Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples

Non-invasive prenatal testing (NIPT) is a powerful screening method for fetal aneuploidy detection, relying on laboratory and computational analysis of cell-free DNA. Although several published computational NIPT analysis tools are available, no prior comprehensive, head-to-head accuracy comparison of the various tools has been published. Here, we compared the outcome accuracies obtained for clinically validated samples with five commonly used computational NIPT aneuploidy analysis tools (WisecondorX, NIPTeR, NIPTmer, RAPIDR, and GIPseq) across various sequencing depths (coverage) and fetal DNA fractions. The sample set included cases of fetal trisomy 21 (Down syndrome), trisomy 18 (Edwards syndrome), and trisomy 13 (Patau syndrome). We determined that all of the compared tools were considerably affected by lower sequencing depths, such that increasing proportions of undetected trisomy cases (false negatives) were observed as the sequencing depth decreased. We summarised our benchmarking results and highlighted the advantages and disadvantages of each computational NIPT software. To conclude, trisomy detection for lower coverage NIPT samples (e.g. 2.5M reads per sample) is technically possible but can, with some NIPT tools, produce troubling rates of inaccurate trisomy detection, especially in low-FF samples.

IDENTIFICATION OF MOST COMMON CONGENITAL ABNORMALITY TYPES AMONG NEWBORN INFANTS: A HOSPITAL-BASED STUDY

The term “congenital abnormalities” signifies a disruption in the normal process of organogenesis occurring before birth: the earlier the insult, the grosser the abnormality. This research is the largest study aimed at identifying the most common congenital abnormality types among newborn infants in the neonatal care unit (NCU) of the Al-Kadhymia teaching hospital, Baghdad, Iraq. This prospective study was carried out during the period from February 1 to August 1, 2011. A total of 2700 neonates were admitted to the NCU, and 100 newborn infants in the nursery care unit were proven to have congenital abnormalities by physical examination alone. The questionnaire for neonatal evaluation included: gestational age, sex, body weight, and type of congenital anomaly. The results showed that of the total (100) affected neonates, 63 (63%) were full term, 55% had neurological abnormalities, followed by 12% with cleft lip and palate and then 11% with chromosomal abnormalities (most of them had Down syndrome, only 3 cases had Edward syndrome, and 1 case had Patau syndrome). It can be concluded that most of the affected newborns were full term, with a slight male predominance. The incidence of neurological abnormalities was higher than other types of birth defects.

Evaluation of Prenatal Central Nervous System Anomalies: Obstetric Management, Fetal Outcomes and Chromosome Abnormalities

Objective: To study the prognostic outcomes of fetuses with prenatally diagnosed central nervous system (CNS) anomalies and describe the obstetric management for those fetuses.Methods: In this retrospective study, fetuses who were detected to have central nervous system by prenatal ultrasound from January 2010 to December 2019 were recruited. Data regarding prenatal diagnosis and obstetric outcome were retrieved from maternal and paediatric records. Prognosis of children who survived till delivery was classified based on their neurodevelopmental outcome within 2 years of life.Results: 365 fetuses were prenatally diagnosed with CNS malformations within the 10-year study period, at a mean gestational age of 24.65±7.37 weeks at diagnosis. Ventriculomegaly (23.36%) was the commonest CNS anomalies diagnosed antenatally. 198 (54.20%) fetuses has associated extra-CNS anomalies, with cardiovascular system being the most common organ system involved with CNS anomalies. Karyotyping was performed in 111 pregnancies, with chromosomal aberrations detected in 53 (49.07%) cases and culture failure in 3 cases. Edward syndrome and Patau syndrome were commonly associated with CNS anomalies. Fetuses with congenital CNS anomalies and abnormal chromosomal karyotyping more likely to be diagnosed earlier by prenatal ultrasound and tend to have poorer obstetric and neurocognitive prognosis. Among the 279 cases whom their pregnancy outcomes were available, 105 (37.63%) pregnancies were electively terminated, 35 (12.54%) pregnancies ended in spontaneous loss while the remaining 139 (49.82%) cases resulted in live births. The decision of TOP largely depends on mean diagnostic gestational age, presence of chromosomal aberrations and abnormal amniotic fluid volume in those fetuses. Ruling out 21 (15.11%) cases which were lost to 2-year follow-up, only 75 (53.96%) infants were still alive by the age of 2 years. Only 32 (23.02%) children with prenatally diagnosed CNS anomalies had normal neurodevelopmental outcome. The presence of multiple CNS anomalies and involvement of extra-CNS anomalies indicated a poorer neurodevelopmental prognosis.Conclusion: Less than 50% of fetuses with prenatally diagnosed CNS anomalies resulted in live births. Even if they survive till delivery, majority passed away within 2 years or had neurodevelopmental disability.

Identification of Chromosome 17 Trisomy in a Cynomolgus Monkey (Macaca fascicularis) by Multicolor FISH Techniques

A female cynomolgus monkey (<i>Macaca fascicularis</i>) with facial features characteristic of Down syndrome showed abnormal behavior, unwariness toward humans, and poor concentration. The number of metaphase chromosomes in blood lymphocytes was examined and found to be 43, which indicated one extra chromosome to the normal diploid number (2n = 42). We then used Q-banding and multicolor FISH techniques to identify the extra chromosome. The results revealed an additional chromosome 17, with no other chromosomal rearrangements, such as translocations. Since no mosaicism or heterozygous variant chromosomes were observed, full trisomy 17 was assessed in this female cynomolgus monkey. Chromosome 17 corresponds to human chromosome 13, and human trisomy 13, known as Patau syndrome, results in severe clinical signs and, often, a short life span; however, this individual has reached an age of 10 years with only mild clinical signs. Although genomic differences exist between human and macaques, this individual’s case could help to reveal the pathological and genetic mechanisms of Patau syndrome.

Type 1 diabetes mellitus presenting with diabetic ketoacidosis in a child with Patau syndrome (trisomy 13) and persistent fetal haemoglobin

A 35-month-old boy with non-mosaic Patau syndrome presented in diabetic ketoacidosis and was diagnosed with type 1 diabetes mellitus. A decision to treat this unanticipated medical problem was made in conjunction with the child’s parent, and he improved with fluid resuscitation and insulin treatment. Acute kidney injury with hypernatraemia complicated his treatment, but this resolved with careful intravenous fluid management. The child survived and was followed up in the diabetes clinic where ongoing management was complicated by persistent fetal haemoglobin, which meant that glycated haemoglobin could not be used to gauge his glucose control.

Neurological findings of a patient with Patau syndrome and a nonusual clinical presentation

Context: Chromosome 13 trisomy, or Patau syndrome (PS), is a genetic condition characterized by multiple findings and usually poor survival rate. However, its clinical presentation can be variable. Case report: A male patient was referred for evaluation due to a syndromic aspect. He was born by normal delivery, at term, weighing 4700 g. On physical exam, at 2 months, two areas of scaly aplasia on the scalp were shown as well as left coloboma of the iris, bulbous nose with small nostrils, ears with oversized helices, micrognathia, umbilical hernia, clinodactyly of the index finger of the hand left and the 4th and 5th toes of the left foot. Echocardiography revealed tetralogy of Fallot. The karyotype showed a free trisomy of chromosome 13 (47, XY, + 13), compatible with the diagnosis of PS. The patient died at 9 months of age due to complications from bronchopneumonia and had evolved with a delay in neuropsychomotor development at that moment. Conclusions: There are findings that stand out among patients with PS and that very often lead to diagnosis, such as micro/anophthalmia, bilateral cleft lip/palate and polydactyly. It is interesting in our case that the patient did not have any of them, which made it difficult to identify. In addition, from a neurological point of view, the findings were quite common; however, in our patient, there was only a delay in neuropsychomotor development, pointing out that the neurological findings can also be quite variable.

Interrupted aortic arch, type A: report of 3 cases

Three cases of interrupted aortic arch of type A (IAA, type A) identified on prenatal ultrasound examination are presented. IAA, type A was a component of 22q11.2 microdeletion syndrome, established by molecular analysis of the aborted fetus`s tissues in the first case and a part of trisomy 13 in the second one. In the third fetus with a normal karyotype, IAA, type A was diagnosed at 31 weeks of gestation and successful cardiac surgery was performed after birth. In a fetus with 22q11.2 microdeletion syndrome, IAA was combined with ascending aorta hypoplasia and ventricular septal defect. In fetuses with Patau syndrome and normal karyotype IAA type A was accompanied by an aortopulmonary window.

Comprehensive analysis of differentially expressed lncRNAs and associated ceRNA networks in Patau syndrome

Objective: LncRNAs are a class of competing for endogenous RNAs (ceRNAs) with no coding ability and have miRNA binding sites that competitively bind to miRNAs and inhibit miRNA-mediated regulation of target genes. In recent years, an increasing number of studies have recognized the biological functions of lncRNAs.Methods: Illumina RNA-Seq technology was used to analyze the cord blood with Patau syndrome (PS) fetal and the peripheral blood of pregnant women to obtain differential expression profiles of lncRNAs, miRNAs, and mRNAs. Further, Combined with bioinformatics analysis of the biological functions of differentially expressed lncRNAs (DElncRNAs). Results: The results showed that 467 DElncRNAs, 8512 differentially expressed mRNAs (DEmRNAs), and 18 differentially expressed miRNAs (DEmiRNAs) were found to be co-expressed in cord blood and peripheral blood. The hsa-miR-15a-5p is located on chromosome 13. We constructed the ceRNA network with hsa-miR-15a-5p, lncRNAs as the bait, and mRNAs as the targe. Conclusion: We consider that the DElncRNAs may indirectly regulate the target gene CLASRP or KARS by binding hsa-miR-15a-5p to participate in the occurrence of PS.

First-trimester presentation of ultrasound findings in trisomy 13 and validation of multiparameter ultrasound-based risk calculation models to detect trisomy 13 in the late first trimester

ObjectivesTo identify the most common ultrasound patterns of markers and anomalies associated with Patau syndrome (PS), to explore the efficacy of multiparameter sonographic protocols in detecting trisomy 13 (T13) and to analyze the influence of maternal age (MA) on screening performance. Methods: The project was a prospective study based on singleton pregnancies referred for a first-trimester screening examination. The scan protocol included nuchal translucency (NT), fetal heart rate (FHR), secondary ultrasound markers [nasal bone (NB), tricuspid regurgitation (TR), ductus venosus reversed a-wave (revDV)] and major anomaly findings. Results: The study population comprised 6133 pregnancies: 6077 cases of euploidy and 56 cases of T13. Statistically significant differences were found in MA, FHR, NT, absence of NB, presence of revDV, TR and single umbilical artery. Fourteen cases of T13 (25%) demonstrated no markers of aneuploidy. The best general detection rate (DR) (DR of 78.6% with an false positive rate (FPR) of 1.2%) was obtained for a cutoff of 1/300 utilizing the “NT+T13” algorithm. The logistic regression model revealed that the central nervous system (CNS) anomalies had the greatest odds ratio (of 205.4) for T13. Conclusions: The effectiveness of the multiparameter sonographic protocol used for T13 screening showed promising results in patients older than 36 years and suboptimal results in patients between 26 and 36 years old. When screening for T13 left heart defects, CNS anomalies, abdominal anomalies, FHR above the 95th percentile, increased NT, revDV and lack of NB should receive specific attention.