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Objectives: To establish the positive predictive values (PPV) of cfDNA testing based on data from a nationwide survey of independent clinical cytogenetics laboratories. Methods: Prenatal diagnostic test results obtained by Italian laboratories between 2013 and March 2020 were compiled for women with positive non-invasive prenatal tests (NIPT), without an NIPT result, and cases where there was sex discordancy between the NIPT and ultrasound. PPV and other summary data were reviewed. Results: Diagnostic test results were collected for 1327 women with a positive NIPT. The highest PPVs were for Trisomy (T) 21 (624/671, 93%) and XYY (26/27, 96.3%), while rare autosomal trisomies (9/47, 19.1%) and recurrent microdeletions (8/55, 14.5%) had the lowest PPVs. PPVs for T21, T18, and T13 were significantly higher when diagnostic confirmation was carried out on chorionic villi (97.5%) compared to amniotic fluid (89.5%) (p < 0.001). In 19/139 (13.9%), of no result cases, a cytogenetic abnormality was detected. Follow-up genetic testing provided explanations for 3/6 cases with a fetal sex discordancy between NIPT and ultrasound. Conclusions: NIPT PPVs differ across the conditions screened and the tissues studied in diagnostic testing. This variability, issues associated with fetal sex discordancy, and no results, illustrate the importance of pre- and post-test counselling.

Copy number variants (CNVs) play important roles in the pathogenesis of several genetic syndromes. Traditional and molecular karyotyping are considered the first-tier diagnostic tests to detect macroscopic and cryptic deletions/duplications. However, their time-consuming and laborious experimental protocols protract diagnostic times from 3 to 15 days. Nanopore sequencing has the ability to reduce time to results for the detection of CNVs with the same resolution of current state-of-the-art diagnostic tests. Nanopore sequencing was compared to molecular karyotyping for the detection of pathogenic CNVs of seven patients with previously diagnosed causative CNVs of different sizes and cellular fractions. Larger chromosomal anomalies included trisomy 21 and mosaic tetrasomy 12p. Among smaller CNVs, two genomic imbalances of 1.3 Mb, a small deletion of 170 kb, and two mosaic deletions (1.2 Mb and 408 kb) were tested. DNA was sequenced and data generated during runs were analyzed in online mode. All pathogenic CNVs were identified with detection time inversely proportional to size and cellular fraction. Aneuploidies were called after only 30 minutes of sequencing, whereas 30 hours were needed to call small CNVs. These results demonstrate the clinical utility of our approach that allows the molecular diagnosis of genomic disorders within a 30-minute to 30-hour time frame and its easy implementation as a routinary diagnostic tool.

Unbalanced Structural Variants (uSVs) play important roles in the pathogenesis of several genetic syndromes. Traditional and molecular karyotyping are considered the first-tier diagnostic tests to detect macroscopic and cryptic deletions/duplications. However, their time-consuming and laborious experimental protocols protract diagnostic times from three to fifteen days. Long read sequencing approaches, such as Oxford Nanopore Technologies (ONT), have the ability to reduce time to results for the detection of uSVs with the same resolution of current state-of-the-art diagnostic tests.Here we compared ONT to molecular karyotyping for the detection of pathogenic uSVs of 7 patients with previously diagnosed causative CNVs of different sizes and allelic fractions. Larger chromosomal anomalies included trisomy 21 and mosaic tetrasomy 12p. Among smaller CNVs we tested two reciprocal genomic imbalances in 7q11.23 (1.367 Mb), a 170 kb deletion encompassing NRXN1 and mosaic 6q27 (1.231 Mb) and 2q23.1 (408 kb) deletions. DNA libraries were prepared following ONT standard protocols and sequenced on the GridION device for 48 h. Data generated during runs were analysed in online mode, using NanoGLADIATOR.We were capable to identify all pathogenic CNVs with detection time inversely proportional to size and allelic fraction. Aneuploidies were called after only 30 minutes of sequencing, while 30 hours were needed to call CNVs < 500 kb also in mosaic state (44%). These results demonstrate the clinical utility of our approach that allows the molecular diagnosis of genomic disorders within a 30 minutes to 30 hours time-frame.

Chromosomal anomalies are well known to be an important cause of infertility, sterility and pregnancy loss. Balanced Reciprocal Translocation Mosaicism (BRTM) is an extremely rare phenomenon, mainly observed in subjects with a normal phenotype accompanied by reproductive failure. To date the mechanism of origin and the incidence of BRTM are poorly defined. Here we describe 10 new cases of BRTM. In 9 cases chromosome analysis revealed the presence of two different cell lines, one with a normal karyotype and the second with an apparently balanced reciprocal translocation. In the remaining case, both cell lines showed two different, but apparently balanced, reciprocal translocations. We document the clinical implications of BRTM, discuss its frequency in our referred population and suggest that carrier individuals might be more frequent than expected.

Objective: Our objective was to retrospectively evaluate whether the levels of cell-free DNA (cfDNA) fetal fraction differed in the first trimester of pregnancies between controls and those who subsequently developed early- or late-onset fetal growth restriction (FGR). Methods: This was a case–control study conducted between May 2015 and May 2018 in 231 low-risk women who had received first trimester screening for major fetal aneuploidies (Panorama, Natera, San Carlos, CA, USA). Early- and late-onset FGR developed in 5 and 16 women, respectively, according to Delphi criteria. Multiples of median (MoM) were used to evaluate the differences in cfDNA fetal fraction between cases and controls. cfDNA fetal fraction was adjusted for gestational age (from 10 + 0 to 13 + 6 gestational weeks) and maternal weight (43–96 kg). Results: The median cfDNA fetal fractions for controls and early- and late-onset FGR were 1.00 (interquartile range [IQR] 0.89–1.12), 0.69 (IQR 0.44–0.84) and 0.93 (IQR 0.83–1.03) MoM, respectively. Statistically lower cfDNA fetal fraction MoM values were observed only in patients with early-onset FGR (Kruskal–Wallis test with Dunn post hoc test). In a 1:35 ratio (one case of early-onset FGR: 35 controls), the mean observed rank of 2.00 ± 2.23 in the cases was significantly lower than the expected 18.97 ± 10.17 (p < 0.001). Conclusions: Low-risk pregnancies that developed early-onset FGR had lower cfDNA fetal fractions than did the matched controls. This result is consistent with the placental dysfunction typical of early-onset FGR. For possible clinical use, the cfDNA fetal fraction would yield a better predictive value if adjusted for maternal weight, since maternal weight affects both cfDNA fetal fraction and the occurrence of FGR.

Objective: To compare the policy of prenatal diagnosis versus first trimester screening of trisomy 21 among pregnant women of advanced age. Methods: A retrospective study was conducted on patients aged ≥35 divided in two groups: patients who requested first trimester combined test and only in case of screen-positive result underwent invasive testing (group A); patients undergoing chorionic villous sampling or amniocentesis as first investigation (group B). The following outcome variables were compared: antenatal detection of trisomy 21, occurrence of trisomy 21 at birth, miscarriage rate, hospitals' costs. Results: 4527 women were included. Of these, 534 (11.80\%) underwent T21 screening whereas 3993 (88.20\%) requested primary invasive testing. In group A, 64 combined test were positive (11.99\%) and 8 trisomy 21 cases were diagnosed (1.50\%); the loss of euploid fetuses after invasive procedure was 4.55\% (2/44). No false-negative case was observed. In group B 57 cases of trisomy 21 were diagnosed (1.43\%), and pregnancy loss rate of chromosomally normal fetuses was 0.45\% (17/3806). The estimated cost was, respectively, 67.720€ for the primary screening versus 1.996.500€ for direct prenatal diagnosis. Conclusion: First trimester screening of trisomy 21 is highly accurate and cost saving among women ≥35.

Objective To contribute to the risk assessment of true fetal mosaicism after detection of a mosaic chromosomal anomaly in chorionic villus samples (CVS) in order to enable more effective counseling and pregnancy management. Methods We retrospectively reviewed 7112 consecutive CVS analyzed on both direct preparations and cultured cells. In 135 out of the 177 cases of mosaicism, we performed cytogenetic follow-up and determined the frequency of confined placental mosaicism (CPM) and true fetal mosaicism according to type and distribution of the cytogenetic abnormality. Results True fetal mosaicism was detected in 38 out of 135 cases (28.15%), confirming the higher incidence of CPM (71.85%). Confirmation rate of CV mosaicism depends on the combination of placental cell lineages affected, chromosome involved and mosaic versus non-mosaic chromosomal anomaly. The overall probability of fetal involvement significantly rises with involvement of mesenchymal cells: 5.88% abnormal cytotrophoblast, 20.96% abnormal mesenchyme and 58.97% anomalies in both tissues. Conclusion Most of the mosaic findings at CVS are unreliable indicators of the fetal karyotype. Our study contributes to large series with cytogenetic information from the different tissues along the cytotrophoblast-extraembrional mesoderm-fetus axis in order to infer clinical relevance of the findings and to enable more effective genetic counseling. © 2014 John Wiley & Sons, Ltd.

Objective To evaluate the alteration in epidermal growth factor-like domain 7 (EGFL7) mRNA expression in maternal blood from pregnancies affected by early-onset intrauterine growth restriction (IUGR) at 20–24 weeks. Method Case–control study encompassing six women with pregnancies affected by IUGR (cases) matched in a 1 : 7 ratio for gestational age and fetal gender with 42 controls. We quantified EGFL7 mRNA expression in normal and IUGR patients. Matched rank–sum analysis and multiples of median were used to evaluate differences of the marker of interest between cases and controls. Spearman regression analysis was used to correlate the estimated fetal weight at blood sampling with the EGFL7 mRNA values. Results The mean observed rank in the IUGR group was significantly higher than that of controls (6.67 vs 4.19, p = 0.01). Pregnancies affected with IUGR exhibited 1.70-fold higher levels of maternal EGFL7 mRNA compared with matched controls (p = 0.014). EGFL7 mRNA values were inversely correlated with estimated fetal weight (Spearman's ρ = −0.429, p = 0.198). Conclusion Early IUGR at 20–24 weeks’ gestation is associated with higher values of EGFL7 expression in maternal plasma. © 2012 John Wiley & Sons, Ltd.

To contribute to the risk assessment of true fetal mosaicism after detection of a mosaic chromosomal anomaly in chorionic villus samples (CVS) in order to enable more effective counseling and pregnancy management.We retrospectively reviewed 7112 consecutive CVS analyzed on both direct preparations and cultured cells. In 135 out of the 177 cases of mosaicism, we performed cytogenetic follow-up and determined the frequency of confined placental mosaicism (CPM) and true fetal mosaicism according to type and distribution of the cytogenetic abnormality.True fetal mosaicism was detected in 38 out of 135 cases (28.15%), confirming the higher incidence of CPM (71.85%). Confirmation rate of CV mosaicism depends on the combination of placental cell lineages affected, chromosome involved and mosaic versus non-mosaic chromosomal anomaly. The overall probability of fetal involvement significantly rises with involvement of mesenchymal cells: 5.88% abnormal cytotrophoblast, 20.96% abnormal mesenchyme and 58.97% anomalies in both tissues.Most of the mosaic findings at CVS are unreliable indicators of the fetal karyotype. Our study contributes to large series with cytogenetic information from the different tissues along the cytotrophoblast-extraembrional mesoderm-fetus axis in order to infer clinical relevance of the findings and to enable more effective genetic counseling.

We report on a fetus presenting with an increased nuchal translucency, in which chorionic villus sampling led to the diagnosis of mosaic trisomy 8. Ultrasound scan performed at 15(+6) weeks revealed bilateral cleft lip and palate, flat facial profile, and arrhinia. Pregnancy was terminated at 16(+6); postmortem examination showed additional findings including hypospadias, bilateral renal dysplasia, and focal portal fibrosis of the liver. In order to confirm the presence of trisomy 8, FISH analysis was performed in abnormal renal and hepatic tissue, which, unexpectedly, showed a higher fraction of cells with only one fluorescent probe signal (43% and 23%, respectively), if compared with normal fetal liver and kidney (3-10%). This finding is consistent with the survival in this fetus of a monosomic cell line after mitotic non-disjunction, which is in contrast with what is generally thought about mosaic trisomy genesis. We hypothesize that the possible persistence of the monosomic cell line, in addition to the variable distribution of aneuploid cells in the body tissues, could explain the high heterogeneity of mosaic trisomy 8 phenotype.

Agenesis of the corpus callosum was identified by ultrasound examination in 35 fetuses between 19 and 37 weeks' gestation. The ultrasound findings included absence of the corpus callosum and cavum septum pellucidum (hypoplasia in one case of partial agenesis of the corpus callosum), a typical 'teardrop' configuration of the lateral ventricles, distension of the interhemispheric fissure, upward displacement of the third ventricle, radiate arrangement of the medial cerebral gyri, and abnormal branching of the anterior cerebral artery. Associated anomalies were identified in 20 fetuses, including heterogeneous malformations and chromosomal aberrations (mosaic-trisomy 8 in three, trisomy 18 in two and partial duplication 8p in one). Five cases of agenesis of the corpus callosum were identified in a population of pregnant patients prospectively investigated because of genetic risk for agenesis of the corpus callosum or related syndromes. In this group, no diagnostic errors were made. Long-term neurological follow-up (6 months to 11 years) was available in 11 infants with antenatal diagnosis of isolated agenesis of the corpus callosum. Normal intellectual development was present in nine, and a low intellect (developmental quotient between 70 and 85) was found in two. It is concluded that fetal agencies of the corpus callosum is associated with elusive sonographic findings that can, however, be accurately identified by targeted examinations. In routine sonograms, an increased atrial width and/or failure to visualize the cavum septum pellucidum should arise the suspicion of fetal agencies of the corpus callosum. Given the high frequency of associated anomalies, prenatal diagnosis of agencies of the corpus callosum dictates the need for a careful survey of fetal anatomy and karyotyping. The prognosis is isolated agencies of the corpus callosum remains uncertain, although it is expected that a normal or boarderline intellectual development will occur in many cases.

The distal region on the short arm of chromosome 9 is of special interest for scientists interested in sex development as well as in the clinical phenotype of patients with the 9p deletion syndrome, characterized by mental retardation, trigonocephaly and other dysmorphic features. Specific genes responsible for different aspects of the phenotype have not been identified. Distal 9p deletions have also been reported in patients with 46,XY sex reversal, with or without 9p deletion syndrome. Within this region the strongest candidates for the gonadal dysgenesis phenotype are the DMRT genes; however, the genetic mechanism is not clear yet. Multiple ligation-dependent probe amplification represents a useful technique to evaluate submicroscopic interstitial or distal deletions that would help the definition of the minimal sex reversal region on 9p and could lead to the identification of gene(s) responsible of the 46,XY gonadal disorders of sex development (DSD). We designed a synthetic probe set that targets genes within the 9p23-9p24.3 region and analyzed a group of XY patients with impaired gonadal development. We characterized a deletion distal to the DMRT genes in a patient with isolated 46,XY gonadal DSD and narrowed down the breakpoint in a patient with a 46,XY del(9)(p23) karyotype with gonadal DSD and mild symptoms of 9p deletion syndrome. The results are compared with other patients described in the literature, and new aspects of sex reversal and the 9p deletion syndrome candidate regions are discussed.

Experience with prenatal karyotyping of 237 fetuses with sonographic evidence of malformation is reported. Abnormal karyotype was found in 40 cases (16.8 per cent): chromosomal aberrations were found in 19 of the 178 fetuses with an isolated structural anomaly (10.6 per cent) and in 21 of the 59 fetuses with multiple malformations (35.6 per cent). Detailed cytogenetic and morphological information concerning fetuses affected by omphalocele, duodenal atresia, hydrocephalus, multicystic kidney, unilateral hydronephrosis and cystic hygroma is reported. The need for a very careful ultrasound evaluation of fetal anatomy in these pregnancies is stressed, as the risk of a chromosomal anomaly depends mainly on the existence of more than one ultrasonically diagnosed structural defect.

First described in 1973 by Alfi et al, 1 the 9p deletion syndrome is a well-recognized (although rare) clinical entity reported in slightly more than 100 cases to date. The head and neck are always involved, typically manifesting long philtrum, microstomia, shortappearing neck, trigonocephaly, epicanthal folds, anteverted nares, midface hypoplasia, upslanting palpebral fissures, and posteriorly angulated and poorly formed ears. Other phenotypical characteristics include hypotonia, widely spaced nipples, mental retardation, square hyperconvex nails, dolichomesophalangy, and an excess of whorls on the fingers. 2 Furthermore, ambiguous genitalia and male-to-female primary sex reversal have been reported in patients with a normal Y chromosome and a terminal 9p deletion. 3,4

A karyotype was obtained from 755 fetuses with structural anomalies detected by sonography between 13 and 40 weeks' gestation. Gestational age was found to have no influence on the prevalence of chromosomal aberrations. The incidence in the second and third trimesters of pregnancy was 15.7 and 17.5 per cent, respectively. The contribution of the different malformations to such proportions did, however, change throughout gestation. Cystic hygroma was by far predominant in the early second trimester, cardiac defects in the late second trimester, and duodenal atresia in late pregnancy. Our findings confirm that karyotyping of malformed fetuses is highly advisable ; the importance of chromosomal investigation is not dependent on the gestational age at detection of the structural defect as the likelihood of finding a chromosomal anomaly during the second and third trimesters is quite similar. Spontaneous intrauterine selection of chromosomally abnormal fetuses is most likely counterbalanced by the limited accuracy of prenatal ultrasound in recognizing many fetal anomalies early in pregnancy.

Cytogenetic analysis was performed in 4860 chorionic villus samples by means of both direct preparation and long-term culture. The results of the analysis were compared with a classification including all theoretical types of combinations between the chromosomal constitution of the cytotrophoblast, extraembryonal mesoderm, and fetus, with the aim of evaluating the cytogenetic variability along the trophoblast—embryo axis. Eighteen of 29 possible combinations were found demonstrating a considerable heterogeneity. A mosaic conceptus was found in 1·5 per cent of cases, with generalized mosaicisms and confined mosaicisms in 0·2 and 1·3 per cent, respectively. Cytogenetic variability along the trophoblast—embryo axis was found in 1·42 per cent of cases. Results possibly leading to diagnostic errors (false-positive and false-negative results) were found in only 1·38 per cent. False-positive results of direct preparation were the most commonly observed discrepancy (0·8 per cent), while the incidence of false-positive results of the culture method and of both methods was 0·31 and 0·16 per cent respectively. The incidence of false-negative results was 0·1 per cent, with false-negative results of direct preparation 0·08 per cent and false-negative results of both methods 0·02 per cent. False-negative results of the culture method were not found. Our data confirm the high diagnostic accuracy of chorionic villus sampling and the utility of the combined use of the two methods in minimizing diagnostic errors and in reducing the need for follow-up amniocentesis.

Among 1041 pregnancies 13 twin gestations were detected by routine ultrasonography prior to genetic amniocentesis at the Department of Prenatal Physiopathology of the University of Bologna. Clear amniotic fluid from both sacs was obtained in 12 of 13 sets of twins. All 12 sets were cytogenetically normal with normal levels of α-fetoprotein. Only one patient spontaneously aborted liveborn immature twins 30 days after the procedure. The technique used to obtain samples of fluid is described in detail and the need for additional counselling prior to amniocentesis in twins is stressed.

Over a 3-year period, 44 ultrasound-guided intravascular transfusions were performed between 18 and 32 weeks on 15 patients with severe erythroblastosis fetalis due to Rh immunization. In 4 fetuses, the first transfusion was performed before 20 weeks, in 6 between 20 and 25 weeks and in the remaining 5 between 25 and 31 weeks. Eight of the 15 fetuses were hydropic at the time of referral. Five transfusions were done in the intrahepatic umbilical vein, 6 were simple transfusions via percutaneous umbilical cord puncture, and 33 were partial exchange. There were 4 intrauterine deaths before 26 weeks, despite successfully performed tranfusions: 3 of these fetuses were severely hydropic, while in the remaining fetus hydrops had been reversed in utero. Following delivery by cesarean section at 32 weeks of gestation, 1 of the neonates developed respiratory distress syndrome and died 17 h after birth. The overall survival rate was 67% (10 of 15 cases): 4 of the 8 hydropic fetuses (50%) and 6 of the 7 nonhydropic fetuses (83%) were alive at birth and survived the perinatal period. Three of the 5 losses occurred among the first 4 cases, while in the last 11 cases the survival rate increased to 82% (9 of 11).