Recommendations for laboratory workflow that better support centralised amalgamation of genomic variant data: findings from CanVIG-UK national molecular laboratory survey.

BACKGROUND: National and international amalgamation of genomic data offers opportunity for research and audit, including analyses enabling improved classification of variants of uncertain significance. Review of individual-level data from National Health Service (NHS) testing of cancer susceptibility genes (2002-2023) submitted to the National Disease Registration Service revealed heterogeneity across participating laboratories regarding (1) the structure, quality and completeness of submitted data, and (2) the ease with which that data could be assembled locally for submission. METHODS: In May 2023, we undertook a closed online survey of 51 clinical scientists who provided consensus responses representing all 17 of 17 NHS molecular genetic laboratories in England and Wales which undertake NHS diagnostic analyses of cancer susceptibility genes. The survey included 18 questions relating to 'next-generation sequencing workflow' (11), 'variant classification' (3) and 'phenotypical context' (4). RESULTS: Widely differing processes were reported for transfer of variant data into their local LIMS (Laboratory Information Management System), for the formatting in which the variants are stored in the LIMS and which classes of variants are retained in the local LIMS. Differing local provisions and workflow for variant classifications were also reported, including the resources provided and the mechanisms by which classifications are stored. CONCLUSION: The survey responses illustrate heterogeneous laboratory workflow for preparation of genomic variant data from local LIMS for centralised submission. Workflow is often labour-intensive and inefficient, involving multiple manual steps which introduce opportunities for error. These survey findings and adoption of the concomitant recommendations may support improvement in laboratory dataflows, better facilitating submission of data for central amalgamation.

Updated variant curation expert panel criteria and pathogenicity classifications for 251 variants for RYR1-related malignant hyperthermia susceptibility.

The ClinGen malignant hyperthermia susceptibility (MHS) variant curation expert panel specified the American College of Medical Genetics and Genomics/Association of Molecular Pathologists (ACMG/AMP) criteria for RYR1-related MHS and a pilot analysis of 84 variants was published. We have now classified an additional 251 variants for RYR1-related MHS according to current ClinGen standards and updated the criteria where necessary. Criterion PS4 was modified such that individuals with multiple RYR1 variants classified as pathogenic (P), likely pathogenic (LP), or variant of uncertain significance (VUS) were not considered as providing evidence for pathogenicity. Criteria PS1 and PM5 were revised to consider LP variants at the same amino-acid residue as providing evidence for pathogenicity at reduced strength. Finally, PM1 was revised such that if PS1 or PM5 are used PM1, if applicable, should be downgraded to supporting. Of the 251 RYR1 variants, 42 were classified as P/LP, 16 as B/LB, and 193 as VUS. The primary driver of 175 VUS classifications was insufficient evidence supporting pathogenicity, rather than evidence against pathogenicity. Functional data supporting PS3/BS3 was identified for only 13 variants. Based on the posterior probabilities of pathogenicity and variant frequencies in gnomAD, we estimated the prevalence of individuals with RYR1-related MHS pathogenic variants to be between 1/300 and 1/1075, considerably higher than current estimates. We have updated ACMG/AMP criteria for RYR1-related MHS and classified 251 variants. We suggest that prioritization of functional studies is needed to resolve the large number of VUS classifications and allow for appropriate risk assessment. RYR1-related MHS pathogenic variants are likely to be more common than currently appreciated.

Germline mismatch repair (MMR) gene analyses from English NHS regional molecular genomics laboratories 1996-2020: development of a national resource of patient-level genomics laboratory records.

OBJECTIVE: To describe national patterns of National Health Service (NHS) analysis of mismatch repair (MMR) genes in England using individual-level data submitted to the National Disease Registration Service (NDRS) by the NHS regional molecular genetics laboratories. DESIGN: Laboratories submitted individual-level patient data to NDRS against a prescribed data model, including (1) patient identifiers, (2) test episode data, (3) per-gene results and (4) detected sequence variants. Individualised per-laboratory algorithms were designed and applied in NDRS to extract and map the data to the common data model. Laboratory-level MMR activity audit data from the Clinical Molecular Genetics Society/Association of Clinical Genomic Science were used to assess early years' missing data. RESULTS: Individual-level data from patients undergoing NHS MMR germline genetic testing were submitted from all 13 English laboratories performing MMR analyses, comprising in total 16 722 patients (9649 full-gene, 7073 targeted), with the earliest submission from 2000. The NDRS dataset is estimated to comprise >60% of NHS MMR analyses performed since inception of NHS MMR analysis, with complete national data for full-gene analyses for 2016 onwards. Out of 9649 full-gene tests, 2724 had an abnormal result, approximately 70% of which were (likely) pathogenic. Data linkage to the National Cancer Registry demonstrated colorectal cancer was the most frequent cancer type in which full-gene analysis was performed. CONCLUSION: The NDRS MMR dataset is a unique national pan-laboratory amalgamation of individual-level clinical and genomic patient data with pseudonymised identifiers enabling linkage to other national datasets. This growing resource will enable longitudinal research and can form the basis of a live national genomic disease registry.

Rapid nursing redeployment from a specialist ward to a COVID-19 high-dependency setting.

BACKGROUND: Redeployment in health care can have a negative impact on the mental wellbeing of staff. Advanced planning and provisions for wellbeing support for health professionals has been recommended following previous pandemics. At the authors' institution nurses were redeployed overnight from a specialist cystic fibrosis ward to a COVID-19 high-dependency unit. AIM: To evaluate nurses' wellbeing following this redeployment during the first wave of the COVID-19 pandemic. METHOD: A mixed online survey, consisting of both open and closed questions, based on literature, preliminary results of the Impact of COVID-19 on the Nursing and Midwifery Workforce (ICON) study and staff feedback. This was sent to 28 nurses to explore their feelings and experiences of redeployment to a COVID-19 environment. Purposive sampling was used to select study participants while thematic analysis and descriptive statistics were used to analyse the data. FINDINGS: The survey had an 86% response rate. Using thematic analysis three key themes emerged: redeployment anxiety, lack of organisational preparedness and newfound teamworking. More than half (57%) of respondents expressed anxiety and concern when told of their redeployment; 52% reported that they did not receive adequate support from senior staff and management. However, 74% reported that they felt their nursing was positively influenced by support and teamwork from those in patient-facing roles. Twenty-five percent reported that they were looking for a new job or leaving their current role. CONCLUSION: This study examines the effects that redeployment to a COVID-19 environment has had on nurses. It highlights the need for further improvement to ensure redeployed staff are supported to safeguard their mental wellbeing.

ADHD symptoms and diagnosis in adult preterms: systematic review, IPD meta-analysis, and register-linkage study.

BACKGROUND: This study examined differences in ADHD symptoms and diagnosis between preterm and term-born adults (≥18 years), and tested if ADHD is related to gestational age, birth weight, multiple births, or neonatal complications in preterm borns. METHODS: (1) A systematic review compared ADHD symptom self-reports and diagnosis between preterm and term-born adults published in PubMed, Web of Science, and PROQUEST until April 2021; (2) a one-stage Individual Participant Data(IPD) meta-analysis (n = 1385 preterm, n = 1633 term; born 1978-1995) examined differences in self-reported ADHD symptoms[age 18-36 years]; and (3) a population-based register-linkage study of all live births in Finland (01/01/1987-31/12/1998; n = 37538 preterm, n = 691,616 term) examined ADHD diagnosis risk in adulthood (≥18 years) until 31/12/2016. RESULTS: Systematic review results were conflicting. In the IPD meta-analysis, ADHD symptoms levels were similar across groups (mean z-score difference 0.00;95% confidence interval [95% CI] -0.07, 0.07). Whereas in the register-linkage study, adults born preterm had a higher relative risk (RR) for ADHD diagnosis compared to term controls (RR = 1.26, 95% CI 1.12, 1.41, p < 0.001). Among preterms, as gestation length (RR = 0.93, 95% CI 0.89, 0.97, p < 0.001) and SD birth weight z-score (RR = 0.88, 95% CI 0.80, 0.97, p < 0.001) increased, ADHD risk decreased. CONCLUSIONS: While preterm adults may not report higher levels of ADHD symptoms, their risk of ADHD diagnosis in adulthood is higher. IMPACT: Preterm-born adults do not self-report higher levels of ADHD symptoms, yet are more likely to receive an ADHD diagnosis in adulthood compared to term-borns. Previous evidence has consisted of limited sample sizes of adults and used different methods with inconsistent findings. This study assessed adult self-reported symptoms across 8 harmonized cohorts and contrasted the findings with diagnosed ADHD in a population-based register-linkage study. Preterm-born adults may not self-report increased ADHD symptoms. However, they have a higher risk of ADHD diagnosis, warranting preventive strategies and interventions to reduce the presentation of more severe ADHD symptomatology in adulthood.

Oil contamination of sediments by freeze-drying versus air-drying for organic geochemical analysis.

Freeze-drying is widely used in geochemical laboratories for preparing wet solid environmental samples such as sediments and soils before being analyzed for their contents and states of various metal elements and labile organic components that may be temperature- and/or redox-sensitive. Screening bulk geochemical analysis of two Artic lake sediment samples prepared by freeze-drying displayed unexpectedly high contents of labile organic matter (OM) represented by the Rock-Eval S1 peaks (e.g., 8.12 and 4.84 mg HC/g sediment). The amount of labile OM was reduced greatly for the freeze-dried sediment samples after a thorough cleaning of the freeze-drier sample chamber (e.g., 2.75 and 1.46 mg HC/g sediment), but was still significantly higher than that of the equivalent air-dried samples (e.g., 0.76 and 0.23 mg HC/g sediment). Compositional analysis of the labile OM fractions by gas chromatography (GC) of both freeze-dried and air-dried aliquots of the same sediments indicates the presence of unresolved complex mixture (UCM) humps of C10-C23 hydrocarbons in the freeze-dried samples. In contrast, air-dried samples, either real sediments or blank laboratory materials represented by clean sand and thermally spent shale, do not show the C10-C23 hydrocarbon UCM humps on their GC traces. The hydrocarbon UCM humps persist in the freeze-dried samples even they further went through air-drying at ambient conditions. Both bulk and compositional analytical results in this work appear to indicate the potential risk of introduction of external hydrocarbons to the prepared materials during freeze-drying process, especially if an aged freeze-drier was used without being thoroughly cleaned and if pump oil and cooling fluids were components of the device.

Screening of potential novel candidate genes in schwannomatosis patients.

Schwannomatosis comprises a group of hereditary tumor predisposition syndromes characterized by, usually benign, multiple nerve sheath tumors, which frequently cause severe pain that does not typically respond to drug treatments. The most common schwannomatosis-associated gene is NF2, but SMARCB1 and LZTR1 are also associated. There are still many cases in which no pathogenic variants (PVs) have been identified, suggesting the existence of as yet unidentified genetic risk factors. In this study, we performed extended genetic screening of 75 unrelated schwannomatosis patients without identified germline PVs in NF2, LZTR1, or SMARCB1. Screening of the coding region of DGCR8, COQ6, CDKN2A, and CDKN2B was carried out, based on previous reports that point to these genes as potential candidate genes for schwannomatosis. Deletions or duplications in CDKN2A, CDKN2B, and adjacent chromosome 9 region were assessed by multiplex ligation-dependent probe amplification analysis. Sequencing analysis of a patient with multiple schwannomas and melanomas identified a novel duplication in the coding region of CDKN2A, disrupting both p14ARF and p16INK4a. Our results suggest that none of these genes are major contributors to schwannomatosis risk but the possibility remains that they may have a role in more complex mechanisms for tumor predisposition.

Reclassification of clinically-detected sequence variants: Framework for genetic clinicians and clinical scientists by CanVIG-UK (Cancer Variant Interpretation Group UK).

PURPOSE: Variant classifications may change over time, driven by emergence of fresh or contradictory evidence or evolution in weighing or combination of evidence items. For variant classifications above the actionability threshold, which is classification of likely pathogenic or pathogenic, clinical actions may be irreversible, such as risk-reducing surgery or prenatal interventions. Variant reclassification up or down across the actionability threshold can therefore have significant clinical consequences. Laboratory approaches to variant reinterpretation and reclassification vary widely. METHODS: Cancer Variant Interpretation Group UK is a multidisciplinary network of clinical scientists and genetic clinicians from across the 24 Molecular Diagnostic Laboratories and Clinical Genetics Services of the United Kingdom (NHS) and Republic of Ireland. We undertook surveys, polls, and national meetings of Cancer Variant Interpretation Group UK to evaluate opinions about clinical and laboratory management regarding variant reclassification. RESULTS: We generated a consensus framework on variant reclassification applicable to cancer susceptibility genes and other clinical areas, which provides explicit recommendations for clinical and laboratory management of variant reclassification scenarios on the basis of the nature of the new evidence, the magnitude of evidence shift, and the final classification score. CONCLUSION: In this framework, clinical and laboratory resources are targeted for maximal clinical effect and minimal patient harm, as appropriate to all resource-constrained health care settings.

Quantifying prediction of pathogenicity for within-codon concordance (PM5) using 7541 functional classifications of BRCA1 and MSH2 missense variants.

PURPOSE: Conditions and thresholds applied for evidence weighting of within-codon concordance (PM5) for pathogenicity vary widely between laboratories and expert groups. Because of the sparseness of available clinical classifications, there is little evidence for variation in practice. METHODS: We used as a truthset 7541 dichotomous functional classifications of BRCA1 and MSH2, spanning 311 codons of BRCA1 and 918 codons of MSH2, generated from large-scale functional assays that have been shown to correlate excellently with clinical classifications. We assessed PM5 at 5 stringencies with incorporation of 8 in silico tools. For each analysis, we quantified a positive likelihood ratio (pLR, true positive rate/false positive rate), the predictive value of PM5-lookup in ClinVar compared with the functional truthset. RESULTS: pLR was 16.3 (10.6-24.9) for variants for which there was exactly 1 additional colocated deleterious variant on ClinVar, and the variant under examination was equally or more damaging when analyzed using BLOSUM62. pLR was 71.5 (37.8-135.3) for variants for which there were 2 or more colocated deleterious ClinVar variants, and the variant under examination was equally or more damaging than at least 1 colocated variant when analyzed using BLOSUM62. CONCLUSION: These analyses support the graded use of PM5, with potential to use it at higher evidence weighting where more stringent criteria are met.

Quantifying evidence toward pathogenicity for rare phenotypes: The case of succinate dehydrogenase genes, SDHB and SDHD.

PURPOSE: The weight of the evidence to attach to observation of a novel rare missense variant in SDHB or SDHD in individuals with the rare neuroendocrine tumors, pheochromocytomas and paragangliomas (PCC/PGL), is uncertain. METHODS: We compared the frequency of SDHB and SDHD very rare missense variants (VRMVs) in 6328 and 5847 cases of PCC/PGL, respectively, with that of population controls to generate a pan-gene VRMV likelihood ratio (LR). Via windowing analysis, we measured regional enrichments of VRMVs to calculate the domain-specific VRMV-LR (DS-VRMV-LR). We also calculated subphenotypic LRs for variant pathogenicity for various clinical, histologic, and molecular features. RESULTS: We estimated the pan-gene VRMV-LR to be 76.2 (54.8-105.9) for SDHB and 14.8 (8.7-25.0) for SDHD. Clustering analysis revealed an SDHB enriched region (ɑɑ 177-260, P = .001) for which the DS-VRMV-LR was 127.2 (64.9-249.4) and an SDHD enriched region (ɑɑ 70-114, P = .000003) for which the DS-VRMV-LR was 33.9 (14.8-77.8). Subphenotypic LRs exceeded 6 for invasive disease (SDHB), head-and-neck disease (SDHD), multiple tumors (SDHD), family history of PCC/PGL, loss of SDHB staining on immunohistochemistry, and succinate-to-fumarate ratio >97 (SDHB, SDHD). CONCLUSION: Using methodology generalizable to other gene-phenotype dyads, the LRs relating to rarity and phenotypic specificity for a single observation in PCC/PGL of a SDHB/SDHD VRMV can afford substantial evidence toward pathogenicity.

Wide Band Gap Chalcogenide Semiconductors.

Wide band gap semiconductors are essential for today's electronic devices and energy applications because of their high optical transparency, controllable carrier concentration, and tunable electrical conductivity. The most intensively investigated wide band gap semiconductors are transparent conductive oxides (TCOs), such as tin-doped indium oxide (ITO) and amorphous In-Ga-Zn-O (IGZO), used in displays and solar cells, carbides (e.g., SiC) and nitrides (e.g., GaN) used in power electronics, and emerging halides (e.g., γ-CuI) and 2D electronic materials (e.g., graphene) used in various optoelectronic devices. Compared to these prominent materials families, chalcogen-based (Ch = S, Se, Te) wide band gap semiconductors are less heavily investigated but stand out because of their propensity for p-type doping, high mobilities, high valence band positions (i.e., low ionization potentials), and broad applications in electronic devices such as CdTe solar cells. This manuscript provides a review of wide band gap chalcogenide semiconductors. First, we outline general materials design parameters of high performing transparent semiconductors, as well as the theoretical and experimental underpinnings of the corresponding research methods. We proceed to summarize progress in wide band gap (EG > 2 eV) chalcogenide materials-namely, II-VI MCh binaries, CuMCh2 chalcopyrites, Cu3MCh4 sulvanites, mixed-anion layered CuMCh(O,F), and 2D materials-and discuss computational predictions of potential new candidates in this family, highlighting their optical and electrical properties. We finally review applications-for example, photovoltaic and photoelectrochemical solar cells, transistors, and light emitting diodes-that employ wide band gap chalcogenides as either an active or passive layer. By examining, categorizing, and discussing prospective directions in wide band gap chalcogenides, this Review aims to inspire continued research on this emerging class of transparent semiconductors and thereby enable future innovations for optoelectronic devices.

Building social accountability to improve reproductive, maternal, newborn and child health in Nigeria.

BACKGROUND: Like many places in Nigeria, Niger, a predominantly rural and poor state in the north of the country, has high fertility, low contraceptive prevalence, and high maternal mortality. This paper presents a descriptive, contextualized case study of a social accountability campaign run by the nongovernmental organization White Ribbon Alliance Nigeria to strategically mobilize collective action to demand quality maternal health care and improve government responsiveness to those demands. We treat maternal health as a component of reproductive health, while recognizing it as a less contested area. METHODS: Data come from more than 40 interviews with relevant actors in Niger State in 2017 and 2018 during the initial phase of the campaign, and follow-up interviews with White Ribbon Alliance Nigeria staff in 2019 and 2021. Other data include White Ribbon Alliance Nigeria's monthly reports. We analyzed these data both deductively and inductively using qualitative techniques. RESULTS: During its first phase, the campaign used advocacy techniques to convince the previously reticent state government to engage with citizens, and worked to amplify citizen voice by hosting community dialogues and town halls, training a cadre of citizen journalists, and shoring up ward health development committees. Many of these efforts were unsustainable, however, so during the campaign's second phase, White Ribbon Alliance Nigeria worked to solidify state commitment to durable accountability structures intended to survive beyond the campaign's involvement. Key challenges have included a nontransparent state budget release process and the continued need for significant support from White Ribbon Alliance Nigeria. CONCLUSION: These findings reveal the significant time and resource inputs associated with implementing a strategic social accountability campaign, important compromises around the terminology used to describe "accountability," and the constraints on government responsiveness posed by unrealistic budgeting procedures. The campaign's contributions towards increased social accountability for maternal health should, however, also benefit accountability for reproductive health, as informed and empowered woman are better prepared to demand health services in any sector.

Combining evidence for and against pathogenicity for variants in cancer susceptibility genes: CanVIG-UK consensus recommendations.

Accurate classification of variants in cancer susceptibility genes (CSGs) is key for correct estimation of cancer risk and management of patients. Consistency in the weighting assigned to individual elements of evidence has been much improved by the American College of Medical Genetics (ACMG) 2015 framework for variant classification, UK Association for Clinical Genomic Science (UK-ACGS) Best Practice Guidelines and subsequent Cancer Variant Interpretation Group UK (CanVIG-UK) consensus specification for CSGs. However, considerable inconsistency persists regarding practice in the combination of evidence elements. CanVIG-UK is a national subspecialist multidisciplinary network for cancer susceptibility genomic variant interpretation, comprising clinical scientist and clinical geneticist representation from each of the 25 diagnostic laboratories/clinical genetic units across the UK and Republic of Ireland. Here, we summarise the aggregated evidence elements and combinations possible within different variant classification schemata currently employed for CSGs (ACMG, UK-ACGS, CanVIG-UK and ClinGen gene-specific guidance for PTEN, TP53 and CDH1). We present consensus recommendations from CanVIG-UK regarding (1) consistent scoring for combinations of evidence elements using a validated numerical 'exponent score' (2) new combinations of evidence elements constituting likely pathogenic' and 'pathogenic' classification categories, (3) which evidence elements can and cannot be used in combination for specific variant types and (4) classification of variants for which there are evidence elements for both pathogenicity and benignity.

Experimental Human Pneumococcal Colonization in Older Adults Is Feasible and Safe, Not Immunogenic.

Rationale: Pneumococcal colonization is key to the pathogenesis of invasive disease but is also immunogenic in young adults, protecting against recolonization. Colonization is rarely detected in older adults, despite high rates of pneumococcal disease.Objectives: To establish experimental human pneumococcal colonization in healthy adults aged 50-84 years, to measure the immune response to pneumococcal challenge, and to assess the protective effect of prior colonization against autologous strain rechallenge.Methods: Sixty-four participants were inoculated with Streptococcus pneumoniae (serotype 6B; 80,000 cfu in each nostril). Colonization was determined by bacterial culture of nasal wash, and humoral immune responses were assessed by anticapsular and antiprotein IgG concentrations.Measurements and Main Results: Experimental colonization was established in 39% of participants (25/64) with no adverse events. Colonization occurred in 47% (9/19) of participants aged 50-59 compared with 21% (3/14) in those aged ≥70 years. Previous pneumococcal polysaccharide vaccination did not protect against colonization. Colonization did not confer serotype-specific immune boosting, with a geometric mean titer (95% confidence interval) of 2.7 µg/ml (1.9-3.8) before the challenge versus 3.0 (1.9-4.7) 4 weeks after colonization (P = 0.53). Furthermore, pneumococcal challenge without colonization led to a drop in specific antibody concentrations from 2.8 µg/ml (2.0-3.9) to 2.2 µg/ml (1.6-3.0) after the challenge (P = 0.006). Antiprotein antibody concentrations increased after successful colonization. Rechallenge with the same strain after a median of 8.5 months (interquartile range, 6.7-10.1) led to recolonization in 5/16 (31%).Conclusions: In older adults, experimental pneumococcal colonization is feasible and safe but demonstrates different immunological outcomes compared with younger adults in previous studies.

Ternary nitride semiconductors in the rocksalt crystal structure.

Inorganic nitrides with wurtzite crystal structures are well-known semiconductors used in optical and electronic devices. In contrast, rocksalt-structured nitrides are known for their superconducting and refractory properties. Breaking this dichotomy, here we report ternary nitride semiconductors with rocksalt crystal structures, remarkable electronic properties, and the general chemical formula Mgx TM 1-xN (TM = Ti, Zr, Hf, Nb). Our experiments show that these materials form over a broad metal composition range, and that Mg-rich compositions are nondegenerate semiconductors with visible-range optical absorption onsets (1.8 to 2.1 eV) and up to 100 cm2 V-1⋅s-1 electron mobility for MgZrN2 grown on MgO substrates. Complementary ab initio calculations reveal that these materials have disorder-tunable optical absorption, large dielectric constants, and electronic bandgaps that are relatively insensitive to disorder. These ternary Mgx TM 1-xN semiconductors are also structurally compatible both with binary TMN superconductors and main-group nitride semiconductors along certain crystallographic orientations. Overall, these results highlight Mgx TM 1-xN as a class of materials combining the semiconducting properties of main-group wurtzite nitrides and rocksalt structure of superconducting transition-metal nitrides.

Assessing the utility of long-read nanopore sequencing for rapid and efficient characterization of mobile element insertions.

Short-read next generation sequencing (NGS) has become the predominant first-line technique used to diagnose patients with rare genetic conditions. Inherent limitations of short-read technology, notably for the detection and characterization of complex insertion-containing variants, are offset by the ability to concurrently screen many disease genes. "Third-generation" long-read sequencers are increasingly being deployed as an orthogonal adjunct technology, but their full potential for molecular genetic diagnosis has yet to be exploited. Here, we describe three diagnostic cases in which pathogenic mobile element insertions were refractory to characterization by short-read sequencing. To validate the accuracy of the long-read technology, we first used Sanger sequencing to confirm the integration sites and derive curated benchmark sequences of the variant-containing alleles. Long-read nanopore sequencing was then performed on locus-specific amplicons. Pairwise comparison between these data and the previously determined benchmark alleles revealed 100% identity of the variant-containing sequences. We demonstrate a number of technical advantages over existing wet-laboratory approaches, including in silico size selection of a mixed pool of amplification products, and the relative ease with which an automated informatics workflow can be established. Our findings add to a growing body of literature describing the diagnostic utility of long-read sequencing.

Maternal Hypertensive Pregnancy Disorders and Mental and Behavioral Disorders in the Offspring: a Review.

PURPOSE OF REVIEW: We review here recent original research and meta-analytic evidence on the associations of maternal hypertensive pregnancy disorders and mental and behavioral disorders in the offspring. RECENT FINDINGS: Seven meta-analyses and 11 of 16 original research studies published since 2015 showed significant associations between maternal hypertensive pregnancy disorders and offspring mental and behavioral disorders. Evidence was most consistent in meta-analyses and high-quality cohort studies. The associations, independent of familial confounding, were observed on different mental and behavioral disorders in childhood and schizophrenia in adulthood. Preterm birth and small-for-gestational age birth emerged as possible moderators and mediators of the associations. Cross-sectional and case-control studies yielded inconsistent findings, but had lower methodological quality. Accumulating evidence from methodologically sound studies shows that maternal hypertensive pregnancy disorders are associated with an increased risk of mental and behavioral disorders in the offspring in childhood. More studies on adult mental disorders are needed.

Cancer Variant Interpretation Group UK (CanVIG-UK): an exemplar national subspecialty multidisciplinary network.

Advances in technology have led to a massive expansion in the capacity for genomic analysis, with a commensurate fall in costs. The clinical indications for genomic testing have evolved markedly; the volume of clinical sequencing has increased dramatically; and the range of clinical professionals involved in the process has broadened. There is general acceptance that our early dichotomous paradigms of variants being pathogenic-high risk and benign-no risk are overly simplistic. There is increasing recognition that the clinical interpretation of genomic data requires significant expertise in disease-gene-variant associations specific to each disease area. Inaccurate interpretation can lead to clinical mismanagement, inconsistent information within families and misdirection of resources. It is for this reason that 'national subspecialist multidisciplinary meetings' (MDMs) for genomic interpretation have been articulated as key for the new NHS Genomic Medicine Service, of which Cancer Variant Interpretation Group UK (CanVIG-UK) is an early exemplar. CanVIG-UK was established in 2017 and now has >100 UK members, including at least one clinical diagnostic scientist and one clinical cancer geneticist from each of the 25 regional molecular genetics laboratories of the UK and Ireland. Through CanVIG-UK, we have established national consensus around variant interpretation for cancer susceptibility genes via monthly national teleconferenced MDMs and collaborative data sharing using a secure online portal. We describe here the activities of CanVIG-UK, including exemplar outputs and feedback from the membership.

Combinatorial Synthesis of Magnesium Tin Nitride Semiconductors.

Nitride materials feature strong chemical bonding character that leads to unique crystal structures, but many ternary nitride chemical spaces remain experimentally unexplored. The search for previously undiscovered ternary nitrides is also an opportunity to explore unique materials properties, such as transitions between cation-ordered and -disordered structures, as well as to identify candidate materials for optoelectronic applications. Here, we present a comprehensive experimental study of MgSnN2, an emerging II-IV-N2 compound, for the first time mapping phase composition and crystal structure, and examining its optoelectronic properties computationally and experimentally. We demonstrate combinatorial cosputtering of cation-disordered, wurtzite-type MgSnN2 across a range of cation compositions and temperatures, as well as the unexpected formation of a secondary, rocksalt-type phase of MgSnN2 at Mg-rich compositions and low temperatures. A computational structure search shows that the rocksalt-type phase is substantially metastable (>70 meV/atom) compared to the wurtzite-type ground state. Spectroscopic ellipsometry reveals optical absorption onsets around 2 eV, consistent with band gap tuning via cation disorder. Finally, we demonstrate epitaxial growth of a mixed wurtzite-rocksalt MgSnN2 on GaN, highlighting an opportunity for polymorphic control via epitaxy. Collectively, these findings lay the groundwork for further exploration of MgSnN2 as a model ternary nitride, with controlled polymorphism, and for device applications, enabled by control of optoelectronic properties via cation ordering.

Cas9-based enrichment and single-molecule sequencing for precise characterization of genomic duplications.

The widespread use of genome-wide diagnostic screening methods has greatly increased the frequency with which incidental (but possibly pathogenic) copy number changes affecting single genes are detected. These findings require validation to allow appropriate clinical management. Deletion variants can usually be readily validated using a range of short-read next-generation sequencing (NGS) strategies, but the characterization of duplication variants at nucleotide resolution remains challenging. This presents diagnostic problems, since pathogenicity cannot generally be assessed without knowing the structure of the variant. We have used a novel Cas9 enrichment strategy, in combination with long-read single-molecule nanopore sequencing, to address this need. We describe the nucleotide-level resolution of two problematic cases, both of whom presented with neurodevelopmental problems and were initially investigated by array CGH. In the first case, an incidental 1.7-kb imbalance involving a partial duplication of VHL exon 3 was detected. This variant was inherited from the patient's father, who had a history of renal cancer at 38 years. In the second case, an incidental ~200-kb de novo duplication that included DMD exons 30-44 was resolved. In both cases, the long-read data yielded sufficient information to enable Sanger sequencing to define the rearrangement breakpoints, and creation of breakpoint-spanning PCR assays suitable for testing of relatives. Our Cas9 enrichment and nanopore sequencing approach can be readily adopted by molecular diagnostic laboratories for cost-effective and rapid characterization of challenging duplication-containing alleles. We also anticipate that in future this method may prove useful for characterizing acquired translocations in tumor cells, and for precisely identifying transgene integration sites in mouse models.