Identifying factors and causal chains associated with optimal implementation of Lynch syndrome tumor screening: An application of coincidence analysis.

PURPOSE: This study compared Lynch syndrome universal tumor screening (UTS) across multiple health systems (some of which had two or more distinct UTS programs) to understand multi-level factors that may impact the successful implementation of complex programs. METHODS: Data from 66 stakeholder interviews were used to conduct multi-value coincidence analysis (mv-CNA) and identify key factors that consistently make a difference in whether UTS programs were implemented and optimized at the system level. RESULTS: The selected CNA model revealed combinations of conditions that distinguish 4 optimized UTS programs, 10 non-optimized programs, and 4 systems with no program. Fully optimized UTS programs had both a maintenance champion and a positive inner setting. Two independent paths were unique to non-optimized programs: 1) positive attitudes and a mixed inner setting, or 2) limited planning & engaging among stakeholders. Negative views about UTS evidence or lack of knowledge about UTS led to a lack of planning and engaging, which subsequently prevented program implementation. CONCLUSION: The model improved our understanding of program implementation in health care systems and informed the creation of a toolkit to guide UTS implementation, optimization, and changes. Our findings and toolkit may serve as a use case to increase the successful implementation of other complex precision health programs.

Universal online self-help ACT interventions for youth: A systematic review.

Previous reviews of online self-help have not exclusively focussed on universally delivered Acceptance and Commitment Therapy (ACT). This systematic review aimed to evaluate the effectiveness of universal online self-help ACT interventions for young people. Relevant databases were searched for studies examining ACT interventions that were delivered universally, online and as self-help (guided and unguided) to young people aged 10 to 25-years-old. Eleven studies met inclusion criteria. These were assessed for quality and findings summarised using a narrative synthesis. Outcomes on mental health, well-being and ACT processes were reviewed, and results across studies were mixed. Most studies found significant improvements in mental health and well-being outcomes following the ACT intervention; however less than half found improvements in ACT process measures. Subgroups, such as those with elevated mental health symptoms, had better outcomes. There were no changes in measures of psychological inflexibility. However, methodological issues limited the interpretation of findings. Heterogeneity between studies and methodological issues made it difficult for this review to draw conclusions regarding the effectiveness of universal online self-help ACT interventions for young people. Future research with consistent approaches is needed across these types of interventions to improve methodological rigour to determine whether these interventions are effective.

Luminal breast epithelial cells from wildtype and BRCA mutation carriers harbor copy number alterations commonly associated with breast cancer.

Cancer-associated mutations have been documented in normal tissues, but the prevalence and nature of somatic copy number alterations and their role in tumor initiation and evolution is not well understood. Here, using single cell DNA sequencing, we describe the landscape of CNAs in >42,000 breast epithelial cells from women with normal or high risk of developing breast cancer. Accumulation of individual cells with one or two of a specific subset of CNAs (e.g. 1q gain and 16q, 22q, 7q, and 10q loss) is detectable in almost all breast tissues and, in those from BRCA1 or BRCA2 mutations carriers, occurs prior to loss of heterozygosity (LOH) of the wildtype alleles. These CNAs, which are among the most common associated with ductal carcinoma in situ (DCIS) and malignant breast tumors, are enriched almost exclusively in luminal cells not basal myoepithelial cells. Allele-specific analysis of the enriched CNAs reveals that each allele was independently altered, demonstrating convergent evolution of these CNAs in an individual breast. Tissues from BRCA1 or BRCA2 mutation carriers contain a small percentage of cells with extreme aneuploidy, featuring loss of TP53 , LOH of BRCA1 or BRCA2 , and multiple breast cancer-associated CNAs in addition to one or more of the common CNAs in 1q, 10q or 16q. Notably, cells with intermediate levels of CNAs are not detected, arguing against a stepwise gradual accumulation of CNAs. Overall, our findings demonstrate that chromosomal alterations in normal breast epithelium partially mirror those of established cancer genomes and are chromosome- and cell lineage-specific.

Implementing evidence-based assertions of clinical actionability in the context of secondary findings: Updates from the ClinGen Actionability Working Group.

PURPOSE: The ClinGen Actionability Working Group (AWG) developed an evidence-based framework to generate actionability reports and scores of gene-condition pairs in the context of secondary findings from genome sequencing. Here we describe the expansion of the framework to include actionability assertions. METHODS: Initial development of the actionability rubric was based on previously scored adult gene-condition pairs and individual expert evaluation. Rubric refinement was iterative and based on evaluation, feedback, and discussion. The final rubric was pragmatically evaluated via integration into actionability assessments for 27 gene-condition pairs. RESULTS: The resulting rubric has a 4-point scale (limited, moderate, strong, and definitive) and uses the highest-scoring outcome-intervention pair of each gene-condition pair to generate a preliminary assertion. During AWG discussions, predefined criteria and factors guide discussion to produce a consensus assertion for a gene-condition pair, which may differ from the preliminary assertion. The AWG has retrospectively generated assertions for all previously scored gene-condition pairs and are prospectively asserting on gene-condition pairs under assessment, having completed over 170 adult and 188 pediatric gene-condition pairs. CONCLUSION: The AWG expanded its framework to provide actionability assertions to enhance the clinical value of their resources and increase their utility as decision aids regarding return of secondary findings.

Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes.

The extent of cell-to-cell variation in tumor mitochondrial DNA (mtDNA) copy number and genotype, and the phenotypic and evolutionary consequences of such variation, are poorly characterized. Here we use amplification-free single-cell whole-genome sequencing (Direct Library Prep (DLP+)) to simultaneously assay mtDNA copy number and nuclear DNA (nuDNA) in 72,275 single cells derived from immortalized cell lines, patient-derived xenografts and primary human tumors. Cells typically contained thousands of mtDNA copies, but variation in mtDNA copy number was extensive and strongly associated with cell size. Pervasive whole-genome doubling events in nuDNA associated with stoichiometrically balanced adaptations in mtDNA copy number, implying that mtDNA-to-nuDNA ratio, rather than mtDNA copy number itself, mediated downstream phenotypes. Finally, multimodal analysis of DLP+ and single-cell RNA sequencing identified both somatic loss-of-function and germline noncoding variants in mtDNA linked to heteroplasmy-dependent changes in mtDNA copy number and mitochondrial transcription, revealing phenotypic adaptations to disrupted nuclear/mitochondrial balance.

Genetically guided precision medicine clinical decision support tools: a systematic review.

OBJECTIVES: Patient care using genetics presents complex challenges. Clinical decision support (CDS) tools are a potential solution because they provide patient-specific risk assessments and/or recommendations at the point of care. This systematic review evaluated the literature on CDS systems which have been implemented to support genetically guided precision medicine (GPM). MATERIALS AND METHODS: A comprehensive search was conducted in MEDLINE and Embase, encompassing January 1, 2011-March 14, 2023. The review included primary English peer-reviewed research articles studying humans, focused on the use of computers to guide clinical decision-making and delivering genetically guided, patient-specific assessments, and/or recommendations to healthcare providers and/or patients. RESULTS: The search yielded 3832 unique articles. After screening, 41 articles were identified that met the inclusion criteria. Alerts and reminders were the most common form of CDS used. About 27 systems were integrated with the electronic health record; 2 of those used standards-based approaches for genomic data transfer. Three studies used a framework to analyze the implementation strategy. DISCUSSION: Findings include limited use of standards-based approaches for genomic data transfer, system evaluations that do not employ formal frameworks, and inconsistencies in the methodologies used to assess genetic CDS systems and their impact on patient outcomes. CONCLUSION: We recommend that future research on CDS system implementation for genetically GPM should focus on implementing more CDS systems, utilization of standards-based approaches, user-centered design, exploration of alternative forms of CDS interventions, and use of formal frameworks to systematically evaluate genetic CDS systems and their effects on patient care.

Case report: Simultaneous measurement of intracranial pressure and lumbar intrathecal pressure during epidural patch therapy for treating spontaneous intracranial hypotension syndrome. Spontaneous intracranial hypotension or spontaneous intraspinal hypovolume?

Objectives: Spontaneous intracranial hypotension (SIH) is frequently complicated by subacute subdural hematoma (SDH) and more rarely by bilateral thalamic ischemia. Here, we report a case of SIH-related SDH treated with three epidural patches (EPs), with follow-up of the intracranial pressure and lumbar intrathecal pressure. Methods: A 46-year-old man presented bilateral thalamic ischemia, then a growing SDH. After failure of urgent surgical evacuation, he underwent three saline EPs, two dynamic myelography examinations and one digital subtraction angiography-phlebography examination. However, because of no dural tear and no obstacle to the venous drainage of the vein of Galen, no therapeutic procedure was available, and the patient died. Results: The case exhibited a progressive increase in the transmission of lumbar intrathecal pressure to intracranial pressure during the three EPs. The EPs may have successfully treated the SIH, but the patient did not recover consciousness because of irreversible damage to both thalami. Conclusion: Clinicians should be aware of the bilateral thalamic ischemia picture that may be the presenting sign of SIH. Moreover, the key problem in the pathophysiology of SIH seems to be intraspinal and intracranial volumes rather than pressures. Therefore, intracranial hypotension syndrome might actually be an intraspinal hypovolume syndrome.

Associations between disordered eating, internalizing symptoms, and behavioral and neural correlates of response inhibition in preadolescence.

Response inhibition difficulties are reported in individuals with eating disorders (EDs), anxiety, and depression. Although ED symptoms and internalizing symptoms co-occur in preadolescence, there is limited research examining associations between these symptoms and response inhibition in this age group. This study is the first to investigate the associations between behavioral and neural markers of response inhibition, disordered eating (DE), and internalizing symptoms in a community sample of preadolescents. Forty-eight children (M age = 10.95 years, 56.3% male) completed a Go/NoGo task, whereas electroencephalography was recorded. Self-report measures of DE and internalizing symptoms were collected. Higher levels of anxiety and depression were associated with neural markers of suboptimal response inhibition (attenuated P3NoGo amplitudes) in preadolescence. In contrast, higher levels of depression were associated with greater response inhibition at a behavioral level. These findings suggest internalizing symptoms in preadolescence are associated with P3-indexed difficulties in evaluation and monitoring, but these are not sufficient to disrupt behavioral performance on a response inhibition task. This pattern may reflect engagement of compensatory processes to support task performance. DE was not significantly associated with response inhibition, suggesting that difficulties in response inhibition may only be reliably observed in more chronic and severe DE and ED presentations.

Allele-specific transcriptional effects of subclonal copy number alterations enable genotype-phenotype mapping in cancer cells.

Subclonal copy number alterations are a prevalent feature in tumors with high chromosomal instability and result in heterogeneous cancer cell populations with distinct phenotypes. However, the extent to which subclonal copy number alterations contribute to clone-specific phenotypes remains poorly understood. We develop TreeAlign, which computationally integrates independently sampled single-cell DNA and RNA sequencing data from the same cell population. TreeAlign accurately encodes dosage effects from subclonal copy number alterations, the impact of allelic imbalance on allele-specific transcription, and obviates the need to define genotypic clones from a phylogeny a priori, leading to highly granular definitions of clones with distinct expression programs. These improvements enable clone-clone gene expression comparisons with higher resolution and identification of expression programs that are genomically independent. Our approach sets the stage for dissecting the relative contribution of fixed genomic alterations and dynamic epigenetic processes on gene expression programs in cancer.

Genomics in nephrology: identifying informatics opportunities to improve diagnosis of genetic kidney disorders using a human-centered design approach.

BACKGROUND: Genomic kidney conditions often have a long lag between onset of symptoms and diagnosis. To design a real time genetic diagnosis process that meets the needs of nephrologists, we need to understand the current state, barriers, and facilitators nephrologists and other clinicians who treat kidney conditions experience, and identify areas of opportunity for improvement and innovation. METHODS: Qualitative in-depth interviews were conducted with nephrologists and internists from 7 health systems. Rapid analysis identified themes in the interviews. These were used to develop service blueprints and process maps depicting the current state of genetic diagnosis of kidney disease. RESULTS: Themes from the interviews included the importance of trustworthy resources, guidance on how to order tests, and clarity on what to do with results. Barriers included lack of knowledge, lack of access, and complexity surrounding the case and disease. Facilitators included good user experience, straightforward diagnoses, and support from colleagues. DISCUSSION: The current state of diagnosis of kidney diseases with genetic etiology is suboptimal, with information gaps, complexity of genetic testing processes, and heterogeneity of disease impeding efficiency and leading to poor outcomes. This study highlights opportunities for improvement and innovation to address these barriers and empower nephrologists and other clinicians who treat kidney conditions to access and use real time genetic information.

Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc.

Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because of unknown sample purity, tumor ploidy, and general intra-tumor heterogeneity. Here, we present CNAqc, an evolution-inspired method to perform the computational validation of clonal and subclonal CNAs detected from bulk DNA sequencing. CNAqc is validated using single-cell data and simulations, is applied to over 4000 TCGA and PCAWG samples, and is incorporated into the validation process for the clinically accredited bioinformatics pipeline at Genomics England. CNAqc is designed to support automated quality control procedures for tumor somatic data validation.

Using implementation science to develop a familial hypercholesterolemia screening program in primary care: The CARE-FH study.

BACKGROUND: We designed the Collaborative Approach to Reach Everyone with Familial Hypercholesterolemia (CARE-FH) clinical trial to improve FH screening in primary care and facilitate guideline-based care. OBJECTIVE: The goal was to incorporate perspectives from end-users (healthcare system leaders, primary care clinicians, cardiologists, genetic counselors, nurses, and clinic staff) and improve translation of screening guidance into practice. METHODS: We partnered with end-users to sequentially define the current state of FH screening, assess acceptability, feasibility, and appropriateness of implementing an FH screening program, and select clinically actionable strategies at the patient-, clinician-, and system-level to be deployed as a package in the CARE-FH clinical trial. Methods informed by implementation science and human centered design included: contextual inquiries, surveys, and deliberative engagement sessions. RESULTS: Screening for FH occurred rarely in primary care, and then only after a cardiovascular event or sometimes due to a family history of high cholesterol or early heart attack. Surveys suggested FH screening in primary care was acceptable, appropriate, and feasible. Reported and observed barriers to screening include insufficient time at patient encounters to screen, cost and convenience of testing for patients, and knowledge regarding causes of dyslipidemia. Facilitators included clear guidance on screening criteria and new therapies to treat FH. These results led to the development of multilevel strategies that were presented to end-users, modified, and then pilot tested in one primary care clinic. CONCLUSIONS: A refined implementation strategy package for FH screening was created with a goal of improving FH awareness, identification, and initiation of guideline-based care. CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/study/NCT05284513?id=NCT05284513&rank=1 Unique Identifier: NCT05284513.

A meta-ethnography of autistic people's experiences of social camouflaging and its relationship with mental health.

LAY ABSTRACT: Some autistic people describe trying to hide autistic behaviour and seem more neurotypical. Researchers called this 'social camouflaging' and have linked it with mental health difficulties. We used a step-by-step approach to identify research where autistic people talk about social camouflaging to explore the relationship between camouflaging and poor mental health. Thirteen studies were combined. The results describe how society negatively impacts autistic people's mental health, and camouflaging is a way to try and cope with this. Many autistic people find their camouflaging strategies have accidental negative consequences which also affect their mental health. Strategies which seemed 'successful' involved a lot of self-monitoring, were very mentally demanding or were very habitual and seemed to have more of an effect on mental health. This might be important for clinicians who support autistic people with mental health difficulties.

An exploration of the relationship between loneliness, the severity of eating disorder-related symptoms and the experience of the 'anorexic voice'.

OBJECTIVES: Many individuals with eating disorders (EDs) report the experience of an 'Anorexic voice' (AV). Negative experiences of loneliness are also often associated with EDs. This study sought to explore the relationship between experiences of loneliness, the frequency of the AV and the impact of this on ED symptom severity. DESIGN: 165 individuals (mean age 27.54 years) who accessed online forums relating to EDs participated in this study. The sample included individuals who have experienced an AV [AV group (N = 141)] and those who have not [non-AV group (N = 23)]. METHODS: The study utilised self-report measures via an online questionnaire to explore the predictive validity of loneliness and frequency of the AV on ED symptom severity. RESULTS: Confirmatory analysis (AV group only) demonstrated the significance of the independent variables individually predicting ED symptom severity. However, a significant interaction was not found between the two primary variables in predicting ED symptom severity, more significantly than the influence of either variable alone. Exploratory analysis considered the differences between the two groups (AV and Non-AV), as well as considering alternate predictors. CONCLUSIONS: The findings offer insight into possible drivers behind engagement with the AV, as part of ED presentations in the community.

Should secondary pharmacogenomic variants be actively screened and reported when diagnostic genome-wide sequencing is performed in a child?

This white paper was prepared by the Global Alliance for Genomics and Health Regulatory and Ethics Work Stream's Pediatric Task Team to review and provide perspective with respect to ethical, legal, and social issues regarding the return of secondary pharmacogenomic variants in children who have a serious disease or developmental disorder and are undergoing exome or genome sequencing to identify a genetic cause of their condition. We discuss actively searching for and reporting pharmacogenetic/genomic variants in pediatric patients, different methods of returning secondary pharmacogenomic findings to the patient/parents and/or treating clinicians, maintaining these data in the patient's health record over time, decision supports to assist using pharmacogenetic results in future treatment decisions, and sharing information in public databases to improve the clinical interpretation of pharmacogenetic variants identified in other children. We conclude by presenting a series of points to consider for clinicians and policymakers regarding whether, and under what circumstances, routine screening and return of pharmacogenomic variants unrelated to the indications for testing is appropriate in children who are undergoing genome-wide sequencing to assist in the diagnosis of a suspected genetic disease.

Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup.

OBJECTIVE: Given the importance AI in genomics and its potential impact on human health, the American Medical Informatics Association-Genomics and Translational Biomedical Informatics (GenTBI) Workgroup developed this assessment of factors that can further enable the clinical application of AI in this space. PROCESS: A list of relevant factors was developed through GenTBI workgroup discussions in multiple in-person and online meetings, along with review of pertinent publications. This list was then summarized and reviewed to achieve consensus among the group members. CONCLUSIONS: Substantial informatics research and development are needed to fully realize the clinical potential of such technologies. The development of larger datasets is crucial to emulating the success AI is achieving in other domains. It is important that AI methods do not exacerbate existing socio-economic, racial, and ethnic disparities. Genomic data standards are critical to effectively scale such technologies across institutions. With so much uncertainty, complexity and novelty in genomics and medicine, and with an evolving regulatory environment, the current focus should be on using these technologies in an interface with clinicians that emphasizes the value each brings to clinical decision-making.

Evaluation of Malignant Hyperthermia Features in Patients with Pathogenic or Likely Pathogenic RYR1 Variants Disclosed through a Population Genomic Screening Program.

BACKGROUND: Malignant hyperthermia (MH) susceptibility is a heritable musculoskeletal disorder that can present as a potentially fatal hypermetabolic response to triggering anesthesia agents. Genomic screening for variants in MH-associated genes RYR1 and CACNA1S provides an opportunity to prevent morbidity and mortality. There are limited outcomes data from disclosing variants in RYR1, the most common MH susceptibility gene, in unselected populations. The authors sought to identify the rate of MH features or fulminant episodes after triggering agent exposure in an unselected population undergoing genomic screening including actionable RYR1 variants. METHODS: The MyCode Community Health Initiative by Geisinger (USA) is an electronic health record-linked biobank that discloses pathogenic and likely pathogenic variants in clinically actionable genes to patient-participants. Available electronic anesthesia and ambulatory records for participants with actionable RYR1 results returned through December 2020 were evaluated for pertinent findings via double-coded chart reviews and reconciliation. Descriptive statistics for observed phenotypes were calculated. RESULTS: One hundred fifty-two participants had an actionable RYR1 variant disclosed during the study period. None had previous documented genetic testing for MH susceptibility; one had previous contracture testing diagnosing MH susceptibility. Sixty-eight participants (44.7%) had anesthesia records documenting triggering agent exposure during at least one procedure. None received dantrolene treatment or had documented muscle rigidity, myoglobinuria, hyperkalemia, elevated creatine kinase, severe myalgia, or tea-colored urine. Of 120 possibly MH-related findings (postoperative intensive care unit admissions, hyperthermia, arterial blood gas evaluation, hypercapnia, or tachycardia), 112 (93.3%) were deemed unlikely to be MH events; 8 (6.7%) had insufficient records to determine etiology. CONCLUSIONS: Results demonstrate a low frequency of classic intraanesthetic hypermetabolic phenotypes in an unselected population with actionable RYR1 variants. Further research on the actionability of screening for MH susceptibility in unselected populations, including economic impact, predictors of MH episodes, and expanded clinical phenotypes, is necessary.

Transforming ovarian cancer care by targeting minimal residual disease.

Frontline treatment and resultant cure rates in patients with advanced ovarian cancer have changed little over the past several decades. Here, we outline a multidisciplinary approach aimed at gaining novel therapeutic insights by focusing on the poorly understood minimal residual disease phase of ovarian cancer that leads to eventual incurable recurrences.