Objective To categorise the variants of uncertain significance found with prenatal chromosomal microarray and determine the proportion of such variants that are associated with a well-known phenotype in order to establish how often they remain truly of uncertain significance. Design Retrospective cohort study.

The identification of supernumerary marker chromosomes (SMC) at prenatal diagnosis is problematic, particularly for the prediction of phenotype. The assessment of phenotypic risk is based on the size, morphology and origin of the SMC. Fluorescence in situ hybridization (FISH) characterization and family studies are also employed to aid in determining the significance of a prenatally ascertained SMC. Generally, SMC containing euchromatin are more likely to be associated with abnormal phenotypes and SMC without euchromatin are more likely to result in normal phenotypes. The smallest of SMC, minute SMC (minSMC) appear as dot-like or centric fragments and are particularly difficult to identify and characterize. Previous empirical observations suggested that the risk of phenotypic abnormality in prenatally ascertained minSMC was ≤5%. We identified minSMC in chorionic villus samples (CVS) or amniocytes from 11 unrelated pregnancies. The chromosomal origin of each minSMC was identified by sequential FISH analysis with chromosome-specific centromere probes. Further FISH analysis with whole chromosome paint probes was undertaken to assess each minSMC for the presence or absence of euchromatin, since the presence of euchromatin may be associated with a higher risk of abnormality. Two minSMC were shown to have euchromatin. The first, a minSMC(12) was found in CVS but not confirmed in amniocytes, indicating confined placental mosaicism. The second, a minSMC derived from chromosome 19, was associated with ultrasound abnormalities. Apart from a case with mild speech delay, the remaining minSMC cases without detectable euchromatin had a normal outcome at birth and/or on longer term follow-up. Additional FISH analyses with a telomeric repeat probe showed no signal on any of the minSMC tested, suggesting that they were ring chromosomes in structure. These data further support the concept that minSMC containing euchromatin are more likely to be associated with an abnormal phenotype, although as more data are collected, this may vary by chromosome of origin. The absence of detectable euchromatin, while not guaranteeing a normal result, is most likely to have a normal outcome. The present report and previous studies do not yet allow any significant adjustment of the empirical ≤5% risk estimate for minSMC identified at prenatal diagnosis. However, reporting of additional cases with characterization of the minSMC and particularly with long-term follow-up will, in time, allow for more accurate risk estimates and provide prognostic information.

A case of lethal hypophosphatasia providing new insights into the perinatal benign form of hypophosphatasia and expression of the ALPL gene Brun-Heath I, Chabrol E, Fox M, Drexler K, Petit C, Taillandier A, De Mazancourt P, Serre J-L, Mornet E. A case of lethal hypophosphatasia providing new insights into the perinatal benign form of hypophosphatasia and expression of the ALPL gene.

We sought to determine the yield of whole exome sequencing (WES) in determining the genetic etiology of fetal pleural effusions. STUDY DESIGN: We examined a retrospective cohort series of all cases of fetal pleural effusions visualized by prenatal ultrasound at a single center between May 1, 2016 and May 31, 2017. Prenatal and postnatal medical records were examined for clinical presentation and diagnostic workup. Fetal pleural effusions attributed to twin sharing, red cell alloimmunization, or structural anomalies were excluded, as were cases with a genetic diagnosis confirmed by karyotype or microarray analysis. The remaining cases were offered WES. WES was performed on cases submitted for either clinical sequencing or sequencing under the Baylor-Hopkins Center for Mendelian Genomics' research sequencing platform. RESULTS: Twenty-four fetuses with pleural effusions were evaluated by prenatal ultrasound. Eleven cases (45.8%) were excluded due to twin-transfusion (3 cases), twin anemia polycythemia sequence (1 case), Rh disease (2 cases), congenital diaphragmatic hernia (2 cases), cystic pulmonary airway malformation (1 case), and fetal teratoma (2 cases). Six additional cases (25%) were excluded due to diagnoses of monosomy X (4 cases), trisomy 21 (1 case), and terminal 7q36 deletion/7p22 duplication (1 case). Of the remaining 7 cases, 5 underwent WES, including 3 parent-proband trios and 2 parent-proband-affected sibling quads. We identified a pathogenic variant in 1 case, a likely pathogenic variant in a second case, and 3 cases with variants of unknown significance with potential for reclassification based on expansion of phenotype (see table). CONCLUSION: Following standard clinical evaluations, a causative etiology remained unknown in 29.2% of prenatally diagnosed pleural effusions. In the present series, WES identified a pathogenic variant in 20% of such cases. Additional variants identified by WES require validation studies for confirmation. WES should be considered in cases of fetal pleural effusions when the standard evaluation is not diagnostic.