatal diagnostic testing after a low-risk screening result was 1 in 1188 for CFTS (n = 37) and 1 in 762 for cfDNA (n = 16) (P = 0.13). The range of chromosomal abnormalities detected after a low-risk cfDNA result included pathogenic copy-number variants (n = 6), triploidy (n = 3), rare autosomal trisomies (n = 3) and monosomy X (n = 2).

CONCLUSIONS

Our state-wide record-linkage analysis delineated the utilization and clinical performance of the multitude of prenatal screening pathways available to pregnant women. The sensitivity of cfDNA for T21, T18 and T13 was clearly superior to that of CFTS. While there was no statistically significant difference in the residual risk of any major chromosomal abnormality after a low-risk CFTS or cfDNA result, there were fewer live infants diagnosed with a major chromosomal abnormality in the cfDNA cohort. These data provide valuable population-based evidence to inform practice recommendations and health policies. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Association between mild stimulated IVF/M cycle and early embryo arrest in sub fertile women with/without PCOS

BACKGROUND

The in vitro maturation (IVM) technique has physical and financial benefits, but a lower efficiency and outcome that is still unclear whether it is related to polycystic ovary syndrome (PCOS) itself or the IVM procedure. In this study, we analyzed the clinical and laboratory outcomes of an optimized IVM protocol in patients with and without PCOS. We also discussed the possible reasons for early embryo arrest in the IVM cycle.

METHODS

This prospective study involved 58 PCOS patients and 56 non-PCOS patients who underwent mild stimulated IVF combined IVM (IVF/M) cycles. The clinical and laboratory outcomes were compared between the two groups. Also, metaphase II (MII) oocytes were obtained after IVM from the two groups, and in vivo MII oocytes randomly collected from IVF patients were examined for mitochondrial function using a laser scanning confocal microscope (LSCM). The aneuploidy rate for arrested cleavage embryos from IVM and IVF oocytes were screened using Next Generation Sequencing (NGS).

RESULTS

Mildly stimulated IVF/M resulted in cumulative clinical pregnancy and implantation rates (40.2, 28.7% in the PCOS group vs. 41.9, 36% in the non-PCOS group), respectively. The blastocyst formation rates were comparable (28% vs. 28.2%) in PCOS and non-PCOS groups, respectively. Using LSCM, there was a significant decrease in the mitochondrial membrane potential of IVM oocytes compared with the control IVF oocytes (P < 0.001), but no significant difference between the PCOS and non-PCOS groups. The NGS showed that the aneuploidy rates were comparable (75, 75, and 66.6%) in IVM-PCOS, IVM-non-PCOS, and control IVF arrested embryos, respectively.

CONCLUSIONS

The mildly stimulated IVF/M protocol produced acceptable clinical outcomes in PCOS and non-PCOS patients. IVM itself rather than the PCOS condition adversely affected the embryo development through its effect on mitochondrial function, which appeared to be a possible cause for the embryo arrest in the IVM cycles rather than chromosomal aneuploidy.

Should cell-free DNA testing be used in pregnancy with increased fetal nuchal translucency?

OBJECTIVE

To assess the frequency of atypical chromosomal and submicroscopic anomalies, as well as fetal structural abnormalities, observed on first-trimester ultrasound scan in fetuses with nuchal translucency (NT) thickness > 99^th centile, in order to evaluate the suitability of using standard cell-free DNA (cfDNA) testing as the sole screening test in these pregnancies.

METHODS

This was a retrospective cohort study of 226 fetuses with NT > 99^th centile at 11-14 weeks' gestation, between January 2013 and December 2017, in a clinical setting in which greater than 95% of pregnant women receive first-trimester combined screening. All patients underwent genetic testing by means of quantitative fluorescence polymerase chain reaction and chromosomal microarray analysis, mainly in chorionic villus samples. We assessed the theoretical yield of two cfDNA testing models, targeted cfDNA (chromosomes 21, 18 and 13) and extended cfDNA (chromosomes 21, 18, 13 and sex chromosomes), and compared it with that of cytogenetic testing and ultrasound assessment in the first and second or third trimesters.

RESULTS

In the 226 fetuses analyzed, cytogenetic testing revealed 84 (37%) anomalies, including 68 typical aneuploidies (involving chromosomes 13, 18 or 21), six sex chromosome aneuploidies (four cases of monosomy X and two of trisomy X), three clinically relevant atypical chromosomal anomalies (one trisomy 22, one trisomy 21 mosaicism and one unbalanced translocation), five submicroscopic pathogenic variants and two cases with Noonan syndrome. Targeted and extended cfDNA testing would miss at least 12% (10/84) and 19% (16/84), respectively, of genetic anomalies, accounting for 4.4% and 7.1% of the fetuses with an increased NT, respectively. Finally, of the 142 fetuses with no identified genetic anomaly, a major fetal malformation was observed in 15 (10.6%) fetuses at the early anomaly scan, and in 19 (13.4%) in the second or third trimester.

CONCLUSIONS

cfDNA does not appear to be the appropriate genetic test in fetuses with NT > 99^th centile, given that it would miss 12-19% of genetic anomalies in this group. Additionally, first-trimester ultrasound will identify a major structural abnormality in 11% of the fetuses with NT > 99^th centile and no genetic anomaly. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Chromosomal abnormalities detected by karyotyping and microarray analysis in twins with structural anomalies

OBJECTIVES

To evaluate the incidence and types of chromosomal abnormalities detected in twins with structural anomalies and compare their distribution according to chorionicity and amnionicity and by structural-anomaly type. The added value of chromosomal microarray analysis (CMA) over conventional karyotyping in twins was also estimated.

METHODS

This was a single-center, retrospective analysis of 534 twin pregnancies seen over an 11-year period, in which one or both fetuses were diagnosed with congenital structural anomalies on ultrasound. The ultrasound findings and invasive prenatal diagnostic results were reviewed. Twin pregnancies were categorized as monochorionic monoamniotic (MCMA), monochorionic diamniotic (MCDA) or dichorionic diamniotic (DCDA). Chromosomal abnormalities detected by G-banding karyotyping and/or CMA were analyzed by chorionicity and amnionicity and by structural-anomaly type.

RESULTS

The 534 twin pairs analyzed comprised 25 pairs of MCMA, 112 pairs of MCDA and 397 pairs of DCDA twins. Of the 549 fetuses affected by structural anomalies, 432 (78.7%) underwent invasive prenatal testing and cytogenetic results were obtained. The incidence of overall chromosomal abnormalities in the DCDA fetuses (25.4%) was higher than that in the MCMA (3.7%) and MCDA (15.3%) fetuses. The incidence of aneuploidy was significantly higher in the DCDA group (22.8%) than in the MCMA (0.0%) and MCDA (12.4%) groups. The incidence of chromosomal abnormalities detected in fetuses, with anomalies of the cardiovascular, faciocervical, musculoskeletal, genitourinary and gastrointestinal systems, was higher in the DCDA group than in the MCDA group. In both the DCDA and MCDA groups, hydrops fetalis was associated with the highest incidence of chromosomal abnormality; of these fetuses, 67.6% had Turner syndrome (45,X). Pathogenic copy-number variations (CNVs) undetectable by karyotyping were identified by CMA in five (2.0%; 95% CI, 0.3-3.7%) DCDA fetuses. No pathogenic CNVs were found in MCMA and MCDA twins.

CONCLUSIONS

Dichorionic twins with structural anomalies have a higher risk of chromosomal abnormalities, especially aneuploidies, than do monochorionic twins. The incremental diagnostic yield of CMA over karyotyping seems to be lower (2.0%) in twins than that reported in singleton pregnancy. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Prenatally diagnosed de novo segmental amplification or deletion by microarray-based comparative genomic hybridization: A retrospective study

OBJECTIVE

Prenatal diagnosis of de novo segmental amplification or deletion by microarray-based comparative genomic hybridization (array CGH) is uncommon. The study aimed to know about the incidence, abnormal ultrasound findings, and pregnancy outcomes of prenatally diagnosed de novo segmental amplification or deletion by array CGH.

MATERIALS AND METHODS

Between January 2014 and December 2017, we analyzed pregnant women who received prenatal array CGH (SurePrint G3 Human CGH Microarray Kit, 8 × 60K) at Chang Gung Memorial Hospital, Taiwan. Clinical data on maternal age, reason for fetal karyotyping, sonographic findings, gestational age at delivery, newborn birth weight, and associated anomalies, if any, were obtained by chart review.

RESULTS

A total of 836 specimens (814 amniotic fluid samples, 4 cord blood samples, 18 chorionic villi samples) were analyzed by array CGH during the study period. Of the 56 cases with abnormal array CGH results, 40 had segmental amplification or deletion, 12 had trisomy, three had monosomy, and one had sex chromosome aneuploidy. Of these 40 cases with segmental amplification or deletion, 30 were inherited and 10 were de novo occurrences. The incidence of de novo segmental amplification or deletion was 1.2% (10/836). Abnormal prenatal ultrasound findings occurred in 40% (4/10) of de novo segmental amplification or deletion cases. Among these 10 pregnancies, nine were voluntarily terminated between 22 and 26 weeks of gestation and one was delivered at term.

CONCLUSIONS

Prenatal diagnosis of de novo segmental amplification or deletion by array CGH raises important genetic counseling issues. In our series, the incidence of de novo segmental amplification or deletion in prenatal samples was 1.2%. Abnormal prenatal sonographic findings occurred in 40% of these de novo segmental amplification or deletion cases. Of these de novo segmental amplification or deletion pregnancies, 90% were voluntarily terminated.

Microarray and RASopathy-disorder testing in fetuses with increased nuchal translucency

OBJECTIVES

To determine the incidence of chromosomal abnormalities, submicroscopic chromosomal abnormalities and RASopathy-disorder (RD) pathogenic variants in a cohort of pregnancies with nuchal translucency thickness (NT) ≥ 3.5 mm, and to propose a clinical protocol for surveillance of this group of patients.

METHODS

This was a retrospective chart review of patients referred to The Prenatal Diagnosis and Medical Genetics Program at Mount Sinai Hospital between January 2013 and December 2015, due to NT ≥ 3.5 mm, who underwent chorionic villus sampling or amniocentesis. Patients underwent extensive genetic counseling prior to invasive procedures and testing. Quantitative fluorescence polymerase chain reaction (QF-PCR) was performed as the first-line test for aneuploidy. If the result was negative, patients underwent karyotyping and/or chromosomal microarray analysis (CMA), and if the findings were normal, they had testing for RD pathogenic variants, which included nine known genes. Patients also underwent detailed fetal ultrasound examinations and echocardiography, performed by expert operators.

RESULTS

A total of 226 eligible patients were identified. In 116/226 (51.3%) patients, QF-PCR identified a chromosomal aneuploidy. The remaining 110/226 (48.7%) patients had further genetic testing. Karyotyping/CMA detected an abnormal/pathogenic cytogenetic result in 9/110 (8.2%) patients, as well as five variants of unknown significance (VOUS). RD testing yielded three pathogenic variants (3/103), giving a detection rate of 2.9%, and one VOUS. The optimal NT cut-off for RD screening was 7.9 mm in this population. In 92/110 (83.6%) patients, the genetic investigations were normal. Of these pregnancies, an early (14-16 weeks' gestation) detailed fetal ultrasound examination identified a structural abnormality in 24 (26.1%), 15 (16.3%) had an abnormal detailed ultrasound examination at 18-22 weeks' gestation and fetal echocardiography showed a cardiac abnormality in nine (9.8%). The birth outcome in the 83 pregnancies that had normal genetic investigations and known outcome included seven (8.4%) cases of termination of pregnancy, seven (8.4%) cases of intrauterine fetal death and 69 (83.1%) cases of live birth. Nine (9.8%) patients were lost to follow-up.

CONCLUSIONS

Both CMA and molecular testing for RD are important investigations in pregnancies with NT ≥ 3.5 mm. The use of genetic testing combined with fetal ultrasound examination provides valuable information that can influence pregnancy outcome, and provide recurrence risks, in this patient population. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Non-invasive cell-free fetal DNA testing for aneuploidy: multicenter study of 31 515 singleton pregnancies in southeastern China

OBJECTIVE

To analyze the non-invasive prenatal testing (NIPT) for aneuploidy results of 31 515 singleton pregnancies in Fujian province, southeastern China, and assess its performance in low-, moderate- and high-risk pregnancies.

METHODS

Women were categorized into groups according to whether their risk for fetal abnormality was low, moderate or high. Cell-free plasma DNA extracted from peripheral blood samples was subjected to low-coverage whole-genome sequencing. Standard Z-score analysis of the mapped sequencing reads was used to identify fetal aneuploidy, including the three main trisomies (T21, T18 and T13) and sex chromosome aneuploidy (SCA). NIPT-positive results were confirmed by amniocentesis and karyotyping. The performance of NIPT for detection of T21, T18, T13 and SCA was assessed by calculating the sensitivity and specificity.

RESULTS

The rate of chromosomal abnormality detected by NIPT in the study population was 1.38%. A higher rate of chromosomal abnormality was found in the high-risk group (1.57%) compared to the moderate-risk (1.05%) and low-risk (1.18%) groups (P < 0.05). Sensitivity and specificity, respectively, were 98.96% (95/96) and 99.94% (31 274/31 292) for detection of T21, 100% (25/25) and 99.96% (31 352/31 363) for T18, 100% (7/7) and 99.97% (31 373/31 381) for T13 and 100% (61/61) and 99.74% (31 245/31 327) for SCA. Positive predictive values were high for T21 (84.07%) and T18 (69.44%) and moderate for T13 (46.67%) and SCA (42.66%).

CONCLUSION

Our findings support the application of NIPT for reliable and accurate testing of the general population of reproductive-age women for clinically significant fetal aneuploidy. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Chromosomal rearrangements as a source of new gene formation in Drosophila yakuba

The origins of new genes are among the most fundamental questions in evolutionary biology. Our understanding of the ways that new genetic material appears and how that genetic material shapes population variation remains incomplete. De novo genes and duplicate genes are a key source of new genetic material on which selection acts. To better understand the origins of these new gene sequences, we explored the ways that structural variation might alter expression patterns and form novel transcripts. We provide evidence that chromosomal rearrangements are a source of novel genetic variation that facilitates the formation of de novo exons in Drosophila. We identify 51 cases of de novo exon formation created by chromosomal rearrangements in 14 strains of D. yakuba. These new genes inherit transcription start signals and open reading frames when the 5' end of existing genes are combined with previously untranscribed regions. Such new genes would appear with novel peptide sequences, without the necessity for secondary transitions from non-coding RNA to protein. This mechanism of new peptide formations contrasts with canonical theory of de novo gene progression requiring non-coding intermediaries that must acquire new mutations prior to loss via pseudogenization. Hence, these mutations offer a means to de novo gene creation and protein sequence formation in a single mutational step, answering a long standing open question concerning new gene formation. We further identify gene expression changes to 134 existing genes, indicating that these mutations can alter gene regulation. Population variability for chromosomal rearrangements is considerable, with 2368 rearrangements observed across 14 inbred lines. More rearrangements were identified on the X chromosome than any of the autosomes, suggesting the X is more susceptible to chromosome alterations. Together, these results suggest that chromosomal rearrangements are a source of variation in populations that is likely to be important to explain genetic and therefore phenotypic diversity.

Added value of chromosomal microarray analysis over conventional karyotyping in stillbirth work-up: systematic review and meta-analysis

OBJECTIVE

To assess the added value of chromosomal microarray analysis (CMA) over conventional karyotyping to assess the genetic causes in stillbirth.

METHODS

To identify relevant studies, published in English or Spanish and without publication time restrictions, we performed a systematic search of PubMed, SCOPUS and ISI Web of Science databases, The Cochrane Library and the PROSPERO register of systematic reviews, for case series of fetal loss ≥ 20 weeks of gestation, with normal or suspected normal karyotype, undergoing CMA and with at least five subjects analyzed. To investigate quality, two reviewers evaluated independently the risk of bias using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. For the meta-analysis, the incremental yield of CMA over karyotyping was assessed by single-proportion analysis using a random-effects model (weighting by inverse variance). We assessed heterogeneity between studies and performed a sensitivity analysis and a subgroup analysis of structurally abnormal (malformed or growth-restricted) and normal fetuses.

RESULTS

Included in the meta-analysis were seven studies involving 903 stillborn fetuses which had normal karyotype. The test success rate achieved by conventional cytogenetic analysis was 75%, while that for CMA was 90%. The incremental yield of CMA over conventional karyotyping based on the random-effects model was 4% (95% CI, 3-5%) for pathogenic copy-number variants (pCNVs) and 8% (95% CI, 4-17%) for variants of unknown significance. Subgroup analysis showed a 6% (95% CI, 4-10%) incremental yield of CMA for pCNVs in structurally abnormal fetuses and 3% (95% CI, 1-5%) incremental yield for those in structurally normal fetuses. The pCNV found most commonly was del22q11.21.

CONCLUSIONS

CMA, incorporated into the stillbirth work-up, improves both the test success rate and the detection of genetic anomalies compared with conventional karyotyping. To achieve a genetic diagnosis in stillbirth is particularly relevant for the purpose of counseling regarding future pregnancies. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.

The application of PGT-A for carriers of balanced structural chromosomal rearrangements

The aim of this study was to analyze differences in chromosomal aberrations and euploidy in embryos of each translocation type and gender of carrier in the case series of 10 couples with balanced translocations who underwent IVF with embryos trophectoderm (TE) biopsy and PGT-A to detect chromosomal aberrations. This is a Case Series (Retrospective study). In each case, controlled ovarian hyperstimulation, oocyte insemination with intracytoplasmic sperm injection (ICSI) and cultivation gave multiple blastocysts, that underwent trophectoderm (TE) biopsy with PGT-A analysis using aCGH and NGS. Number of total unbalanced translocations compared to the number of sporadic aneuploid embryos was 39.6% to 39.6% (50% to 50% of all 37 aneuploid embryos). The highest euploidy rate was in male carrier group - 26.7% and the lowest in the Robertsonian translocation carrier group - 18.2%. Sporadic aneuploidy - 68.2% was highest in Robertsonian translocation carrier group and lowest in female group - 11.1%. Chromosomal aberrations related to translocation were highest in female carrier group - 77.8% and lowest in Robertsonian translocation carrier group - 13.6%. Our study showed that expectancy of total embryo aneuploidy rates will be higher in carriers, than in people with normal karyotype. The prevalence of chromosomal aberrations related to translocation was 4.5 times higher in Reciprocal carrier group than in Robertsonian translocation carrier group. Among maternal and paternal carrier groups, the embryos from female carriers had the lowest euploidy rate, unbalanced translocation rate 4.7 times higher than in the male carrier group and higher total aneuploidy rates.

Prenatal diagnosis and pregnancy outcome analysis of thickened nuchal fold in the second trimester

To summarize the results of prenatal diagnoses and pregnancy outcomes of fetuses with thickened nuchal fold (TNF) in the second trimester.From 2009 to 2016, we studied 72 pregnant women with fetal nuchal fold (NF) measurements over 5 mm at 14 to 19 + 6 weeks or 6 mm at 20 to 28 weeks of gestation who received prenatal diagnosis. Karyotypes were first used to detect common chromosomal diseases, and then chromosome microarray analysis (CMA) was performed if karyotypes were normal. Prognoses were followed up by documentation in the hospital or over the telephone.In total, 12 fetuses with chromosomal defects, including 5 pathogenic copy number variants (CNVs) were detected. The risk of chromosomal defects when a TNF was associated with structural malformations (SMs) (35.5%) was much greater than that of an isolated TNF (3.7%) and a TNF associated with soft markers (0%). The rate of SMs when the NF measured ≥10 mm was greater than that NF measured 5 to 7.9 mm or 8 to 9.9 mm. Totally 27 fetuses had adverse pregnancy outcome.A TNF is not only associated with a high risk of trisomy 21 but also with other chromosomal abnormalities, including pathogenic CNVs. The rates of SMs and adverse outcomes increase when the NF thickness increases.

Diagnosis of fetal megacystis with chromosomal abnormality by 2D prenatal ultrasound: A case report

RATIONALE

The pathogenesis of fetal megacystis is divided into obstructive and nonobstructive. Megacystis combined with chromosomal abnormalities is rare and most of the cases are nonobstructive.

PATIENT CONCERNS

The fetus showed posterior urethral obstructive megacystis with features of bladder enlargement, "keyhole" feature, and thick bladder wall.

DIAGNOSES

Here, we present a case of fetal megacystis diagnosed by ultrasound at pregnancy week 15+2 and with multisystem abnormalities.

OUTCOMES

Moreover, the fetus showed edema, umbilical cord cyst, cardiac dysplasia, hook-shaped hand, and strephenopodia. These abnormalities strongly suggested chromosomal abnormalities. The fetus was diagnosed with trisomy 18 by amniocentesis. Posterior urethral obstructive megacystis was confirmed by pathology.

LESSONS

In conclusion, this case suggests that in the presence of fetal megacystis and multisystem abnormalities, causes should be investigated and the possibility of chromosomal abnormalities should be considered in the presence of multisystem developmental abnormalities.

A Retrospective Study of Cytogenetic Results From Amniotic Fluid in 5328 Fetuses With Abnormal Obstetric Sonographic Findings

OBJECTIVES

The purpose of this study was to evaluate the diagnostic utility of karyotype analysis of amniotic fluid for fetuses with abnormal sonographic findings and to determine the detection rates of abnormal karyotypes.

METHODS

We conducted a retrospective study of 5328 fetuses with abnormal sonographic findings in the first or second trimester enrolled from October 1998 and September 2015. Cytogenetic results from amniotic fluid were obtained in all of these pregnancies. Sonographic abnormalities were stratified according to anatomic system involvement.

RESULTS

A total of 238 abnormal karyotypes were encountered in the 5328 fetuses (4.5%). The highest rate of chromosomal anomalies was in fetuses with structural abnormalities in multiple organ systems (25.7%), followed by an abnormal amniotic fluid volume (7.9%), structural abnormalities in a single system (7.3%), multiple nonstructural anomalies (7.2%), isolated placental abnormalities (7.1%), and isolated soft markers for aneuploidy (2.4%; P < .01). Among abnormalities in a single system, gastrointestinal and neck/body fluids had particularly high detection rates (26.1% and 26.2%, respectively). A detailed analysis suggested that the probability of an abnormal karyotype among every anatomic system was statistically significant (P < .01). This study identified several common indications with extremely high abnormal rates: duodenal atresia (53.1%), holoprosencephaly (48.8%), fetal hydrops (39.5%), cerebellar hypoplasia (32.0%), cystic hygroma (31.5%), absent/short nasal bone (11.0%), and bilateral choroid plexus cysts (8.5%).

CONCLUSIONS

Cytogenetic analysis has important clinical utility in a wide range of settings, such as prenatal diagnosis. For fetuses with indications of a highly abnormal detection rate, karyotype analysis should be suggested.

[Contribution of chromosomal microarray analysis by a multidisciplinary prenatal diagnosis center]

OBJECTIVE

Chromosomal analysis by array CGH is a cytogenetic technique that has opened its application to prenatal diagnosis in recent years. The main objective of the study was to analyze the contribution for couples using chromosomal analysis by array CGH in a CPDPN.

METHODS

A retrospective cohort study was conducted in 2015 in a CPDPN. All the patients with array CGH analysis were included in the study. The analysis indications were CN≥3.5mm, ultrasound signs, intra-uterine growth retardation and fetal deaths. Data were collected in the prenatal diagnosis and genetic records.

RESULTS

In total, 155 patients underwent analysis by array CGH, which corresponds to 36% of patients with invasive sampling indication. Fifteen CGH analysis were positive which represents 9.6% of indications. None of those diagnoses was possible with standard karyotype. These positive results have changed the outcome of pregnancy and what to do for a future pregnancy in 54% of cases.

CONCLUSION

Array CGH enables a diagnostic gain despite a delicate interpretation and changes taking care of patients in future pregnancies. These results should be confirmed in a prospective multicenter study.

Can we predict orofacial cleft in future pregnancy?

AIM

The aim of this thesis was not only to define the frequency of all orofacial clefts and their particular types, but also to determine the sex of an embryo or fetus and detect associated developmental and chromosomal abnormalities. Approximately one third of orofacial clefts are a part of chromosomal syndromes.

MATERIALS AND METHODS

Retrospective morphological and cytogenetic study of 43 cases of different types of orofacial clefts between 1992-2014 from miscarriages (spontaneous abortions) and premature births.

RESULTS

Associated abnormalities were found in 34 cases. Most of the anomalies were skeletal anomalies (29), NTD (24) and anomalies of the abdominal wall (9). Most associated anomalies were found in the R III group (93.3 %). Eleven of the successfully cultivated cases (26 %) had a normal karyotype and in 14 of the cases (32 %), numerical or unbalanced structural chromosomal aberrations were found.

CONCLUSION

Our data did not show that isolated clefts were not associated with a higher risk of chromosomal aberrations. Higher percentage of chromosomal aberrations found in isolated clefts in our pool can be explained by the age of the embryos and fetuses - usually between day 43 and week 12. It is nearly impossible to diagnose some associated congenital defects at such an early age. Thanks to the morphological and cytogenetic analysis of embryos and fetuses with orofacial cleft, it is possible to estimate if not determine the etiologic factor which influenced the miscarriage. Additionally, in the case of birth defects, the prognosis for future pregnancy can be offered, which is important information for gynecologist and clinical geneticist (Tab. 5, Fig. 5, Ref. 31).

Quality Requirements for the early Fetal Ultrasound Assessment at 11-13+6 Weeks of Gestation (DEGUM Levels II and III)

The early fetal ultrasound assessment at 11 - 13(+6) weeks of gestation remains the cornerstone of care despite the progress in diagnosing fetal chromosomal defects using cell-free fetal DNA (cffDNA) from the maternal circulation. The measurement of nuchal translucency (NT) allows the risk calculation for the fetal trisomies 21, 18 and 13 but also gives information on those fetal chromosomal defects which are at present unable to be detected using cffDNA. Nuchal translucency is the only auditable parameter at 11 - 13(+6) weeks and gives thus information on the quality of the first trimester anomaly scan. In addition it gives indirect information on the risks for fetal defects and for cardiac anomalies. Also the chances for a healthy live baby can be estimated. As experience with first trimester anomaly scanning increases, and the resolution of the ultrasound equipment has increased substantially, more and more details of the fetal anatomy become accessible at the first trimester scan. Therefore fetal anatomical defects and complex anomalies have become amenable to examination in the first trimester. This guideline describes compulsory and optional parameters for investigation at the first trimester scan and outlines a structured method of examining a first trimester fetus at 11 - 13(+6) weeks of gestation.

[ABERRANT RIGHT SUBCLAVIAN ARTERY (ARSA)--A NEW ULTRASOUND MARKER FOR CHROMOSOMAL FETAL ABNORMALITIES]

The development of the fetal aorta ends with the formation of the aortic arch which normally branches into three blood vessels: 1) a. brachiocephalica (a. innominata), which divides into the right subclavian artery (RSA) and the right carotid artery; 2) the left carotid artery; and 3) the left subclavian artery. Occasionally, RSA originates as a separate fourth branch of the aortic arch, passing behind the trachea with an oblique course to the right shoulder. This rare variant is called an aberrant right subclavian artery (ARSA) and is observed in approximately 2% of normal individuals. On the other hand, the reported incidence of ARSA varies between 25 and 37% in cases with Down syndrome and other chromosomal abnormalities.

OBJECTIVE

To evaluate the success rate of ultrasound visualization of the fetal RSA between 18 and 23 weeks of gestation and to establish the importance of the prenatal diagnosis of ARSA in the risk assessment for fetal chromosomal abnormalities in the second trimester.

RESULTS

Three experienced sonographers scanned 992 fetuses in MC "Markovs", Sofia between 01.09.2013-01.06.2014 with Voluson 730 Expert (GE Healthcare) ultrasound equipment. Visualization of RSA was successful in 92.7% of cases. Overall, 17 cases with ARSA were diagnosed in the study period. ARSA was an isolated sonographic finding in 13 of them. The remaining 4 cases had additional pathology. In the first case ARSA was associated with a short femurand humerus, short nasal bone and borderline nuchal thickness without any other soft markers or structural abnormalities. Trisomy 21 was diagnosed after amniocentesis and the pregnancy was terminated at patient's request. In the second case ARSA was associated with severe polymalformation syndrome. Trisomy 18 was diagnosed by DNA analysis post abortem. In the third case ARSA was associated with an unilateral cleft lip and cleft palate. Abnormalities of the fetal karyotype and Di George syndrome were excluded by amniocentesis. The fourth case was associated with a single umbilical artery without any structural and chromosomal abnormalities. The pregnancy had a favourable perinatal outcome at term.

CONCLUSION

Visualization of RSA and prenatal diagnosis of ARSA in the second trimester is relatively easy in experienced hands. The examination slightly prolongs the fetal morphology scan. Since there is an obvious association between ARSA and chromosomal fetal abnormalities, implementation of its sonographic evaluation in the protocol of fetal echocardiography in the second trimester is strongly recommended.

Association of non-invasive prenatal testing and chromosomal microarray analysis for prenatal diagnostics

The purposes of this study is to examine possibility to use combination of non-invasive prenatal testing (NIPT) and chromosomal microarray analysis (CMA) for prenatal diagnostics and their advantages between combined first-trimester screen with confirmation by karyotyping of CVS or amniocytes. A total of 1968 pregnant women, in this study, have undergone prenatal screening and/or diagnostic tests. NIPT is more suitable and efficient for the detection of aneuploidy. However, this test has limitations for detection deletions/duplications. Use of CMA for confirmation of some NIPT findings or as first test for women with ultrasound abnormalities can detect small imbalances in chromosomes. Combination of NIPT and CMA allows a higher prenatal detection of chromosomal abnormalities.

Blastocyst euploidy and implantation rates in a young (<35 years) and old (≥35 years) presumed fertile and infertile patient population

OBJECTIVE

To examine the relationship between blastocyst euploidy and implantation rates in a presumed fertile patient population.

DESIGN

Retrospective analysis.

SETTING

Private IVF clinic.

PATIENT(S)

IVF patients undergoing comprehensive chromosome screening (CCS).

INTERVENTION(S)

Embryo biopsy at the blastocyst stage with preimplantation genetic screening using CCS.

MAIN OUTCOME MEASURE(S)

Euploidy, chemical pregnancy, and implantation rates.

RESULT(S)

There was no significant difference in the number of euploid blastocysts between presumed fertile (68/118, 57.6%) and infertile (75/132, 56.8%) patients<35 years old. Likewise, there was no significant difference in the number of euploid blastocysts between presumed fertile (42/86, 48.8%) and infertile (97/206, 47.1%) patients≥35 years old. When those same patients underwent a corresponding frozen embryo transfer cycle, presumed fertile patients demonstrated a significantly higher chemical pregnancy rate when compared with infertile patients, 28/33 (84.8%) and 50/81 (61.7%), respectively. Moreover, presumed fertile patients exhibited significantly higher implantation rates compared with infertile patients, 36/42 (85.7%) and 54/109 (66.7%), respectively.

CONCLUSION(S)

When subdivided by maternal age, no significant difference was seen in blastocyst euploidy rates between presumed fertile and infertile patients; however, chemical pregnancy and implantation rates were significantly higher in a presumed fertile patient population even when transferring only euploid blastocysts. This would indicate that infertility, as a disease, may encompass other aspects such as uterine or other unknown embryological factors that can influence outcomes.

Detection of submicroscopic chromosomal aberrations by array-based comparative genomic hybridization in fetuses with congenital heart disease

OBJECTIVES

To evaluate the usefulness of array-based comparative genomic hybridization (aCGH) for prenatal genetic diagnosis of congenital heart disease (CHD), with and without associated anomalies, and to explore the relationship between submicroscopic chromosomal aberrations and CHD.

METHODS

In this prospective study we investigated 76 consecutive singleton fetuses with abnormal cardiac ultrasound findings, normal karyotype and negative or no fluorescence in-situ hybridization results for 22q11.2 deletion syndrome. All pregnancies underwent aCGH in a comprehensive search for chromosomal aberrations. The relationship between copy number variations (CNVs) and CHD was determined by comparing clinical findings to chromosomal databases.

RESULTS

CNVs that were benign or had no clinical significance were detected in 18/76 (23.7%) cases. CNVs of unknown clinical significance (i.e. VOUS) were detected in 4/76 (5.3%) cases. Pathogenic CNVs were detected in 5/76 (6.6%) cases. Fetuses with CHD and additional structural abnormalities demonstrated no difference in number of pathogenic CNVs when compared with fetuses with isolated CHD (7.4% (n = 2/27) vs 6.1% (n = 3/49), P > 0.05).

CONCLUSION

In this study cohort, aCGH analysis significantly improved the detection of submicroscopic chromosomal aberrations in pregnancies with CHD, as compared with conventional cytogenetics. Our results suggest that aCGH can provide additional genetic information in fetuses with abnormal heart findings.

Evolution of prenatal genetics: from point mutation testing to chromosomal microarray analysis

Molecular genetic testing involves DNA analysis using various methods for the purpose of diagnosing genetic disorders. In the prenatal DNA diagnostic setting, fetal DNA is usually tested for a specific single-gene disorder for which the fetal risk is 25% or more. In contrast, cytogenetic testing is often used to detect fetal chromosomal abnormalities in cases that involve a wider range of indications. Classic cytogenetic and DNA-based testing methods provide a range of aberrations detected with different levels of genomic resolution. More recently developed molecular cytogenetic methods provide powerful tools to bridge the technical divide between these related areas. One such hybrid method is microarray-based comparative genomic hybridization. Chromosomal microarray analysis has been applied to clinical testing for unbalanced gains or losses of genomic regions associated with genetic disorders. This technology is poised to have a substantial impact on clinical genetics, including prenatal genetic testing.

Isolated ventricular septal defects in the era of advanced fetal echocardiography: risk of chromosomal anomalies and spontaneous closure rate from diagnosis to age of 1 year

OBJECTIVES

To evaluate, in a cohort of 248 fetuses seen at a tertiary referral center, the frequency of isolated ventricular septal defects (VSD) among all congenital heart defects (CHD), the association with chromosomal and postnatal anomalies and the rate of spontaneous closure.

METHODS

This was a 6-year study on 10,800 women referred for fetal echocardiography, with 995 confirmed cases of CHD. The prevalence and characteristics of VSDs were analyzed, including follow-up until 1 year of age. Multivariate binary logistic regression analysis was performed to test the independent contribution of the ratio of the diameter of the VSD to that of the aorta (VSD/aorta ratio) (< 0.5 or ≥ 0.5) and location of VSD (perimembranous or muscular) in the prediction of spontaneous closure before the age of 1 year.

RESULTS

Two hundred and forty-eight VSDs (24.9% of all CHDs) were diagnosed, of which 216 (87.1%) were muscular and 32 (12.9%) perimembranous. Median gestational age at diagnosis was 30.4 (range, 17-41) weeks and mean size 2.6 ± 0.77 mm. Clinically relevant chromosomal anomalies were found in one (3.1%) perimembranous VSD compared with none in 216 muscular defects (P = 0.12). Postnatal malformations were diagnosed in eight of the 211 cases (3.8%) evaluated at 12 months postpartum. Spontaneous closure occurred prenatally in 13 fetuses (5.2%) and postnatally in 151 of the 198 infants (76.3%) who had an open VSD at birth. Closure was predicted by the VSD/aorta ratio (odds ratio (OR) 0.445 (95% CI, 0.216-0.914); P < 0.03) and location (OR 0.385 (95% CI, 0.160-0.926); P < 0.03).

CONCLUSIONS

In our fetal cardiology unit, isolated muscular VSD is today the most prevalent CHD. In contrast to the findings of postnatal studies, muscular VSDs were more common than perimembranous VSDs. Perimembranous VSDs were associated with a higher risk of chromosomal anomalies than were muscular VSDs, which had a similar risk to those of normal pregnancies. Spontaneous closure of the VSD was frequent and occurred in most cases postnatally.

The role of ductus venosus Doppler flow in the diagnosis of chromosomal abnormalities during the first trimester of pregnancy

BACKGROUND

The ductus venosus (DV) is an intrahepatic end-part of the umbilical vein. Inappropriate first trimester DV Doppler blood flow patterns correspond to a higher risk of chromosomal abnormalities.

OBJECTIVES

The aim of the study was to assess the usefulness of ductus venosus Doppler flow in a first trimester screening for aneuploidies.

MATERIAL AND METHODS

A prospective study included 1526 singleton pregnancies with increased risk of chromosomal abnormalities who underwent prenatal first trimester screening between the years 2006-2009. All ultrasound scans were performed by experienced sonographers and included an assessment of fetal growth, nuchal translucency (NT), nasal bone assessment (NB) and ductus venosus (DV) blood flow. Reversed a-wave (atrial diastole) in the ductus venosus flow pattern was recognized as abnormal. In addition to DV blood flow, the levels of pregnancy-associated plasma protein-A (PAPP-A) and free β - human chorionic gonadotropin (β-hCG) in maternal serum were measured. The risk of chromosomal abnormalities was calculated using the Fetal Medicine Foundation software. The following risk levels were assumed: high risk results - 1:100 or lower, intermediate risk 1:100 - 1:1000, and low risk above 1:1000. In 523 pregnancies, patients underwent amniocentesis and karyotyping.

RESULTS

The authors diagnosed 46 cases with chromosomal abnormalities (using amniocentesis and karyotyping). 29 patients had spontaneous miscarriage, in 21 cases they reported fetuses with congenital malformations (mostly heart defects). Abnormal DV blood flow was recognized in 113 pregnant women (7.4%). The majority of cases affected by abnormal DV blood flow were classified as intermediate and high disorder risk groups - 100 (6.5%). The comparison between a combined test with and without DV assessment revealed that the addition of DV flow pattern results increased sensitivity from 84% to 92% in screening for aneuploidies. The false-positive ratio was between 0.4% and 2.4%.

CONCLUSIONS

Ductus venosus Doppler blood flow examination is useful in the first trimester prenatal diagnostic since it increases the sensitivity of the combined test in the assessment of risk for chromosomal abnormalities. The authors recommend assessing DV blood flow during the first trimester screening in all pregnancies, irrespectively of the chromosomal abnormalities background risk. This procedure in clinical practice seems to be favorable and less complicated.

[Achievement and prospects of the new laboratory of medical cytogenetics]

Chromosomal abnormalities (CA) represent a significant part in the congenital and hereditary diseases of man. Because of the high need for cytogenetic analysis in January, 2011 a new cytogenetic laboratory was established in ICBFM SB RAS. For 1 year and 8 months more than 450 people was examined (including 21 cases with prenatal diagnosis (PD)), and 34 cases of CA was revealed. The diagnostics allows to choose symptomatic treatment for patients with CA or to prevent the birth of a child with serious CA and to plan a family. Our future plans is to develop of PD (amniocentesis) and to use the methods of molecular cytogenetic.

Cell-free fetal DNA testing for fetal aneuploidy and beyond: clinical integration challenges in the US context

The recent release of new, non-invasive prenatal tests for fetal aneuploidy using cell-free fetal DNA (cffDNA) has been hailed as a revolution in prenatal testing and has triggered significant commercial interest in the field. Ongoing research portends the arrival of a wide range of cffDNA tests. However, it is not yet clear how these tests will be integrated into well-established prenatal testing strategies in the USA, as the timing of such testing and the degree to which new non-invasive tests will supplement or replace existing screening and diagnostic tools remain uncertain. We argue that there is an urgent need for policy-makers, regulators and professional societies to provide guidance on the most efficient and ethical manner for such tests to be introduced into clinical practice in the USA.

[Case with intrauterine fetus death: interphase fluorescence in situ hybridization using buccal cells is useful for examining chromosomal abnormalities when placental villus not available]

The proband was a male fetus who died at 18 weeks of gestation. The fetus had growth retardation, hydrocephalus, exophthalmos, and micrognathia. The placental villus was not available. We performed interphase fluorescence in situ hybridization (FISH) using buccal cells of the fetus. The FISH using centromere specific probes for chromosome 7, 8 and 18, and RB1 gene (13q14)-specific probe showed three signals for each chromosome. The sex chromosome composition was XXY by FISH using centromere-specific probes for X and Y chromosomes. Thus, the fetus was diagnosed with triploidy syndrome. This report suggested that interphase FISH using buccal cells is useful for examining chromosomal abnormalities in intrauterine fetal death when placental villus is not available.

Identification of submicroscopic chromosomal aberrations in fetuses with increased nuchal translucency and apparently normal karyotype

OBJECTIVE

Fetal nuchal translucency (NT) is assessed by ultrasonography as a screening tool for aneuploidy at 11 to 13 + 6 weeks' gestation. Fetuses with increased NT but apparently normal karyotype are still at higher risk of structural abnormality and a range of genetic syndromes, which may be related to major and submicroscopic chromosomal abnormalities. The aim of this study was to report the prevalence of submicroscopic chromosomal abnormalities in a cohort of apparently euploid fetuses that presented with increased NT.

METHODS

DNA was extracted from stored chorionic villus samples from fetuses found to have increased NT (> 3.5 mm) during first-trimester screening. These samples were examined by microarray-based comparative genomic hybridization (aCGH) using a 44K oligonucleotide array specifically constructed for prenatal screening. Variations in copy number (CNVs) were reported after excluding known non-pathogenic variants and after validation with multiplex ligation-dependent probe amplification (MLPA) or real-time quantitative polymerase chain reaction (qPCR). The prevalence of pathogenic CNVs is reported and the association with NT and other ultrasound findings described.

RESULTS

CNVs were reported in 6/48 (12.5%) cases by aCGH and the microdeletions or microduplications ranged from 1.1 to 7.9 Mb. Five of these were validated by MLPA/real-time qPCR and four (8.3%) were considered to be pathogenic and clinically significant. The incidence of pathogenic CNVs was 20.0% (2/10) among those cases with other sonographic anomalies and 5.3% (2/38) among those without.

CONCLUSION

aCGH allows detection of submicroscopic chromosomal abnormalities, the prevalence of which may be increased in fetuses with NT > 3.5 mm and an apparently normal karyotype.

Individualized correction for maternal weight in calculating the risk of chromosomal abnormalities with first-trimester screening data

AIM

In the algorithm developed by the Fetal Medicine Foundation (FMF) Germany designed to evaluate the findings of routine first-trimester screening, the false-positive rate (FPR) was determined for the entire study group without stratification by maternal weight. Based on the data received from the continuous audit we were able to identify an increase in the FPR for the weight-related subgroups of patients, particularly for patients with extremely high body weights. The aim of this study was to demonstrate that the variability of the FPR can be reduced through adjusting the concentrations of free β-HCG and PAPP-A measured in the maternal serum by means of a nonlinear regression function modeling the dependence of these values on maternal weight.

MATERIAL AND METHODS

The database used to establish a version of the algorithm enabling control of the FPR over the whole range of maternal weight consisted of n = 123 546 pregnancies resulting in the birth of a child without chromosomal anomalies. The group with positive outcomes covered n = 500 cases of trisomy 21 and n = 159 trisomies 13 or 18. The dependency of the serum parameters free β-HCG and PAPP-A on maternal weight was analyzed in the sample of negative outcomes by means of nonlinear regression. The fitted regression curve was of exponential form with negative slope. Using this model, all individual measurements were corrected through multiplication with a factor obtained as the ratio of the concentration level predicted by the model to belong to the average maternal body weight of 68.2 kg, over the ordinate of that point on the regression curve which belongs to the weight actually measured. Subsequently, the totality of all values of free β-HCG and PAPP-A corrected for deviation from average weight were used as input data for carrying out the construction of diagnostic discrimination rules described in our recent paper for a database to which no corrections for over- or under-weight had been applied. This entailed in particular the construction of new reference bands for the corrected biochemical values as the basis for calculating the degree of extremeness (DOE) measures to replace the more traditional MOMs. In the final and most crucial step, stratified FPRs were computed and compared over a set of intervals partitioning the whole range of maternal weight into 18 classes.

RESULTS

For the posterior risks of both trisomy 21 and 13 / 18 computed from the weight-corrected database, the use of a cutoff value of 1:150 turned out to be an appropriate choice. For T 21, the overall FPR obtained through comparing the individual risks with this cutoff was found to be 3.51 %. The corresponding proportion of ascertained cases of trisomy 21 detected by means of the new algorithm was 86.2 %. For the trisomy 13 / 18 group, the analogous results were a FPR of 2.07 % and a detection rate (DTR) of 83.0 %, respectively. A comparison between the FPRs obtained for the 18 intervals into which the range of maternal weight had been partitioned, showed the deviation of the strata-specific from the overall FPR to be fairly small: for T 21, the FPR ranged from 2.72 to 4.86 %, and the maximum was found in the group of 87.5 - 95.0 kg. For women with a weight of more than 120 kg, the FPR was only slightly above the FPR for the total sample (3.69 as compared to 3.51 %). Similar results were obtained for the discrimination rule constructed for diagnosing T 13 / 18: here, the minimum FPR (1.17 %) was found for patients weighing more than 120 kg, whereas the maximum (2.66 %) occurred in the interval 75.0 - 77.5 kg.

CONCLUSION

In this study we demonstrated that the new algorithm developed by the FMF Germany to estimate risks for fetal trisomies 21 and 13 / 18 combines very good misclassification rates with a far-reaching stability of the false-positive rate against even extreme deviations from the average maternal weight.

Biochemical and morphological effects of hypoxic environment on human embryonic stem cells in long-term culture and differentiating embryoid bodies

The mammalian reproductive tract is known to contain 1.5-5.3% oxygen (O(2)), but human embryonic stem cells (hESCs) derived from preimplantation embryos are typically cultured under 21% O(2) tension. The aim of this study was to investigate the effects of O(2) tension on the long-term culture of hESCs and on cell-fate determination during early differentiation. hESCs and embryoid bodies (EBs) were grown under different O(2) tensions (3, 12, and 21% O(2)). The expression of markers associated with pluripotency, embryonic germ layers, and hypoxia was analyzed using RTPCR, immunostaining, and Western blotting. Proliferation, apoptosis, and chromosomal aberrations were examined using BrdU incorporation, caspase-3 immunostaining, and karyotype analysis, respectively. Structural and morphological changes of EBs under different O(2) tensions were comparatively examined using azan- and hematoxylineosin staining, and scanning and transmission electron microscopy. Mild hypoxia (12% O(2)) increased the number of cells expressing Oct4/Nanog and reduced BrdU incorporation and aneuploidy. The percentage of cells positive for active caspase-3, which was high during normoxia (21% O(2)), gradually decreased when hESCs were continuously cultured under mild hypoxia. EBs subjected to hypoxia (3% O(2)) exhibited well-differentiated microvilli on their surface, secreted high levels of collagen, and showed enhanced differentiation into primitive endoderm. These changes were associated with increased expression of Foxa2, Sox17, AFP, and GATA4 on the EB periphery. Our data suggest that mild hypoxia facilitates the slow mitotic division of hESCs in long-term culture and reduces the frequency of chromosomal abnormalities and apoptosis. In addition, hypoxia promotes the differentiation of EBs into extraembryonic endoderm.

[Preimplantation genetic diagnosis in prevention of genetic diseases --diagnostic of spinal muscular atrophy (SMA)]

INTRODUCTION

Preimplantation genetic diagnosis, PGD, is an established procedure allowing genetic research of the oocyte or embryo before implantation to the uterus. A neurodegenerative disorder known as spinal muscular atrophy (SMA) is the second most common lethal autosomal recessive disease in Caucasians, after cystic fibrosis. There are three clinically different types of the disease, with type I (Werding-Hoffman Disease) being the most severe. Around 98% of clinical cases of SMA are caused by the homozygous absence of a region of exons 7 and 8 of the telomeric copy of the SMN gene (SMN1) on chromosome 5 (5q13.3).

OBJECTIVES

The aim of the present work was to performed PGD for SMA in 5 couples who had already had a child affected with SMA.

MATERIAL AND METHODS

All patients underwent a standard IVF procedure associated with intracytoplasmic sperm injection. 6-8 cell embryos were biopsied on day 3 of culture. Single cell nested PCR-RFLP protocol for PGD of SMA was used for the detection of the mutation.

RESULTS

In the course of IVF-PGD procedures all patients had a transfer of embryos without SMN1 deletions. Four out of the five couples delivered healthy babies.

CONCLUSIONS

Preimplantation genetic diagnosis (PGD) of monogenic disorders is a very efficient method, especially for patients whose previous child is homozygous for genetic disorders. It offers new possibilities for the treatment for genetic disease carriers.

Decision making and attitudes towards invasive prenatal diagnosis in the early second trimester

PURPOSE

To investigate the impact of the a priori attitude, nondirective counselling and targeted second trimester ultrasound examination on the decision process concerning invasive prenatal diagnosis in the second trimester.

MATERIAL AND METHODS

A prospective study including 696 high-risk pregnancies at 15 to 18 weeks' gestation, performed from 2005-2007. Attitudes towards invasive prenatal testing were explored before and after genetic counselling and targeted ultrasound examination in a tertiary referral centre.

RESULTS

Initially, 311 (44.7%) women intended to have an invasive testing (group 1), 150 women (21.5%) were against an invasive procedure (group 2), and 235 women (33.8%) wanted to make their final decision depending on the sonographic result (group 3). The total rate of amniocentesis was 87.1%, 5.3% and 13.6%, respectively. Overall, the a priori decision was sparsely influenced by the ultrasound examination. Only 12.9% (40/311) and 5.3% (8/150) of the primarily determined women (group 1, 2) changed their opinion. However, in the initially undecided group, 86.7% declined an amniocentesis after a normal ultrasound scan.

CONCLUSION

The referral indication and the a priori opinion are the strongest influencing factors with regard to invasive testing and the ultrasound scan has a low impact in those preselected patients. However, ultrasound has an important reassuring aspect in women willing to use ultrasound as assistance in the process of decision making.

Isolated single umbilical artery and fetal karyotype

OBJECTIVE

To determine the need for fetal karyotyping in cases of an isolated single umbilical artery (SUA) identified during the second-trimester routine anomaly scan.

METHODS

All patients booked for antenatal care and delivery in our hospital are offered two ultrasound scans in pregnancy, one at 11-13 weeks' gestation as part of screening for chromosomal defects and another at 20-23 weeks for detailed fetal examination. In addition we examine patients referred from other hospitals because of suspected fetal abnormalities during their routine second-trimester scan. We performed a search of the database to retrieve all cases with an SUA and reviewed the ultrasound findings, fetal karyotype and pregnancy outcome.

RESULTS

There were 643 cases with SUA, including 424 (65.9%) where the condition was isolated, 133 (20.7%) with one major fetal defect and 86 (13.4%) with multiple defects. The incidence of chromosomal abnormalities was 0% in the isolated SUA group, 3.7% in those with one defect and 50.7% in those with multiple defects. The commonest chromosomal abnormalities were trisomy 18, trisomy 13 and triploidy, which together accounted for 82.9% of cases.

CONCLUSION

The finding of an SUA should prompt the sonographer to search for fetal defects and if these are found the risk for chromosomal abnormalities is increased. In cases of apparently isolated SUA there is no evidence of increased risk of chromosomal abnormalities.

Tumor suppressor gene alterations of spontaneously malignant transformed cells from human embryonic muscle in vitro

Recent research has shown that mesenchymal stem cells (MSCs) which were cultured for long time could transform malignantly, the transformation mechanism is not clear yet, it might be associated with the activation of oncogenes and inactivation of tumor suppressor genes. In our initial investigation, we found that the cells arising from human embryonic muscle could spontaneously transform into malignancy in vitro and we obtained 6 immortalized cell lines. In this study, polymerase chain reaction (PCR) was used to assay several tumor suppressor genes of these cell lines, and homozygous deletions within chromosomal band 9p2l including MTAP (methylthioadenosine phosphorylase), p16 and p15 were detected. PCR products of p53 exons 7 and 8 of these novel tumor cell lines were assayed by sequencing, and the results showed high prevalence of mutations in these regions, the mutation rate reached as high as 8% in exon 7 and 14% in exon 8, and all of them were point mutations, the intron 7 changed more significantly, including piece deletion, insertion, frameshift and point mutation, it showed almost no similarity to that of the wt p53 sequence, that was totally different from other p53 mutation data published. All the mutation sequences were identical in 6 cell lines, this suggest that there may be a common mutation mechanism and strong selective advantage in these novel tumor cell lines over long-term culture. In conclusion, our research shows that the inactivation of tumor suppressor genes may play an important role in the process of malignant transformation of embryonic muscle cells in vitro.

Increased nuchal translucency with normal karyotype: a follow-up study of 100 cases supplemented with CGH and MLPA analyses

OBJECTIVE

To evaluate whether high-resolution comparative genomic hybridization (HR-CGH) and subtelomeric and syndrome-specific multiplex ligation-dependent probe amplification (MLPA) would detect minor chromosomal aberrations in fetuses with increased nuchal translucency thickness (NT) and normal karyotype on conventional karyotyping.

METHODS

Chorionic villus samples from 100 fetuses with NT > or = 99(th) percentile and normal G-banding analysis and MLPA for detection of aneuploidies for chromosomes 13, 18, 21, X and Y were included. Examinations were supplemented by HR-CGH and MLPA for syndromes and subtelomeric regions. Pregnancy outcome was followed up.

RESULTS

Among 80 liveborn children who were followed up, three (4%) had syndromes involving mental retardation, including a case of Sotos syndrome caused by a de novo mutation. 15% of fetuses were lost during pregnancy due to abnormalities and termination. The rate of adverse outcome overall was 18%. HR-CGH and MLPA did not detect any chromosomal aberrations associated with the syndromes.

CONCLUSION

The rate of adverse outcome was similar to levels recorded in the literature. Using CGH and MLPA did not increase the detection rate of genetic disease, which supports the current approach of repeated ultrasound examinations in these high-risk pregnancies.

Long-term outcome for children born after a first-trimester measurement of increased nuchal translucency with a normal karyotype: a retrospective analysis

PURPOSE

To study the outcome of pregnancy in chromosomally normal fetuses with increased nuchal translucency with respect to fetal loss, structural defects genetic syndromes, and neurological outcome.

MATERIALS AND METHODS

Retrospective analysis and telephone interview. All included pregnancies underwent a mid-trimester anomaly scan.

RESULTS

279 pregnancies were included. The overall live birth rate was 81.4 %, and decreased as the NT measurement increased. The most common structural defect was cardiac anomalies (7 %). If the second-trimester anomaly scan was uneventful, the chance of a healthy live birth was 92 %. The number of unexpected neurodevelopmental delays after a normal scan during mid-trimester was 1.1 %.

CONCLUSION

Counseling should emphasize that if the karyotype is normal and no fetal structural malformations were missed prenatally after resolution of nuchal thickening, the prognosis is positive.

Diagnostic performance of routine ultrasound screening for fetal abnormalities in an unselected Swedish population in 2000-2005

OBJECTIVES

To determine the detection rate of fetal malformations and chromosomal abnormalities and the rate of false-positive ultrasound diagnoses at routine ultrasound examinations carried out by specially trained midwives in an unselected pregnant population from 2000 to 2005, and to describe the consequences of true-positive and false-positive ultrasound diagnoses of fetal malformations.

METHODS

A retrospective analysis was undertaken of all babies born in Malmö, Sweden, between January 2000 and December 2005 by mothers residing in Malmö and of all fetuses with an ultrasound diagnosis of malformation made in the same time interval at the two units performing all routine pregnancy scans in Malmö. All women underwent two routine scans, at 18 and 32 weeks, including scrutiny of the fetal anatomy. Detection rates and false-positive rates were calculated per fetus.

RESULTS

The prevalence of chromosomally abnormal fetuses was 0.31% (52/16 775); that of chromosomally normal fetuses with major and minor malformations was 1.80% (302/16 775) and 1.32% (222/16 775), respectively. The detection rate of fetuses with major malformations but normal chromosomes was 68% (205/302), with a detection rate at < 22 weeks of 37% (112/302). In addition, 46% (24/52) of all chromosomally abnormal fetuses were diagnosed before birth because a malformation was detected at ultrasound imaging, 33% (17/52) being detected at < 22 gestational weeks. In all, 68 pregnancies were terminated because of an ultrasound diagnosis of fetal malformation (0.4% of all pregnancies and 47% of the pregnancies in which a fetal malformation was detected by ultrasound examination before 22 weeks). A false-positive ultrasound diagnosis of malformation was made in 0.19% (31/16 180) of the normally formed fetuses and in 20 (0.12%) fetuses the abnormal finding persisted during pregnancy. No fetus assigned a false-positive diagnosis was lost by termination of pregnancy, but most were subjected to one or more unnecessary interventions before birth (e.g. amniocentesis), at birth (e.g. Cesarean section) or after birth (e.g. electrocardiogram, X-ray, ultrasound examination or treatment with antibiotics).

CONCLUSIONS

In a screening program consisting of one fetal anomaly scan at 18 weeks and another at 32 weeks the detection rate of major malformations in chromosomally normal fetuses was 68% with a detection rate of 37% at < 22 weeks. The corresponding detection rates of chromosomally abnormal fetuses were 46% and 33%. Fewer than one in 500 screened fetuses had an ultrasound diagnosis of an anomaly that was not confirmed after birth.

Antenatal detection of cleft lip with or without cleft palate: incidence of associated chromosomal and structural anomalies

OBJECTIVE

To ascertain how many fetuses with prenatally diagnosed cleft lip with or without cleft palate have associated congenital structural and/or chromosomal abnormalities and whether there is an association with the anatomical type of cleft lip or palate.

METHODS

This was a retrospective review of infants referred to the North-West England Regional Cleft Lip and Palate (CLAP) team between January 2000 and January 2006. Referrals made to the Regional Fetal Management Unit (FMU) in the same time period were investigated to identify the corresponding antenatal ultrasound findings and data on termination of pregnancy and intrauterine fetal death.

RESULTS

Over the 6-year period investigated, 570 infants were referred to the FMU and/or CLAP team. Among these, there were 24 terminations of pregnancy, two intrauterine fetal deaths and one early neonatal death identified. Data on 69 of the 543 patients that survived were incomplete. Of 188 cases with unilateral and 34 cases with bilateral cleft lip +/- palate there were no karyotypical abnormalities without other structural abnormalities. The incidence of associated structural abnormalities varied with the anatomical type of cleft: that of unilateral cleft lip +/- palate was 9.8% (19/194), that of bilateral cleft lip and palate was 25% (11/44) and that of midline cleft lip and palate was 100% (11/11). None of 252 cases with isolated cleft palate was identified antenatally; of these, 5.6% (n = 14) had either karyotypical or associated structural abnormalities and 21.0% (n = 53) had a genetic syndrome as an underlying diagnosis.

CONCLUSIONS

It is essential to tailor the antenatal counseling of patients to the specific scan diagnosis, considering both the anatomical type of cleft and the presence or absence of associated abnormalities. It is inappropriate to offer invasive testing to all patients. The use of three-dimensional ultrasound as an adjunct should be considered in these patients to improve the accuracy of prenatal diagnosis.

Ultrasonographic diagnosis of fetal structural abnormalities in prenatal screening at 11-14 weeks

PURPOSE

The aim of the study was to determine the detection rate of structural abnormalities at the 11-14 week ultrasound examination as a part of two-stage screening process in low-risk pregnancies.

MATERIALS AND METHODS

A total of 1085 consecutive low-risk pregnant women participated in screening by two-stage ultrasonography for the estimation of the sensitivity of the first and second trimester ultrasound scans in the detection of major anomalies as a part of routine screening.

RESULTS

Of 1085 pregnancies, 21 (1.93%) fetuses had at least one major structural defect considered detectable by routine ultrasound screening; 14 (1.29%) were identified at early screening and an additional 5 (0.47%) at late screening. Two abnormalities were not detected prenatally, and data were obtained from the patients after delivery.

CONCLUSION

The majority of fetal structural abnormalities can be detected by sonographic screening at 11-14 weeks, but detailed fetal anatomic survey performed at 18-22 weeks should not be abandoned.

Marked abnormal quadruple screen in a patient with severe preeclampsia at 20 weeks with a triploid fetus

Severe preeclampsia rarely occurs prior to 20 weeks of gestation except in pregnancies with triploidy. The patient reported herein is a 29-year-old primigravida who developed severe preeclampsia at 20 weeks of gestation. Evaluation of the pregnancy demonstrated a markedly abnormal quadruple screen. Amniocentesis demonstrated a fetus with triploidy, despite a normal appearance.

[The genetic sonogram]

Mid-trimester soft sonographic markers have been linked with aneuploidies. This article describes the individual sonographic markers used in the genetic sonograms, and reviews the current relevant Literature. The significant soft markers are: nuchal thickness, echogenic bowel, shortened limbs and absence of nasal bone. The soft markers which are not significant as an isolated finding in young patients but are significant in combination with the biochemical markers, or in older age are: intracardiac echogenic focus, choroid pLexus cyst, pyelectasis and single umbilical artery. There are several other reported findings which might be linked to chromosomal abnormalities including hypoplasia of the middle phalanx of the fifth digit, sandal gap, ear size, brachycephaly, cervical cyst, iliac angle and others. These findings shouLd not be considered as soft markers since they were reported only in small series or case reports. The aneuploidy risk should be calcuLated on the basis of age, nuchal translucency, biochemical screening and anomaly scan. If the calculated risk for aneupLoidy exceeds 1:380, an invasive karyotyping procedure should be recommended. Adoption of this approach will reduce the unnecessary invasive tests, reduce abortion rate and will increase the detection rate of aneuploidy.

Incidence and development of zygotes exhibiting abnormal pronuclear disposition after identification of two pronuclei at the fertilization check

OBJECTIVE

To determine the incidence, developmental potential, and clinical implications of embryos having one pronucleus (1PN) or three pronuclei (3PN) at early cleavage, despite exhibiting 2PN at the fertilization check.

DESIGN

Retrospective cohort study.

SETTING

Hospital-based academic medical center.

PATIENT(S)

All IVF cycles from January 2006 through May 2008 having 2PN zygotes that subsequently transitioned to 1PN or 3PN before cleavage, matched to cycles having 2PN zygotes progressing to cleavage without intervening abnormal pronuclear disposition.

INTERVENTION(S)

Standard IVF protocol.

MAIN OUTCOME MEASURE(S)

Incidence, day 3 development, and implantation rates of 2PN zygotes transitioning to 1PN and 3PN states before cleavage, compared with normal embryos.

RESULT(S)

The incidences of 1PN and 3PN zygotes were 2.9% and 0.4%, respectively. Both types of abnormal zygote showed slower day 3 cleavage, although only the 1PNs exhibited higher fragmentation and asymmetry compared with controls. The 1PN zygotes had a 6.4% implantation rate and viable pregnancy rate of 1.3%. Of the nine 3PN zygotes transferred, none implanted.

CONCLUSION(S)

Two-pronuclear zygotes transitioning through 1PN or 3PN states tend to develop into poorer-quality embryos than 2PN control zygotes. Patients should be counseled regarding the very low likelihood of viable pregnancy after transfer of these abnormally developing zygotes.