Detailed characterization of chromosomal abnormalities, a common cause for congenital abnormalities and pregnancy loss, is critical for elucidating genes for human fetal development. Here, 2,186 ...product‐of‐conception samples were tested for copy‐number variations (CNVs) at two clinical diagnostic centers using whole‐genome sequencing and high‐resolution chromosomal microarray analysis. We developed a new gene discovery approach to predict potential developmental genes and identified 275 candidate genes from CNVs detected from both datasets. Based on Mouse Genome Informatics (MGI) and Zebrafish model organism database (ZFIN), 75% of identified genes could lead to developmental defects when mutated. Genes involved in embryonic development, gene transcription, and regulation of biological processes were significantly enriched. Especially, transcription factors and gene families sharing specific protein domains predominated, which included known developmental genes such as HOX, NKX homeodomain genes, and helix‐loop‐helix containing HAND2, NEUROG2, and NEUROD1 as well as potential novel developmental genes. We observed that developmental genes were denser in certain chromosomal regions, enabling identification of 31 potential genomic loci with clustered genes associated with development.
Identification of critical genes for human early development within CNVs associated with pregnancy loss reveals the genomic clusters of developmental genes in the human genome.
Defects in the cohesin pathway are associated with cohesinopathies, notably Cornelia de Lange syndrome (CdLS). We aimed to delineate pathogenic variants in known and candidate cohesinopathy genes ...from a clinical exome perspective.
We retrospectively studied patients referred for clinical exome sequencing (CES, N = 10,698). Patients with causative variants in novel or recently described cohesinopathy genes were enrolled for phenotypic characterization.
Pathogenic or likely pathogenic single-nucleotide and insertion/deletion variants (SNVs/indels) were identified in established disease genes including NIPBL (N = 5), SMC1A (N = 14), SMC3 (N = 4), RAD21 (N = 2), and HDAC8 (N = 8). The phenotypes in this genetically defined cohort skew towards the mild end of CdLS spectrum as compared with phenotype-driven cohorts. Candidate or recently reported cohesinopathy genes were supported by de novo SNVs/indels in STAG1 (N = 3), STAG2 (N = 5), PDS5A (N = 1), and WAPL (N = 1), and one inherited SNV in PDS5A. We also identified copy-number deletions affecting STAG1 (two de novo, one of unknown inheritance) and STAG2 (one of unknown inheritance). Patients with STAG1 and STAG2 variants presented with overlapping features yet without characteristic facial features of CdLS.
CES effectively identified disease-causing alleles at the mild end of the cohensinopathy spectrum and enabled characterization of candidate disease genes.
Abstract
Kagomé metals are widely recognized, versatile platforms for exploring topological properties, unconventional electronic correlations, magnetic frustration, and superconductivity. In the
R
V
...6
Sn
6
family of materials (
R
= Sc, Y, Lu), ScV
6
Sn
6
hosts an unusual charge density wave ground state as well as structural similarities with the
A
V
3
Sb
5
system (
A
= K, Cs, Rb). In this work, we combine Raman scattering spectroscopy with first-principles lattice dynamics calculations to reveal phonon mixing processes in the charge density wave state of ScV
6
Sn
6
. In the low temperature phase, we find at least four new peaks in the vicinity of the V-containing totally symmetric mode near 240 cm
−1
suggesting that the density wave acts to mix modes of
P
6/
m
m
m
and
$$R\bar{3}m$$
R
3
¯
m
symmetry - a result that we quantify by projecting phonons of the high symmetry state onto those of the lower symmetry structure. We also test the stability of the short-range ordered density wave state under compression and propose that both physical and chemical pressure quench the effect. We discuss these findings in terms of symmetry and the structure-property trends that can be unraveled in this system.
Degradation of proteins by the ubiquitin-proteasome system (UPS) is an essential biological process in the development of eukaryotic organisms. Dysregulation of this mechanism leads to numerous human ...neurodegenerative or neurodevelopmental disorders. Through a multi-center collaboration, we identified six de novo genomic deletions and four de novo point mutations involving PSMD12, encoding the non-ATPase subunit PSMD12 (aka RPN5) of the 19S regulator of 26S proteasome complex, in unrelated individuals with intellectual disability, congenital malformations, ophthalmologic anomalies, feeding difficulties, deafness, and subtle dysmorphic facial features. We observed reduced PSMD12 levels and an accumulation of ubiquitinated proteins without any impairment of proteasome catalytic activity. Our PSMD12 loss-of-function zebrafish CRISPR/Cas9 model exhibited microcephaly, decreased convolution of the renal tubules, and abnormal craniofacial morphology. Our data support the biological importance of PSMD12 as a scaffolding subunit in proteasome function during development and neurogenesis in particular; they enable the definition of a neurodevelopmental disorder due to PSMD12 variants, expanding the phenotypic spectrum of UPS-dependent disorders.
In this chapter, we provide a systematic overview of the published guidelines and validation procedures for fluorescence in situ hybridization (FISH) probes for clinical diagnostic use. FISH ...probes-which are classified as molecular probes or analyte-specific reagents (ASRs)-have been extensively used in vitro for both clinical diagnosis and research. Most commercially available FISH probes in the United States are strictly regulated by the U.S. Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), the Centers for Medicare & Medicaid Services (CMS) the Clinical Laboratory Improvement Amendments (CLIA), and the College of American Pathologists (CAP). Although home-brewed FISH probes-defined as probes made in-house or acquired from a source that does not supply them to other laboratories-are not regulated by these agencies, they too must undergo the same individual validation process prior to clinical use as their commercial counterparts. Validation of a FISH probe involves initial validation and ongoing verification of the test system. Initial validation includes assessment of a probe's technical specifications, establishment of its standard operational procedure (SOP), determination of its clinical sensitivity and specificity, development of its cutoff, baseline, and normal reference ranges, gathering of analytics, confirmation of its applicability to a specific research or clinical setting, testing of samples with or without the abnormalities that the probe is meant to detect, staff training, and report building. Ongoing verification of the test system involves testing additional normal and abnormal samples using the same method employed during the initial validation of the probe.
The brain is sensitive to the dose of MeCP2 such that small fluctuations in protein quantity lead to neuropsychiatric disease. Despite the importance of MeCP2 levels to brain function, little is ...known about its regulation. In this study, we report eleven individuals with neuropsychiatric disease and copy-number variations spanning NUDT21, which encodes a subunit of pre-mRNA cleavage factor Im. Investigations of MECP2 mRNA and protein abundance in patient-derived lymphoblastoid cells from one NUDT21 deletion and three duplication cases show that NUDT21 regulates MeCP2 protein quantity. Elevated NUDT21 increases usage of the distal polyadenylation site in the MECP2 3' UTR, resulting in an enrichment of inefficiently translated long mRNA isoforms. Furthermore, normalization of NUDT21 via siRNA-mediated knockdown in duplication patient lymphoblasts restores MeCP2 to normal levels. Ultimately, we identify NUDT21 as a novel candidate for intellectual disability and neuropsychiatric disease, and elucidate a mechanism of pathogenesis by MeCP2 dysregulation via altered alternative polyadenylation.
This two-site randomised trial compared the effectiveness of a voluntary sector-led, community-based diabetes prevention programme to a waiting-list control group at 6 months, and included an ...observational follow-up of the intervention arm to 12 months.
Adults aged 18-75 years at increased risk of developing type 2 diabetes due to elevated blood glucose and being overweight were recruited from primary care practices at two UK sites, with data collected in participants' homes or community venues. Participants were randomised using an online central allocation service. The intervention, comprising the prototype "Living Well, Taking Control" (LWTC) programme, involved four weekly two-hour group sessions held in local community venues to promote changes in diet and physical activity, plus planned follow-up contacts at two, three, six, nine and 12 months alongside 5 hours of additional activities/classes. Waiting list controls received usual care for 6 months before accessing the programme. The primary outcome was weight loss at 6 months. Secondary outcomes included glycated haemoglobin (HbA1c), blood pressure, physical activity, diet, health status and well-being. Only researchers conducting analyses were blinded.
The target sample of 314 participants (157 each arm) was largely representative of local populations, including 44% men, 26% from ethnic minorities and 33% living in deprived areas. Primary outcome data were available for 285 (91%) participants (141 intervention, 144 control). Between baseline and 6 months, intervention participants on average lost more weight than controls (- 1.7 kg, 95% CI - 2.59 to - 0.85). Higher attendance was associated with greater weight loss (- 3.0 kg, 95% CI - 4.5 to - 1.5). The prototype LWTC programme more than doubled the proportion of participants losing > 5% of their body weight (21% intervention vs. 8% control, OR 2.83, 95% CI 1.36 to 5.90) and improved self-reported dietary behaviour and health status. There were no impacts on HbA1c, blood pressure, physical activity and well-being at 6 months and, amongst intervention participants, few further changes from six to 12-months (e.g. average weight re-gain 0.36 kg, 95% CI - 0.20 to 0.91). There were no serious adverse events but four exercise-related injuries were reported in the intervention arm.
This voluntary sector-led diabetes prevention programme reached a broad spectrum of the population and had modest effects on weight-related outcomes, but limited impacts on other diabetes risk factors.
Trial registration number: ISRCTN70221670, 5 September 2014 Funder (National Institute for Health Research School for Public Health Research) project reference number: SPHR-EXE-PES-COM.
van der Waals materials are exceptionally responsive to external stimuli. Pressure-induced layer sliding, metallicity, and superconductivity are fascinating examples. Inspired by opportunities in ...this area, we combined high-pressure optical spectroscopies and first-principles calculations to reveal piezochromism in MnPS3. Dramatic color changes (green → yellow → red → black) take place as the charge gap shifts across the visible regime and into the near infrared, moving systematically toward closure at a rate of approximately −50 meV/GPa. This effect is quenched by the appearance of the insulator–metal transition. In addition to uncovering an intriguing and tunable functionality that is likely to appear in other complex chalcogenides, the discovery that piezochromism can be deterministically controlled at room temperature accelerates the development of technologies that take advantage of stress-activated modification of electronic structure.
Background
A comprehensive evaluation of bariatric surgery is required to inform decision-making. This will include measures of benefit and risk. It is possible that stakeholders involved with ...surgery value these outcomes differently, although this has not previously been explored. This study aimed to investigate and compare how professionals and patients prioritise outcomes of bariatric surgery.
Methods
Systematic reviews and qualitative interviews created an exhaustive list of outcomes. This informed the development of a 130-item questionnaire, structured in four sections (complications of surgery; clinical effectiveness; signs, symptoms, and other measures; quality of life). Health professionals and patients rated the importance of each item on a 1–9 scale. Items rated 8–9 by at least 70 % of the participants were considered prioritised. Items prioritised in each section were compared between professionals and patients and interrater agreement assessed using kappa statistics (
ĸ
).
Results
One hundred sixty-eight out of four hundred fifty-nine professionals (36.6 %) and 90/465 patients (19.4 %) completed the questionnaire. Professionals and patients prioritised 18 and 25 items, respectively, with 10 overlapping items and 23 discordant items (
ĸ
0.363). Examples of items prioritised by both included ‘diabetes’ and ‘leakage from bowel joins’. Examples of discordant items included ‘re-admission rates’ (professionals only) and ‘excess skin’ (patients only). Poor agreement was seen in the ‘quality of life’ section (0 overlapping items, 8 discordant,
ĸ
−0.036).
Conclusions
Although there was some overlap of outcomes prioritised by professionals and patients, there were important differences. We recommend that the views of all relevant health professionals and patients are considered when deciding on outcomes to evaluate bariatric surgery.
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