Population screening shows risk of inherited cancer and familial hypercholesterolemia in Oregon.

The Healthy Oregon Project (HOP) is a statewide effort that aims to build a large research repository and influence the health of Oregonians through providing no-cost genetic screening to participants for a next-generation sequencing 32-gene panel comprising genes related to inherited cancers and familial hypercholesterolemia. This type of unbiased population screening can detect at-risk individuals who may otherwise be missed by conventional medical approaches. However, challenges exist for this type of high-throughput testing in an academic setting, including developing a low-cost high-efficiency test and scaling up the clinical laboratory for processing large numbers of samples. Modifications to our academic clinical laboratory including efficient test design, robotics, and a streamlined analysis approach increased our ability to test more than 1,000 samples per month for HOP using only one dedicated HOP laboratory technologist. Additionally, enrollment using a HIPAA-compliant smartphone app and sample collection using mouthwash increased efficiency and reduced cost. Here, we present our experience three years into HOP and discuss the lessons learned, including our successes, challenges, opportunities, and future directions, as well as the genetic screening results for the first 13,670 participants tested. Overall, we have identified 730 pathogenic/likely pathogenic variants in 710 participants in 24 of the 32 genes on the panel. The carrier rate for pathogenic/likely pathogenic variants in the inherited cancer genes on the panel for an unselected population was 5.0% and for familial hypercholesterolemia was 0.3%. Our laboratory experience described here may provide a useful model for population screening projects in other states.

Impact of the COVID-19 pandemic on a post-mortem CT service for adult non-suspicious death.

Due to the COVID-19 pandemic, the post-mortem computed tomography (PMCT) service was expanded from three to seven cases per day to help mortuary services and avoid invasive autopsy. Additional targeted angiography and pulmonary ventilation procedures were stopped and triage rules relaxed to allow more indications to be scanned, including those requiring toxicology. A service evaluation was performed for the first 3-months of the COVID-19 pandemic compared to the equivalent period the previous year to study the impact of these changes. It was found that, despite the increase in deaths regionally, coronial referrals remained about 100 per month, a reduction in referral rate. The number undergoing PMCT rose from 28% to 74% of cases. Turnaround time remained the same. For cases triaged to PMCT, the need for subsequent autopsy increased from 7.9% to 15.8%. No significant changes were seen in diagnosis rates, including cardiac or respiratory. There was an increase in patients with coronary death without severe coronary calcification who underwent autopsy after PMCT. These may have been diagnosed by targeted coronary angiography. Fifty-three cases requiring toxicology/biochemistry had PMCT, with 38 having PMCT only. In 8/11 (72.7%) cases with normal PMCT and toxicology as the key diagnostic test, autopsy was performed prior to results. This suggests the pathology team were reluctant to risk an "unascertained" outcome. This study shows that it is possible to increase PMCT services by widening referral criteria and by limiting the use of enhanced imaging techniques, without significantly changing diagnosis rates of key diseases; however, selectively restarting targeted angiography may help avoid autopsy in some cases.

The 10-year trajectory of aggressive behaviours in autistic individuals.

BACKGROUND: Aggressive behaviours are common in people with neurodevelopmental conditions, contributing to poorer quality of life and placement breakdown. However, there is limited empirical research documenting the prevalence and persistence of aggressive behaviours in autism. In this longitudinal study, aggressive behaviours were investigated in a sample of autistic individuals over 10 years. METHODS: Caregivers of autistic individuals, both with and without intellectual disability, completed questionnaires relating to the presence of aggressive behaviours at T1 [N = 229, mean age in years 11.8, standard deviation (SD) 5.9], T2 (T1 + 3 years, N = 81, mean age in years 15.1, SD 5.9) and T3 (T1 + 10 years, N = 54, mean age in years 24.5, SD 8.1). Analyses examined the presence and persistence of aggressive behaviours and the predictive value of established correlates of aggression. RESULTS: Aggressive behaviours were common at baseline (61.6%) but only persistent in 30% of the sample over 10 years. Higher composite scores of overactivity and impulsivity at T1 were significantly associated with the persistence of aggressive behaviours at T2 (P = 0.027) and T3 (P = 0.012) with medium effect size. CONCLUSIONS: Aggressive behaviours are common in autism, but reduce with age. Behavioural correlates of attention deficit hyperactivity disorder (ADHD) predict the presence and persistence of aggressive behaviour and as such may be useful clinical indicators to direct proactive intervention resources to ameliorate aggressive behaviours.

An evaluation of a novel bowel preparation regimen and its effect on the utility of colon capsule endoscopy: a prospective cohort study with historical controls.

BACKGROUND: The aim of this study was to evaluate the efficacy of a novel bowel preparation and booster regimen for colon capsule endoscopy (CCE) using macrogol, phospho-soda and gastrografin, compared with a control regimen consisting of polyethylene glycol and sodium picosulfate. METHODS: This was a prospective cohort study using historical controls. Symptomatic patients undergoing CCE between 11/07/2021 and 21/12/2021 using the novel regimen were included. Symptomatic patients who underwent CCE in the ScotCap evaluation using the control regimen were used as historical controls. We measured the rate of complete test (visualisation of the whole colon and rectum), adequate bowel preparation, successful test (complete and adequate bowel preparation) and need for further test following CCE. The rate of adverse events was also collected. RESULTS: Patients undergoing CCE using the new and control regimen were 200 and 316, respectively. The median age, age range and proportion of female patients in the new and control regimen cohorts was 61 vs 60 years, 16-86 vs 20-83 years, and 60.5% vs 56.6%. The rate of complete test, adequate bowel reparation and successful test for the new and control regimen was 69% vs 72.2%, 86.6% vs 80.7% and 60.5% vs 65.8%. Comparing the new and control regimen, 39.5% vs 37.3% of patients required no test following CCE, 26% vs 32.6% required a colonoscopy, 31.5% vs 21.5% required a flexible sigmoidoscopy and 3% vs 2.9% required a computed tomography colonogram. No adverse events were reported using the new regimen compared to 2 (0.6%) in the control group. CONCLUSIONS: The rate of adequate bowel preparation has improved following the introduction of a new regimen. However, further work is needed to increase the complete test rate. A significant proportion of patients continue to avoid colonoscopy following CCE.

Artificial intelligence (AI)-assisted exome reanalysis greatly aids in the identification of new positive cases and reduces analysis time in a clinical diagnostic laboratory.

PURPOSE: Artificial intelligence (AI) and variant prioritization tools for genomic variant analysis are being rapidly developed for use in clinical diagnostic testing. However, their clinical utility and reliability are currently limited. Therefore, we performed a validation of a commercial AI tool (Moon) and a comprehensive reanalysis of previously collected clinical exome sequencing cases using an open-source variant prioritization tool (Exomiser) and the now-validated AI tool to test their feasibility in clinical diagnostics. METHODS: A validation study of Moon was performed with 29 positive cases determined by previous manual analysis. After validation, reanalysis was performed on 80 previously manually analyzed nondiagnostic exome cases using Moon. Finally, a comparison between Moon and Exomiser was completed regarding their ability to identify previously completed positive cases and to identify new positive cases. RESULTS: Moon correctly selected the causal variant(s) in 97% of manually analyzed positive cases and identified 7 new positive cases. Exomiser correctly identified the causal gene in 85% of positive cases and agreed with Moon by ranking the new gene in its top 10 list 43% of the time. CONCLUSION: The use of AI in diagnostic laboratories greatly enhances exome sequencing analysis by reducing analysis time and increasing the diagnostic rate.

Age and the anaesthetist: considerations for the individual anaesthetist and workforce planning: Guidelines about the ageing anaesthetic workforce from the Association of Anaesthetists: Guidelines for the ageing anaesthetic workforce from the Association of Anaesthetists.

There is clear evidence of a growing workforce gap and this is compounded by demographic data that show the current workforce is ageing. Within the current workforce, more doctors are taking voluntary early retirement and the loss of these experienced clinicians from departments can have wide-ranging effects. Older doctors are at risk of age-related health problems (e.g. sight, musculoskeletal, menopause) and are more susceptible to the effects of fatigue, which may increase the risk of error and or complaint. The purpose of this working party and advocacy campaign was to address concerns over the number of consultants retiring at the earliest opportunity and whether a different approach could extend the working career of consultant anaesthetists and SAS doctors. This could be viewed as 'pacing your career'. The earlier this is considered in a clinician's career the greater the potential mitigation on individuals.

An update on oral cavity cancer: epidemiological trends, prevention strategies and novel approaches in diagnosis and prognosis.

In the UK, the incidence of oral cavity cancer continues to rise, with an increase of around 60% over the past 10 years. Many patients still present with advanced disease, often resulting in locoregional recurrence and poor outcomes, which has not changed significantly for over four decades. Changes in aetiology may also be emerging, given the decline of smoking in developed countries. Therefore, new methods to better target prevention, improve screening and detect recurrence are needed. High-throughput 'omics' technologies appear promising for future individual-level diagnosis and prognosis. However, given this is a relatively rare cancer with significant intra-tumour heterogeneity and variation in patient response, reliable biomarkers have been difficult to elucidate. From a public health perspective, implementing these novel technologies into current services would require substantial practical, financial and ethical considerations. This may be difficult to justify and implement at present, therefore focus remains on early detection using new patient-led follow-up strategies. This paper reviews the latest evidence on epidemiological trends in oral cavity cancer to help identify at risk groups, population-based approaches for prevention, in addition to potential cutting-edge approaches in the diagnosis and prognosis of this disease.

Preconception Carrier Screening by Genome Sequencing: Results from the Clinical Laboratory.

Advances in sequencing technologies permit the analysis of a larger selection of genes for preconception carrier screening. The study was designed as a sequential carrier screen using genome sequencing to analyze 728 gene-disorder pairs for carrier and medically actionable conditions in 131 women and their partners (n = 71) who were planning a pregnancy. We report here on the clinical laboratory results from this expanded carrier screening program. Variants were filtered and classified using the latest American College of Medical Genetics and Genomics (ACMG) guideline; only pathogenic and likely pathogenic variants were confirmed by orthologous methods before being reported. Novel missense variants were classified as variants of uncertain significance. We reported 304 variants in 202 participants. Twelve carrier couples (12/71 couples tested) were identified for common conditions; eight were carriers for hereditary hemochromatosis. Although both known and novel variants were reported, 48% of all reported variants were missense. For novel splice-site variants, RNA-splicing assays were performed to aid in classification. We reported ten copy-number variants and five variants in non-coding regions. One novel variant was reported in F8, associated with hemophilia A; prenatal testing showed that the male fetus harbored this variant and the neonate suffered a life-threatening hemorrhage which was anticipated and appropriately managed. Moreover, 3% of participants had variants that were medically actionable. Compared with targeted mutation screening, genome sequencing improves the sensitivity of detecting clinically significant variants. While certain novel variant interpretation remains challenging, the ACMG guidelines are useful to classify variants in a healthy population.

Emerging Therapeutic Potential of Mesenchymal Stem/Stromal Cells in Preeclampsia.

PURPOSE OF REVIEW: Preeclampsia is a dangerous pregnancy condition affecting both the mother and offspring. It is a multifactorial disease with poorly understood pathogenesis, lacking effective treatments. Maternal immune response, inflammation and oxidative stress leading to endothelial dysfunction are the most prominent pathogenic processes implicated in preeclampsia development. Here, we give a detailed overview of the therapeutic applications and mechanisms of mesenchymal stem/stromal cells (MSCs) as a potential new treatment for preeclampsia. RECENT FINDINGS: MSCs have gained growing attention due to low immunogenicity, easy cultivation and expansion in vitro. Accumulating evidence now suggests that MSCs act primarily through their secretomes facilitating paracrine signalling that leads to potent immunomodulatory, pro-angiogenic and regenerative therapeutic effects. MSCs have been studied in different animal models of preeclampsia demonstrating promising result, which support further investigations into the therapeutic effects and mechanisms of MSC-based therapies in preeclampsia, steering these therapies into clinical trials.

International validation of a risk prediction algorithm for patients with malignant colorectal polyps.

AIM: The optimal management strategy for patients with endoscopically resected malignant colorectal polyps (MCP) has yet to be defined. The aim of this study was to validate a published decision-making tool, termed the Scottish Polyp Cancer Study (SPOCS) algorithm, on a large international population. METHODS: The SPOCS algorithm allocates patients to risk groups based on just two variables: the polyp resection margin and the presence of lymphovascular invasion (LVI). The risk groups are termed low (clear margin, LVI absent), medium (clear margin, LVI present) or high (involved/non-assessable margin). The International Polyp Cancer Collaborative was formed to validate the algorithm on data from Australia, Denmark, UK and New Zealand. RESULTS: In total, 1423 patients were included in the final dataset. 680/1423 (47.8%) underwent surgical resection and 108/680 (15.9%) had residual disease (luminal disease 8.8%, lymph node metastases 8.8%). The SPOCS algorithm classified 602 patients as low risk (in which 1.5% had residual disease), 198 patients as medium risk (in which 7.1% had residual disease) and 484 as high risk (in which 14.5% had residual disease) (P < 0.001, χ2 test). Receiver operating characteristic curve analysis demonstrated good accuracy of the algorithm in predicting residual disease (area under the curve 0.732, 95% CI 0.687-0.778, P < 0.001). When patients were designated as low risk, the negative predictive value was 98.5%. CONCLUSION: The SPOCS algorithm can be used to predict the risk of residual disease in patients with endoscopically resected MCPs. Surgery can be safely avoided in patients who have a clear margin of excision and no evidence of LVI.

Genetic and phenotypic consequences of early domestication in black soldier flies (Hermetia illucens).

The black soldier fly, Hermetia illucens, is an emerging biotechnological agent with its larvae being effective converters of organic waste into usable bio-products including protein and lipids. To date, most operations use unimproved commercial populations produced by mass rearing, without cognisance of specific breeding strategies. The genetic and phenotypic consequences of these commercial practices remain unknown and could have a significant impact on long-term population viability and productivity. The aim of this study was thus to assess the genetic and phenotypic changes during the early phases of colony establishment and domestication in the black soldier fly. An experimental colony was established from wild founder flies and a new microsatellite marker panel was developed to assess population genetic parameters along with the phenotypic characteristics of each generational cohort under captive breeding. The experimental colony was characterised by a small effective population size, subsequent loss of genetic diversity and rapid genetic and phenotypic differentiation between the generational cohorts. Ultimately, the population collapsed by the fifth generation, most likely owing to the adverse effect of inbreeding depression following the fixation of deleterious alleles. Species with r-selected life history characteristics (e.g. short life-span, high fecundity and low larval survival) are known to pose particular challenges for genetic management. The current study suggests that sufficient genetic and phenotypic variations exist in the wild population and that domestication and strain development could be achieved with careful population augmentation and selection during the early stages of colony establishment.

Woman to Woman: Implementation of a Cervical Cancer Education Training Program for Grenadian Lay Health Advisors.

The reduction in cervical cancer (CC) in developed countries, due mainly to Pap testing, has not filtered down to Caribbean countries including Grenada despite accessible screening. This is attributed to a lack of knowledge and low screening. Researchers in low resource settings successfully trained lay health advisors (LHAs), using theory-based, culturally relevant interventions to reverse this trend. The use of LHAs in Grenada was not documented in the literature; therefore, the purpose of this study was to implement and evaluate a culturally relevant curriculum in an effort to educate Grenadian LHAs on CC. Using convenience sampling, 8 Grenadian women were recruited from the parishes with the highest rates of CC. They participated in Woman to Woman (W2W), a 2-day CC, and human papilloma virus (HPV) prevention education program facilitated by local content experts. W2W was adapted from an evidence-based curriculum and tailored for the Grenadian context. Training consisted of modules on CC and HPV. Knowledge of LHAs was measured pre- and post-intervention. Summative evaluation was assessed using a focus group discussion. There was a significant increase in CC knowledge among LHA post-training (p < 0.05) and LHAs had positive opinions about the intervention. They had an enhanced sense of self-efficacy and valued feeling part of a team. The W2W results indicated that an evidence-based and culturally tailored educational intervention has the potential for significant gains in CC and HPV knowledge. Future research will evaluate the LHA-led CC and HPV educational intervention in the community setting.

Correction: Secondary findings from clinical genomic sequencing: prevalence, patient perspectives, family history assessment, and health-care costs from a multisite study.

The originally published version of this Article contained errors in Fig. 2. The numbers below the black arrowheads were incorrect; please see incorrect Figure in associated Correction. These errors have now been corrected in the PDF and HTML versions of the Article.

Secondary findings from clinical genomic sequencing: prevalence, patient perspectives, family history assessment, and health-care costs from a multisite study.

PURPOSE: Clinical sequencing emerging in health care may result in secondary findings (SFs). METHODS: Seventy-four of 6240 (1.2%) participants who underwent genome or exome sequencing through the Clinical Sequencing Exploratory Research (CSER) Consortium received one or more SFs from the original American College of Medical Genetics and Genomics (ACMG) recommended 56 gene-condition pair list; we assessed clinical and psychosocial actions. RESULTS: The overall adjusted prevalence of SFs in the ACMG 56 genes across the CSER consortium was 1.7%. Initially 32% of the family histories were positive, and post disclosure, this increased to 48%. The average cost of follow-up medical actions per finding up to a 1-year period was $128 (observed, range: $0-$678) and $421 (recommended, range: $141-$1114). Case reports revealed variability in the frequency of and follow-up on medical recommendations patients received associated with each SF gene-condition pair. Participants did not report adverse psychosocial impact associated with receiving SFs; this was corroborated by 18 participant (or parent) interviews. All interviewed participants shared findings with relatives and reported that relatives did not pursue additional testing or care. CONCLUSION: Our results suggest that disclosure of SFs shows little to no adverse impact on participants and adds only modestly to near-term health-care costs; additional studies are needed to confirm these findings.

An evidence-based treatment algorithm for colorectal polyp cancers: results from the Scottish Screen-detected Polyp Cancer Study (SSPoCS).

OBJECTIVES: Colorectal polyp cancers present clinicians with a treatment dilemma. Decisions regarding whether to offer segmental resection or endoscopic surveillance are often taken without reference to good quality evidence. The aim of this study was to develop a treatment algorithm for patients with screen-detected polyp cancers. DESIGN: This national cohort study included all patients with a polyp cancer identified through the Scottish Bowel Screening Programme between 2000 and 2012. Multivariate regression analysis was used to assess the impact of clinical, endoscopic and pathological variables on the rate of adverse events (residual tumour in patients undergoing segmental resection or cancer-related death or disease recurrence in any patient). These data were used to develop a clinically relevant treatment algorithm. RESULTS: 485 patients with polyp cancers were included. 186/485 (38%) underwent segmental resection and residual tumour was identified in 41/186 (22%). The only factor associated with an increased risk of residual tumour in the bowel wall was incomplete excision of the original polyp (OR 5.61, p=0.001), while only lymphovascular invasion was associated with an increased risk of lymph node metastases (OR 5.95, p=0.002). When patients undergoing segmental resection or endoscopic surveillance were considered together, the risk of adverse events was significantly higher in patients with incomplete excision (OR 10.23, p<0.001) or lymphovascular invasion (OR 2.65, p=0.023). CONCLUSION: A policy of surveillance is adequate for the majority of patients with screen-detected colorectal polyp cancers. Consideration of segmental resection should be reserved for those with incomplete excision or evidence of lymphovascular invasion.

Actionable exomic incidental findings in 6503 participants: challenges of variant classification.

Recommendations for laboratories to report incidental findings from genomic tests have stimulated interest in such results. In order to investigate the criteria and processes for assigning the pathogenicity of specific variants and to estimate the frequency of such incidental findings in patients of European and African ancestry, we classified potentially actionable pathogenic single-nucleotide variants (SNVs) in all 4300 European- and 2203 African-ancestry participants sequenced by the NHLBI Exome Sequencing Project (ESP). We considered 112 gene-disease pairs selected by an expert panel as associated with medically actionable genetic disorders that may be undiagnosed in adults. The resulting classifications were compared to classifications from other clinical and research genetic testing laboratories, as well as with in silico pathogenicity scores. Among European-ancestry participants, 30 of 4300 (0.7%) had a pathogenic SNV and six (0.1%) had a disruptive variant that was expected to be pathogenic, whereas 52 (1.2%) had likely pathogenic SNVs. For African-ancestry participants, six of 2203 (0.3%) had a pathogenic SNV and six (0.3%) had an expected pathogenic disruptive variant, whereas 13 (0.6%) had likely pathogenic SNVs. Genomic Evolutionary Rate Profiling mammalian conservation score and the Combined Annotation Dependent Depletion summary score of conservation, substitution, regulation, and other evidence were compared across pathogenicity assignments and appear to have utility in variant classification. This work provides a refined estimate of the burden of adult onset, medically actionable incidental findings expected from exome sequencing, highlights challenges in variant classification, and demonstrates the need for a better curated variant interpretation knowledge base.

Venous thromboembolism laboratory testing (factor V Leiden and factor II c.*97G>A), 2018 update: a technical standard of the American College of Medical Genetics and Genomics (ACMG).

Factor V Leiden and factor II c.*97G>A (formerly referred to as prothrombin 20210G>A) are the two most common genetic variants associated with venous thromboembolism (VTE). Testing for these variants is one of the most common referrals in clinical genetics laboratories. While the methodologies for testing these two variants are relatively straightforward, the clinical implementation can be complicated with regard to test indications, risk assessment of occurrence and recurrence of VTE, and related genetic counseling. This document provides an overview of VTE, information about the variants and their influence on risk, considerations before initiating genetic testing, and the clinical and analytical sensitivity and specificity of the tests. Key information that should be included in the laboratory report is also provided. Disease-specific statements are intended to augment the general American College of Medical Genetics and Genomics (ACMG) technical standards for clinical genetics laboratories. Individual laboratories are responsible for meeting the Clinical Laboratory Improvement Amendments (CLIA)/College of American Pathologists (CAP) quality assurance standards with respect to appropriate sample documentation, assay validation, general proficiency testing, and quality control measures. This 2018 edition of the ACMG technical standard updates and supersedes the 2005 edition on this topic. It is designed to be a checklist for genetic testing professionals who are already familiar with the disease and the methods of analysis.

Professional responsibilities regarding the provision, publication, and dissemination of patient phenotypes in the context of clinical genetic and genomic testing: points to consider-a statement of the American College of Medical Genetics and Genomics (ACMG).

Disclaimer: This Points to Consider document is designed as an educational resource to provide best practices for medical genetic clinicians, laboratories, and journals regarding the provision, publication, and dissemination of patient phenotypes in the context of genomic testing, clinical genetic practice, and research. While the goal of the document is the improvement of patient care, the considerations and practices described should not be considered inclusive of all proper considerations and practices or exclusive of others that are reasonably directed to obtaining the same goal. In determining the value of any practice, clinicians, laboratories, and journals should apply their own professional standards and judgment to the specific circumstances presented.The content of this article is solely the responsibility of the authors and does not necessarily represent the official views of the authors' affiliated institutions.