The incremental yield of prenatal exome sequencing over chromosome microarray for congenital heart abnormalities: A systematic review and meta-analysis.

OBJECTIVES: To determine the incremental yield of prenatal exome sequencing (PES) over standard testing in fetuses with an isolated congenital heart abnormality (CHA), CHA associated with extra-cardiac malformations (ECMs) and CHA dependent upon anatomical subclassification. METHODS: A systematic review of the literature was performed using MEDLINE, EMBASE, Web of Science and grey literature January 2010-February 2023. Studies were selected if they included greater than 20 cases of prenatally diagnosed CHA when standard testing (QF-PCR/chromosome microarray/karyotype) was negative. Pooled incremental yield was determined. PROSPERO CRD 42022364747. RESULTS: Overall, 21 studies, incorporating 1957 cases were included. The incremental yield of PES (causative pathogenic and likely pathogenic variants) over standard testing was 17.4% (95% CI, 13.5%-21.6%), 9.3% (95% CI, 6.6%-12.3%) and 35.9% (95% CI, 21.0%-52.3%) for all CHAs, isolated CHAs and CHAs associated with ECMs. The subgroup with the greatest yield was complex lesions/heterotaxy; 35.2% (95% CI 9.7%-65.3%). The most common syndrome was Kabuki syndrome (31/256, 12.1%) and most pathogenic variants occurred de novo and in autosomal dominant (monoallelic) disease causing genes (114/224, 50.9%). CONCLUSION: The likelihood of a monogenic aetiology in fetuses with multi-system CHAs is high. Clinicians must consider the clinical utility of offering PES in selected isolated cardiac lesions.

A report on the impact of rapid prenatal exome sequencing on the clinical management of 52 ongoing pregnancies: a retrospective review.

OBJECTIVE: Studies have shown that prenatal exome sequencing (PES) improves diagnostic yield in cases of fetal structural malformation. We have retrospectively analysed PES cases from two of the largest fetal medicine centres in the UK to determine the impact of results on management of a pregnancy. DESIGN: A retrospective review of clinical case notes. SETTING: Two tertiary fetal medicine centres. POPULATION: Pregnancies with fetal structural abnormalities referred to clinical genetics via a multidisciplinary team. METHODS: We retrospectively reviewed the notes of all patients who had undergone PES. DNA samples were obtained via chorionic villus sampling or amniocentesis. Variants were filtered using patient-specific panels and interpreted using American College of Medical Genetics guidelines. RESULTS: A molecular diagnosis was made in 42% (18/43) ongoing pregnancies; of this group, there was a significant management implication in 44% (8/18). A positive result contributed to the decision to terminate a pregnancy in 16% (7/43) of cases. A negative result had a significant impact on management in two cases by affirming the decision to continue pregnancy. CONCLUSIONS: We demonstrate that the results of PES can inform pregnancy management. Challenges include variant interpretation with limited phenotype information. These results emphasise the importance of the MDT and collecting phenotype and variant data. As this testing is soon to be widely available, we should look to move beyond diagnostic yield as a measure of the value of PES. TWEETABLE ABSTRACT: Prenatal exome sequencing can aid decision-making in pregnancy management; review ahead of routine implementation in NHS.

Biomarker changes associated with the development of resistance to aromatase inhibitors (AIs) in estrogen receptor-positive breast cancer.

BACKGROUND: The purpose of this study was to identify any differences in key biomarkers associated with estrogen action between biopsies taken at diagnosis and at recurrence or progression during treatment with an aromatase inhibitor (AI). PATIENTS AND METHODS: Patients were retrospectively identified from a clinical database as having relapsed or progressed during AI treatment. Immunohistochemistry was carried out against estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), insulin-like growth factor type-1 receptor (IGF1R), insulin receptor substrate-1 (IRS-1), stathmin, phosphatase and tensin homolog and Ki67. RESULTS: Fifty-five pairs of samples were identified with ER- and/or PgR-positive diseases. Four (7%) patients were ER-negative at progression. Overall, PgR levels were lower in the recurrence sample, but 35% of cases remained positive. IGF1R levels decreased significantly. There were no substantial changes in HER2, IRS-1 or stathmin levels to indicate a role in resistance. Higher Ki67 levels at resistance indicate more proliferative disease. CONCLUSIONS: The phenotype of AI-recurrent lesions shows high between-tumour heterogeneity. There is evidence of an increase in Ki67, a reduction in IGF1R and a loss of ER expression in some individuals and some activation of growth factor signalling pathways that may explain resistance in individuals and merit treatment targeted to those pathways. Biopsy at recurrence will be necessary to identify the relevant target for individuals.

Telomere length and early severe social deprivation: linking early adversity and cellular aging.

Accelerated telomere length attrition has been associated with psychological stress and early adversity in adults; however, no studies have examined whether telomere length in childhood is associated with early experiences. The Bucharest Early Intervention Project is a unique randomized controlled trial of foster care placement compared with continued care in institutions. As a result of the study design, participants were exposed to a quantified range of time in institutional care, and represented an ideal population in which to examine the association between a specific early adversity, institutional care and telomere length. We examined the association between average relative telomere length, telomere repeat copy number to single gene copy number (T/S) ratio and exposure to institutional care quantified as the percent of time at baseline (mean age 22 months) and at 54 months of age that each child lived in the institution. A significant negative correlation between T/S ratio and percentage of time was observed. Children with greater exposure to institutional care had significantly shorter relative telomere length in middle childhood. Gender modified this main effect. The percentage of time in institutional care at baseline significantly predicted telomere length in females, whereas the percentage of institutional care at 54 months was strongly predictive of telomere length in males. This is the first study to demonstrate an association between telomere length and institutionalization, the first study to find an association between adversity and telomere length in children, and contributes to the growing literature linking telomere length and early adversity.

Inter-rater reliability of the Pediatric Transplant Rating Instrument (P-TRI): challenges to reliably identifying adherence risk factors during pediatric pre-transplant evaluations.

The purpose of this study was to assess the inter-rater reliability of the P-TRI, a 17-item instrument developed to identify risk factors associated with poor treatment adherence in pediatric solid organ transplant candidates. Because factors influencing treatment adherence may vary with age, the 89 subject samples were divided into pre-adolescent (0-11 yr) and adolescent (12-19 yr) groups. Each subject received two independent P-TRI ratings based on pretransplant psychosocial assessments separately conducted by a PSYC and a SWTC. Inter-rater reliability was assessed using the delta statistic. Overall, agreement was higher in the pre-adolescent group, with delta>0.70 for five items and delta<0.30 for two items. For the adolescent group, one item had a delta>0.70 and seven items had a delta<0.30. Overall, PSYC P-TRI ratings indicated fewer areas of concern on items assessing family dynamics compared with SWTC P-TRI ratings, whereas the reverse was true for items related to psychiatric history. Results highlight the challenges of conducting a reliable pretransplant assessment of adherence-related risk factors and suggest the need for revisions to the P-TRI prior to its use in clinical practice.

Validity, reliability, and transcultural adaptations of the Bayley Scales of Infant and Toddler Development (BSID-III-NL) for children in Suriname.

BACKGROUND: A valid and reliable measure of infant neurodevelopment is needed in Suriname, South America. The Bayley Scales of Infant and Toddler Development, 3rd edition (BSID-III), was created for evaluation of United States infants and toddlers and subsequently validated for use in Dutch speaking infants of the Netherlands (BSID-III-NL). Given that Suriname was a previous Dutch colony and Dutch remains the national language of Suriname, this study sought to evaluate the psychometric properties of the BSID-III-NL in Suriname. AIMS: Given that the cultural context differs between Suriname, the United States, and the Netherlands, the aims of this study were to determine if any cultural adaptations of the BSID-III-NL were needed for Surinamese infants and to evaluate its psychometric properties. METHODS: Two hundred and ninety-nine infants between the ages of 10 to 26 months were assessed in three geographic regions of Suriname between May 2018 and July 2019. Minor adaptations to the BSID-III-NL imagery were made based on the input of Surinamese pediatricians and neuropsychologists who were also involved in the administration of the BSID-III-NL in Suriname. Raw scores were collected for the cognitive, communicative, and motor subscales of the BSID-III-NL. Factor structure was evaluated with exploratory factor analysis and cluster analysis, and reliability of internal consistency was assessed using Cronbach's alpha coefficient for each subscale. RESULTS: Content validity was endorsed by pediatricians and neuropsychologists in Suriname who participated in the administration of the BSID-III-NL. Construct validity was demonstrated through agreement of items from cluster analysis where at least 81.56% of all variability was explained by clustering with correct or incorrect responses and mean raw scores in subscales increased with age group. Cronbach's alpha coefficient was above 0.77 for all subscales. CONCLUSIONS: This internationally validated developmental measure was found to be valid and reliable in assessing neurodevelopment of infants in Suriname.

Caribbean Consortium for Research in Environmental and Occupational Health (CCREOH) Cohort Study: influences of complex environmental exposures on maternal and child health in Suriname.

PURPOSE: The Caribbean Consortium for Research in Environmental and Occupational Health prospective environmental epidemiologic cohort study addresses the impact of chemical and non-chemical environmental exposures on mother/child dyads in Suriname. The study determines associations between levels of environmental elements and toxicants in pregnant women, and birth outcomes and neurodevelopment in their children. PARTICIPANTS: Pregnant women (N=1143) were enrolled from December 2016 to July 2019 from three regions of Suriname: Paramaribo (N=738), Nickerie (N=204) and the tropical rainforest interior (N=201). Infants (N=992) were enrolled at birth. Follow-up will take place until children are 48 months old. FINDINGS TO DATE: Biospecimens and questionnaire data on physiological and psychosocial health in pregnant women have been analysed. 39.1% had hair mercury (Hg) levels exceeding values considered safe by international standards. Median hair Hg concentrations in women from Paramaribo (N=522) were 0.64 µg/g hair (IQRs 0.36-1.09; range 0.00-7.12), from Nickerie (N=176) 0.73 µg/g (IQR 0.45-1.05; range 0.00-5.79) and the interior (N=178) 3.48 µg/g (IQR 1.92-7.39; range 0.38-18.20). 96.1% of women ate fish, respective consumption of the three most consumed carnivorous species, Hoplias aimara, Serrasalmus rhombeus and Cichla ocellaris, known to have high Hg levels, was 44.4%, 19.3% and 26.3%, respectively, and was greater among the interior subcohort. 89% frequently consumed the vegetable tannia, samples of which showed presence of worldwide banned pesticides. 24.9% of pregnant women had Edinburgh Depression Scale scores indicative of probable depression. FUTURE PLANS: Fish consumption advisories are in development, especially relevant to interior women for whom fish consumption is likely to be the primary source of Hg exposure. Effects of potentially beneficial neuroprotective factors in fish that may counter neurotoxic effects of Hg are being examined. A pesticide literacy assessment in pregnant women is in progress. Neurodevelopmental assessments and telomere length measurements of the children to evaluate long-term effects of prenatal exposures to toxicant mixtures are ongoing.

Cell-Free Fetal DNA Testing for Prenatal Diagnosis.

Prenatal diagnosis and screening have undergone rapid development in recent years, with advances in molecular technology driving the change. Noninvasive prenatal testing (NIPT) for Down syndrome as a highly sensitive screening test is now available worldwide through the commercial sector with many countries moving toward implementation into their publically funded maternity systems. Noninvasive prenatal diagnosis (NIPD) can now be performed for definitive diagnosis of some recessive and X-linked conditions, rather than just paternally inherited dominant and de novo conditions. NIPD/T offers pregnant couples greater choice during their pregnancy as these safer methods avoid the risk of miscarriage associated with invasive testing. As the cost of sequencing falls and technology develops further, there may well be potential for whole exome and whole genome sequencing of the unborn fetus using cell-free DNA in the maternal plasma. How such assays can or should be implemented into the clinical setting remain an area of significant debate, but it is clear that the progress made to date for safer prenatal testing has been welcomed by expectant couples and their healthcare professionals.

Assembly of a high-resolution map of the Acadian Usher syndrome region and localization of the nuclear EF-hand acidic gene.

Usher syndrome type 1C (USH1C) occurs in a small population of Acadian descendants from southwestern Louisiana. Linkage and linkage disequilibrium analyses localize USH1C to chromosome 11p between markers D11S1397 and D11S1888, an interval of less than 680 kb. Here, we refine the USH1C linkage to a region less than 400 kb, between genetic markers D11S1397 and D11S1890. Using 17 genetic markers from this interval, we have isolated a contiguous set of 60 bacterial artificial chromosomes (BACs) that span the USH1C critical region. Exon trapping of BAC clones from this region resulted in the recovery of an exon of the nuclear EF-hand acidic (NEFA) gene. However, DNA sequence analysis of the NEFA cDNA from lymphocytes of affected individuals provided no evidence of mutation, making structural mutations in the NEFA protein unlikely as the cellular cause of Acadian Usher syndrome.

The mouse deafness locus (dn) is associated with an inversion on chromosome 19.

Recombination data for the mouse deafness locus (dn) on chromosome 19 are consistent with the presence of an inversion for which one of the breakpoints is between D19Mit14 and D19Mit96, a distance of less than 226 kb. Fluorescence in situ hybridization studies using a bacterial artificial chromosome on interphase (G1) nuclei provide additional support for the presence of an inversion. The dn gene is probably the orthologue of the human DFNB7/DFNB11 gene on chromosome 9.

Smooth muscle specific overexpression of p22phox potentiates carotid artery wall thickening in response to injury.

We hypothesized that transgenic mice overexpressing the p22(phox) subunit of the NADPH oxidase selectively in smooth muscle (Tg(p22smc)) would exhibit an exacerbated response to transluminal carotid injury compared to wild-type mice. To examine the role of reactive oxygen species (ROS) as a mediator of vascular injury, the injury response was quantified by measuring wall thickness (WT) and cross-sectional wall area (CSWA) of the injured and noninjured arteries in both Tg(p22smc) and wild-type animals at days 3, 7, and 14 after injury. Akt, p38 MAPK, and Src activation were evaluated at the same time points using Western blotting. WT and CSWA following injury were significantly greater in Tg(p22smc) mice at both 7 and 14 days after injury while noninjured contralateral carotids were similar between groups. Apocynin treatment attenuated the injury response in both groups and rendered the response similar between Tg(p22smc) mice and wild-type mice. Following injury, carotid arteries from Tg(p22smc) mice demonstrated elevated activation of Akt at day 3, while p38 MAPK and Src activation was elevated at day 7 compared to wild-type mice. Both increased activation and temporal regulation of these signaling pathways may contribute to enhanced vascular growth in response to injury in this transgenic model of elevated vascular ROS.

Refining the DFNB7-DFNB11 deafness locus using intragenic polymorphisms in a novel gene, TMEM2.

The combined DFNB7-DFNB11 deafness locus maps to chromosome 9q13-q21 between markers D9S1806 and D9S769. We have determined the cDNA sequence and genomic structure of a novel gene, TMEM2, that maps to this interval and is expressed in the cochlea. The mouse orthologue of this gene (Tmem2) maps to the murine dn (deafness) locus on mouse chromosome 19. Screens for transmembrane helices reveal the presence of at least one putative transmembrane domain in the TMEM2 protein. To determine whether mutations in TMEM2 cause hearing loss at the DFNB7-DFNB11 locus, we screened the coding region of this gene in DFNB7-DFNB11 affected families by direct sequencing. All DNA variants that segregated with the deafness and changed the predicted amino acid sequence of TMEM2 were common polymorphisms, as demonstrated by allele-specific amplification of pooled control DNA. Northern blot analysis showed no difference in transcript size or expression level of Tmem2 in dn/dn and control mice. The intragenic polymorphisms in TMEM2 represent a novel centromeric boundary for the DFNB7-DFNB11 interval.

Identification and mutation analysis of a cochlear-expressed, zinc finger protein gene at the DFNB7/11 and dn hearing-loss loci on human chromosome 9q and mouse chromosome 19.

The DFNB7/11 locus for autosomal recessive non-syndromic hearing loss (ARNSHL) has been mapped to an approx. 1.5 Mb interval on human chromosome 9q13-q21. We have determined the cDNA sequence and genomic structure of a novel cochlear-expressed gene, ZNF216, that maps to the DFNB7/11 interval. The mouse orthologue of this gene maps to the murine dn (deafness) locus on mouse chromosome 19. The ZNF216 gene is highly conserved between human and mouse, and contains two regions that show homology to the putative zinc linger domains of other proteins. To determine it mutations in ZNF216 might be the cause of hearing loss at the DFNB7/11 locus, we screened the coding region of this gene in DFNB7/11 families by direct sequencing. No potential disease-causing mutations were found. In addition, Northern blot analysis showed no difference in ZNF216 transcript size or abundance between dn and control mice. These data Suggest that the ZNF216 gene is unlikely to be responsible for hearing loss at the DFNB7/11 and dn loci.

Detection of a coronavirus from turkey poults in Europe genetically related to infectious bronchitis virus of chickens.

Intestinal contents of 13-day-old turkey poults in Great Britain were analysed as the birds showed stunting, unevenness and lameness, with 4% mortality. At post mortem examination, the main gross features were fluid caecal and intestinal contents. Histological examination of tissues was largely unremarkable, apart from some sections that showed crypt dilation and flattened epithelia. Negative contrast electron microscopy of caecal contents revealed virus particles, which in size and morphology had the appearance of a coronavirus. RNA was extracted (turkey/UK/412/00) and used in a number of reverse transcription-polymerase chain reactions (RT-PCRs) with the oligonucleotides based on sequences derived from avian infectious bronchitis virus (IBV), a coronavirus of domestic fowl. The RT-PCRs confirmed that turkey/UK/412/00 was a coronavirus and, moreover, showed that it had the same partial gene order (S-E-M-5-N-3' untranslated region) as IBV. This gene order is unlike that of any known mammalian coronavirus, which does not have a gene analogous to the gene 5 of IBV.The gene 5 of the turkey virus had two open reading frames, 5a and 5b, as in IBV and the coronaviruses isolated from turkeys in North America. The turkey/UK/412/00 also resembled IBV, but not mammalian coronaviruses, in having three open reading frames in the gene encoding E protein (gene 3). The percentage differences between the nucleotide sequences of genes 3 and 5 and the 3' untranslated region of turkey/UK/412/00 when compared with those of IBVs were similar to the differences observed when different strains of IBV were compared with each other. No sequences unique to the turkey isolates were identified. These results demonstrate, for the first time, that a coronavirus was associated with disease in turkeys outside of North America and that it is a Group 3 coronavirus, like IBV.

Failure to induce neoplasia in nude mice by injection of disrupted cells from continuous cell lines.

Nude mice were injected subcutaneously with disrupted cells from three continuous cell lines (HeLa, NCTC clone 2472 and Morris hepatoma). No tumours were observed at either the inoculation site or in other organs taken at 35 or 90 days after injection. Live cells from one line (HeLa) produced tumours at the inoculation site after eight to 12 days.

In vitro metabolism of benzo[a]pyrene and dibenzo[def,p]chrysene in rodent and human hepatic microsomes.

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous and often carcinogenic contaminants released into the environment during natural and anthropogenic combustion processes. Benzo[a]pyrene (B[a]P) is the prototypical carcinogenic PAH, and dibenzo[def,p]chrysene (DBC) is a less prevalent, but highly potent transplacental carcinogenic PAH. Both are metabolically activated by isoforms of the cytochrome P450 enzyme superfamily to form reactive carcinogenic and cytotoxic metabolites. Metabolism of B[a]P and DBC was studied in hepatic microsomes of male Sprague-Dawley rats, naïve and pregnant female B6129SF1/J mice, and female humans, corresponding to available pharmacokinetic data. Michaelis-Menten saturation kinetic parameters including maximum rates of metabolism (VMAX, nmol/min/mg microsomal protein), affinity constants (KM, µM), and rates of intrinsic clearance (CLINT, ml/min/kg body weight) were calculated from substrate depletion data. CLINT was also estimated from substrate depletion data using the alternative in vitro half-life method. VMAX and CLINT were higher for B[a]P than DBC, regardless of species. Clearance for both B[a]P and DBC was highest in naïve female mice and lowest in female humans. Clearance rates of B[a]P and DBC in male rat were more similar to female human than to female mice. Clearance of DBC in liver microsomes from pregnant mice was reduced compared to naïve mice, consistent with reduced active P450 protein levels and elevated tissue concentrations and residence times for DBC observed in previous in vivo pharmacokinetic studies. These findings suggest that rats are a more appropriate model organism for human PAH metabolism, and that pregnancy's effects on metabolism should be further explored.

Changes in breast cancer biomarkers in the IGF1R/PI3K pathway in recurrent breast cancer after tamoxifen treatment.

Development of resistance to the antioestrogen tamoxifen occurs in a large proportion of patients with oestrogen receptor-positive (ER+) breast cancer and is an important clinical challenge. While loss of ER occurs in c.20% of tamoxifen-resistant tumours, this cannot be the sole explanation for tamoxifen treatment failure. PI3K pathway activation, including by insulin-like growth factor receptor 1 (IGF1R), has been implicated in some resistance models. The primary aim was to determine whether evidence exists in clinical breast cancer for a role of IGF1R and/or the PI3K pathway, in acquisition of resistance to tamoxifen. Invasive primary and recurrent tamoxifen-resistant tumours from the same patient (n=77) were assessed for changes in ER, progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), IGF1R, stathmin, PTEN expression and PIK3CA mutations where possible. ER and PgR levels were significantly reduced at recurrence with 22 and 45%, respectively, showing negative status at this time. Acquisition of HER2 overexpression occurred in 6% of cases. IGF1R expression was significantly reduced in both ER+ and ER- recurrences and stathmin levels increased. A positive association between stathmin and IGF1R emerged in recurrent samples, despite their opposing relationships with ER, suggesting some coalescence of their activities may be acquired. The data confirm loss of ER and PgR and gain of HER2 in some tamoxifen-resistant tumours. There is no evidence for IGF1R gain in tamoxifen resistance; increases in stathmin levels suggest that activation of the PI3K pathway may have contributed, but PTEN loss and PIK3CA hotspot mutations were relatively rare.