Whole-exome sequencing of BRCA-negative breast cancer patients and case-control analyses identify variants associated with breast cancer susceptibility.

BACKGROUND: For the majority of individuals with early-onset or familial breast cancer referred for genetic testing, the genetic basis of their familial breast cancer remains unexplained. To identify novel germline variants associated with breast cancer predisposition, whole-exome sequencing (WES) was performed. METHODS: WES on 290 BRCA1/BRCA2-negative Singaporeans with early-onset breast cancer and/or a family history of breast cancer was done. Case-control analysis against the East-Asian subpopulation (EAS) from the Genome Aggregation Database (gnomAD) identified variants enriched in cases, which were further selected by occurrence in cancer gene databases. Variants were further evaluated in repeated case-control analyses using a second case cohort from the database of Genotypes and Phenotypes (dbGaP) comprising 466 early-onset breast cancer patients from the United States, and a Singapore SG10K_Health control cohort. RESULTS: Forty-nine breast cancer-associated germline pathogenic variants in 37 genes were identified in Singapore cases versus gnomAD (EAS). Compared against SG10K_Health controls, 13 of 49 variants remain significantly enriched (False Discovery Rate (FDR)-adjusted p < 0.05). Comparing these 49 variants in dbGaP cases against gnomAD (EAS) and SG10K_Health controls revealed 23 concordant variants that were significantly enriched (FDR-adjusted p < 0.05). Fourteen variants were consistently enriched in breast cancer cases across all comparisons (FDR-adjusted p < 0.05). Seven variants in GPRIN2, NRG1, MYO5A, CLIP1, CUX1, GNAS and MGA were confirmed by Sanger sequencing. CONCLUSIONS: In conclusion, we have identified pathogenic variants in genes associated with breast cancer predisposition. Importantly, many of these variants were significant in a second case cohort from dbGaP, suggesting that the strategy of using case-control analysis to select variants could potentially be utilized for identifying variants associated with cancer susceptibility.

Awareness, Knowledge, Attitude, and Practice of Teledentistry among Dental Practitioners during COVID-19: A Systematic Review and Meta-Analysis.

Background and Objectives: This systemic review aims to appraise and analyse the awareness, knowledge, attitude, and practice of teledentistry among dental practitioners during COVID-19. Materials and Methods: This review was registered in the PROSPERO database (CRD42021283404). Cross-sectional articles on dental practitioners' perceptions towards teledentistry published between March 2020 and September 2021 were searched in ten online databases (PubMed, Google Scholar, Web of Science, ScienceDirect, Cochrane, EMBASE, SIGLE, EBSCO, LILACS, and Open Grey). The Joanna Briggs Institute critical appraisal tool was employed to analyse the risk of bias (RoB) of each article, whereas the Oxford Centre for Evidence-Based Medicine recommendation tool was used to evaluate the level of evidence. Data were analysed using the DerSimonian-Laird random effect model based on a single-arm approach. Results: Six studies were included and demonstrated Level 3 evidence. A single-arm meta-analysis revealed that dental practitioners had a high level of awareness (70.4%) and attitude (72.5%) towards teledentistry during the COVID-19 pandemic, but their knowledge level (57.9%) was moderate with a poor practice level (35.8%). A substantial heterogeneity was observed with the overall I2 ranging from 90.78% to 98.21%. Furthermore, meta-regression indicated that the sample size of each study had a significant (p < 0.05) impact on the degree of data heterogeneity. Conclusions: Despite their high degree of awareness and attitude, dental practitioners demonstrated moderate knowledge and relatively poor practice of teledentistry during the COVID-19 pandemic. More well-designed studies are warranted to investigate the alternatives for enhancing dental practitioners' knowledge and practice of teledentistry interventions.

Machine learning unveils an immune-related DNA methylation profile in germline DNA from breast cancer patients.

BACKGROUND: There is an unmet need for precise biomarkers for early non-invasive breast cancer detection. Here, we aimed to identify blood-based DNA methylation biomarkers that are associated with breast cancer. METHODS: DNA methylation profiling was performed for 524 Asian Chinese individuals, comprising 256 breast cancer patients and 268 age-matched healthy controls, using the Infinium MethylationEPIC array. Feature selection was applied to 649,688 CpG sites in the training set. Predictive models were built by training three machine learning models, with performance evaluated on an independent test set. Enrichment analysis to identify transcription factors binding to regions associated with the selected CpG sites and pathway analysis for genes located nearby were conducted. RESULTS: A methylation profile comprising 51 CpGs was identified that effectively distinguishes breast cancer patients from healthy controls achieving an AUC of 0.823 on an independent test set. Notably, it outperformed all four previously reported breast cancer-associated methylation profiles. Enrichment analysis revealed enrichment of genomic loci associated with the binding of immune modulating AP-1 transcription factors, while pathway analysis of nearby genes showed an overrepresentation of immune-related pathways. CONCLUSION: This study has identified a breast cancer-associated methylation profile that is immune-related to potential for early cancer detection.

Autoimmune manifestations of CTLA-4 haploinsufficiency in two patients of Southeast Asian ethnicity.

We report 2 patients who first developed cutaneous manifestations, followed by autoimmune phenomena, infections, and hypogammaglobulinemia. They were initially diagnosed with common variable immunodeficiency; however, the diagnosis was revised to cytotoxic T-lymphocyte antigen 4 haploinsufficiency after genetic and functional testing.

TPMT and NUDT15 testing for thiopurine therapy: A major tertiary hospital experience and lessons learned.

Variants in thiopurine methyltransferase (TPMT) and nudix hydrolase 15 (NUDT15) are associated with an accumulation of cytotoxic metabolites leading to increased risk of drug-related toxicity with standard doses of thiopurine drugs. We established TPMT and NUDT15 genetic testing for clinical use and evaluated the utilization, service outcomes and potential value of multi-gene PGx testing for 210 patients that underwent pharmacogenetics (PGx) testing for thiopurine therapy with the aim to optimize service delivery for future prescribing. The test was most commonly ordered for Gastroenterology (40.0%) and Neurology (31.4%), with an average turnaround time of 2 days. Following testing, 24.3% patients were identified as intermediate or poor metabolizers, resulting in 51 recommendations for a drug or dose change in thiopurine therapy, which were implemented in 28 (54.9%) patients. In the remaining patients, 14 were not adjusted and 9 had no data available. Focusing on drug gene interactions available for testing in our laboratory, multi-gene PGx results would present opportunities for treatment optimization for at least 33.8% of these patients who were on 2 or more concurrent medications with actionable PGx guidance. However, the use of PGx panel testing in clinical practice will require the development of guidelines and education as revealed by a survey with the test providers. The evaluation demonstrated successful implementation of single gene PGx testing and this experience guides the transition to a pre-emptive multi-gene testing approach that provides the opportunity to improve clinical care.

Non-Faradaic Promotion of Ethylene Hydrogenation under Oscillating Potentials.

The acceleration of Faradaic reactions by oscillating electric potentials has emerged as a viable tool to enhance electrocatalysis, but the non-Faradaic dynamic promotion of thermal catalytic processes remains to be proven. Here, we present experimental evidence showing that oscillating potentials are capable of enhancing the rate of ethylene hydrogenation despite no promotion effect being observed under static potentials. The non-Faradaic dynamic enhancement reaches up to 553% on a Pd/C electrode when cycling between -0.25 and 0.55 VNHE under optimized conditions with a frequency of around 0.1 Hz and a duty cycle of 99%. Under those conditions, the catalytic reaction rates were promoted beyond the rate of charge transfer to the electrode surface, confirming the non-Faradaic nature of the process. Experiments in different electrolytes reveal a good correlation between the catalytic enhancement and the double-layer capacitance, a measure for the interfacial electric field strength. Preliminary kinetic data is consistent with cyclic removal of adsorbates from the surface at negative potential and the subsequent adsorption of H2 and C2H4 and hydrogenation reaction at the positively polarized surface.

Promoting heterogeneous catalysis beyond catalyst design.

Despite the indisputable success of conventional approaches to manipulate the performance of heterogeneous catalysts by tuning the composition and structure of active sites, future research on catalysis engineering will likely go beyond the catalyst itself. Recently, several auxiliary promotion methods, either promoting the activity of reagents or enabling optimized adsorbate-catalyst interactions, have been proven as viable strategies to enhance catalytic reactions. Those auxiliary promotion methods range from electric/magnetic fields and electric potentials to mechanic stress, significantly altering the properties of reagent molecules and/or the surface characteristics of nanostructured catalysts. Apart from static enhancement effects, they in principle also allow for spatially and temporally variable modifications of catalyst surfaces. While some of those methods have been demonstrated, some are only theoretically predicted, opening exciting avenues for future experimental advances. Besides fundamental descriptions and comparisons of each activation method, in this perspective we plan to provide examples for the applications of those techniques for a variety of catalytic reactions as diverse as N2 and CO2 hydrogenation as well as electrochemical water splitting. Finally, we provide a unifying view and guidelines for future research into the use of promotion methods, generating deeper understanding of the complex dynamics on the nanoparticle surface under auxiliary promotion and the expansion of auxiliary techniques to different sustainability-related reactions.

Patient with multiple acyl-CoA dehydrogenase deficiency disease and ETFDH mutations benefits from riboflavin therapy: a case report.

BACKGROUND: Lipid storage myopathy (LSM) is a diverse group of lipid metabolic disorders with great variations in the clinical phenotype and age of onset. Classical multiple acyl-CoA dehydrogenase deficiency (MADD) is known to occur secondary to mutations in electron transfer flavoprotein dehydrogenase (ETFDH) gene. Whole exome sequencing (WES) with clinical correlations can be useful in identifying genomic alterations for targeted therapy. CASE PRESENTATION: We report a patient presented with severe muscle weakness and exercise intolerance, suggestive of LSM. Diagnostic testing demonstrated lipid accumulation in muscle fibres and elevated plasma acyl carnitine levels. Exome sequencing of the proband and two of his unaffected siblings revealed compound heterozygous mutations, c.250G > A (p.Ala84Thr) and c.770A > G (p.Tyr257Cys) in the ETFDH gene as the probable causative mutations. In addition, a previously unreported variant c.1042C > T (p.Arg348Trp) in ACOT11 gene was found. This missense variant was predicted to be deleterious but its association with lipid storage in muscle is unclear. The diagnosis of MADD was established and the patient was treated with riboflavin which resulted in rapid clinical and biochemical improvement. CONCLUSIONS: Our findings support the role of WES as an effective tool in the diagnosis of highly heterogeneous disease and this has important implications in the therapeutic strategy of LSM treatment.

Non-invasive detection of actionable mutations in advanced non-small-cell lung cancer using targeted sequencing of circulating tumor DNA.

OBJECTIVE: To evaluate the feasibility of detecting actionable gene mutations in circulating tumor DNA (ctDNA) in patients with advanced non-small-cell lung cancer (NSCLC) using targeted next-generation sequencing (NGS). MATERIALS AND METHODS: In total 50 plasma samples from patients newly diagnosed with advanced NSCLC or resistant to first-line tyrosine kinase inhibitors (TKIs) were subjected to deep sequencing on a seven-gene panel (BRAF, EGFR, ERBB2, KRAS, NRAS, PIK3CA, PTEN) incorporated with molecular barcodes to improve accuracy in variant detection. When possible, results were compared with those from matched tissue samples. RESULTS: At least one alteration in the ctDNA was detected in 44 out of 50 patients (88%); EGFR was the most frequently mutated gene. Half the total number of patients (50%, 25 of 50) had at least one actionable genetic alteration with targeted therapies available for treatment. Our results showed a high concordance rate of 81% in detection of EGFR mutation between 26 matched tissue and plasma samples. For progressive patients, from whom tissue is mostly unavailable, the resistant EGFR T790 M mutation was validated using the droplet digital polymerase chain reaction (ddPCR), yielding a concordance of 92% between alternative platforms. CONCLUSION: Our study demonstrated that therapeutically actionable mutations can be detected with high accuracy in ctDNA using NGS. This promising approach offers alternative and non-invasive diagnostic methods for treatment guidance and clinical monitoring.

Analysis of Genetic Variation in CYP450 Genes for Clinical Implementation.

BACKGROUND: Genetic determinants of drug response remain stable throughout life and offer great promise to patient-tailored drug therapy. The adoption of pharmacogenetic (PGx) testing in patient care requires accurate, cost effective and rapid genotyping with clear guidance on the use of the results. Hence, we evaluated a 32 SNPs panel for implementing PGx testing in clinical laboratories. METHODS: We designed a 32-SNP panel for PGx testing in clinical laboratories. The variants were selected using the clinical annotations of the Pharmacogenomics Knowledgebase (PharmGKB) and include polymorphisms of CYP2C9, CYP2C19, CYP2D6, CYP3A5 and VKORC1 genes. The CYP2D6 gene allele quantification was determined simultaneously with TaqMan copy number assays targeting intron 2 and exon 9 regions. The genotyping results showed high call rate accuracy according to concordance with genotypes identified by independent analyses on Sequenome massarray and droplet digital PCR. Furthermore, 506 genomic samples across three major ethnic groups of Singapore (Malay, Indian and Chinese) were analysed on our workflow. RESULTS: We found that 98% of our study subjects carry one or more CPIC actionable variants. The major alleles detected include CYP2C9*3, CYP2C19*2, CYP2D6*10, CYP2D6*36, CYP2D6*41, CYP3A5*3 and VKORC1*2. These translate into a high percentage of intermediate (IM) and poor metabolizer (PM) phenotypes for these genes in our population. CONCLUSION: Genotyping may be useful to identify patients who are prone to drug toxicity with standard doses of drug therapy in our population. The simplicity and robustness of this PGx panel is highly suitable for use in a clinical laboratory.