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Developments within genetic testing may increase demands on general practitioners to advise about family history of breast cancer (FHBC). This descriptive, qualitative study, investigated women's views of GP consultations about FHBC and their context. Participants were women from the general population who had experienced a primary care consultation in which FHBC was mentioned, as reported by the practitioner. Information about women's views of consultation context was obtained from 72 telephone interviews. More in-depth information about context and women's evaluations of FHBC consultations were obtained from a sub-sample of 20 face to face interviews. FHBC was rarely the main focus of consultations. It featured as a part of an overall discussion of breast symptoms, treatment and cancer risk. Women's understanding of heredity and disease was often idiosyncratic and might differ from biomedical models. A main task for clinicians appeared to be appropriate reassurance. Failure to reassure was linked to a failure to provide explanations at the woman's level of understanding. Clinicians cannot assume that patients share their perceptions of the mechanisms of disease and heredity. Instead they need to ascertain the patient's understanding and provide explanations accordingly. GPs need to have, or access, enough knowledge to inform and reassure. [ABSTRACT FROM AUTHOR]

Several immune checkpoint inhibitors (ICIs) have already been introduced into clinical practice or are in advanced phases of clinical experimentation. Extensive efforts are being made to identify robust biomarkers to select patients who may benefit from treatment with ICIs. Tumor mutation burden (TMB) may be a relevant biomarker of response to ICIs in different tumor types; however, its clinical use is challenged by the analytical methods required for its evaluation. The possibility of using targeted next-generation sequencing panels has been investigated as an alternative to the standard whole exome sequencing approach. However, no standardization exists in terms of genes covered, types of mutations included in the estimation of TMB, bioinformatics pipelines for data analysis, and cut-offs used to discriminate samples with high, intermediate or low TMB. Bioinformatics serve a relevant role in the analysis of targeted sequencing data and its standardization is essential to deliver a reliable test in clinical practice. In the present study, cultured and formalin-fixed, paraffin-embedded cell lines were analyzed using a commercial panel for TMB testing; the results were compared with data from the literature and public databases, demonstrating a good correlation. Additionally, the correlation between high tumor mutation burden and microsatellite instability was confirmed. The bioinformatics analyses were conducted using two different pipelines to highlight the challenges associated with the development of an appropriate analytical workflow., Competing Interests: NN has received speaker's fee and is on the advisory boards of the following companies: Astra-Zeneca, Bayer, Illumina, Incyte, MSD, Merck KgA, J&J, Qiagen, Roche, Thermo Fisher Scientific, Inc. CA, FH and RC are Thermo Fisher Scientific, Inc. employees. Thermo Fisher Scientific, Inc. is the supplier of the Oncomine Tumor Mutation Load assay used within the study. The other authors declare no competing interests., (Copyright: © Fenizia et al.)

Tumor mutation burden (TMB) is evaluated as a biomarker of response to immunotherapy. We present the efforts of the Onconetwork Immuno-Oncology Consortium to validate a commercial targeted sequencing test for TMB calculation. A three-phase study was designed to validate the Oncomine Tumor Mutational Load (OTML) assay at nine European laboratories. Phase 1 evaluated reproducibility and accuracy on seven control samples. In phase 2, six formalin-fixed, paraffin-embedded samples tested with FoundationOne were reanalyzed with the OTML panel to evaluate concordance and reproducibility. Phase 3 involved analysis of 90 colorectal cancer samples with known microsatellite instability (MSI) status to evaluate TMB and MSI association. High reproducibility of TMB was demonstrated among the sites in the first and second phases. Strong correlation was also detected between mean and expected TMB in phase 1 (r 2  = 0.998) and phase 2 (r 2  = 0.96). Detection of actionable mutations was also confirmed. In colorectal cancer samples, the expected pattern of MSI-high/high-TMB and microsatellite stability/low-TMB was present, and gene signatures produced by the panel suggested the presence of a POLE mutation in two samples. The OTML panel demonstrated robustness and reproducibility for TMB evaluation. Results also suggest the possibility of using the panel for mutational signatures and variant detection. Collaborative efforts between academia and companies are crucial to accelerate the translation of new biomarkers into clinical research., (Copyright © 2021 Association for Molecular Pathology and American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.)

Aims: To determine the career decision intentions of graduating doctors, and the relationship between these intentions and the predicted medical workforce needs in New Zealand in 10 years' time., Methods: A workforce forecasting model developed by the Ministry of Health (MOH) has been used to predict the proportion of doctors required in each medical specialty in 2028 in New Zealand. The future work intentions of recently graduated doctors at the Universities of Auckland and Otago were collected from the Medical Student Outcomes Data (MSOD), and compared with these predicted needs., Results: Between 2013 and 2017, 2,292 doctors graduated in New Zealand, of whom 1,583 completed the MSOD preferences section (response rate 69%). Of these only 50.1% had decided on a future medical specialty. The most popular were surgical specialties (26.2%), general practice (20.7%), and internal medicine (11.0%). Compared to the MOH workforce forecast model there appears to be insufficient interest in general practice at the time of graduation., Conclusions: To shape the medical workforce to meet forecast needs, multiple stakeholders will need to collaborate, with a special focus on the early postgraduate years, as many doctors have yet to decide on specialisation., Competing Interests: Dr Bagg was Head of the Medical Programme at the University of Auckland until February 2019. Ms Verstappen and Dr Poole report grants from Health Workforce New Zealand during the conduct of the study.

For over a decade, the Medical Schools Outcomes Database and Longitudinal Tracking Project (MSOD) has collected data from medical students in Australia and New Zealand. This project aims to explore how individual student background or attributes might interact with curriculum or early postgraduate training to affect eventual career choice and location. In New Zealand, over 4,000 students have voluntarily provided information at various time points, and the project is at a stage where some firm conclusions are starting to be drawn. This paper presents the background to the project along with some early results and future directions., Competing Interests: Dr Poole and Ms Verstappen report grants from Health Workforce New Zealand during the conduct of the study.

Background: Public involvement adds value to numerous aspects of health research, yet few studies have attempted to evaluate its impact on research. Evidence of such impact is needed to develop recommendations for best practice and ensure adequate resourcing., Aim: To evaluate public involvement within a large interdisciplinary Science, Technology, Engineering and Mathematics (STEM) research project that focused on digital health., Methods: The evaluation was conducted with members of the project's Public Advisory Groups (PAG) and with researchers who had participated in involvement activities. Two questionnaires were designed based on a public involvement value systems and clusters framework., Results: Responses from members of the PAG (n = 10) were mostly positive towards normative values, which include moral, ethical and political aspects of involvement in research, and towards values concerning the conduct of public involvement and best practices. Researchers' responses (n = 16) indicated they felt that involvement was generally effective and increased the quality, relevance and generalizability of their work. However, their responses about the validity of involvement in research were varied. They also highlighted several challenges including how well public involvement impacted on research, how decisions made in the research might differ from the views generated from public involvement, and barriers to researchers' participation., Discussion and Conclusion: Our evaluation suggests that members of the public and the researchers value involvement. However, there is a need to consider how to embed public involvement to an even greater extent in STEM contexts and a need to address any barriers for researchers' own involvement., (© 2018 The Authors. Health Expectations published by John Wiley & Sons Ltd.)

Background: Tumor mutational burden (TMB) is an increasingly important biomarker for immune checkpoint inhibitors. Recent publications have described strong association between high TMB and objective response to mono- and combination immunotherapies in several cancer types. Existing methods to estimate TMB require large amount of input DNA, which may not always be available., Methods: In this study, we develop a method to estimate TMB using the Oncomine Tumor Mutation Load (TML) Assay with 20 ng of DNA, and we characterize the performance of this method on various formalin-fixed, paraffin-embedded (FFPE) research samples of several cancer types. We measure the analytical performance of TML workflow through comparison with control samples with known truth, and we compare performance with an orthogonal method which uses matched normal sample to remove germline variants. We perform whole exome sequencing (WES) on a batch of FFPE samples and compare the WES TMB values with TMB estimates by the TML assay., Results: In-silico analyses demonstrated the Oncomine TML panel has sufficient genomic coverage to estimate somatic mutations with a strong correlation (r 2 =0.986) to WES. Further, in silico prediction using WES data from three separate cohorts and comparing with a subset of the WES overlapping with the TML panel, confirmed the ability to stratify responders and non-responders to immune checkpoint inhibitors with high statistical significance. We found the rate of somatic mutations with the TML assay on cell lines and control samples were similar to the known truth. We verified the performance of germline filtering using only a tumor sample in comparison to a matched tumor-normal experimental design to remove germline variants. We compared TMB estimates by the TML assay with that from WES on a batch of FFPE research samples and found high correlation (r 2 =0.83). We found biologically interesting tumorigenesis signatures on FFPE research samples of colorectal cancer (CRC), lung, and melanoma origin. Further, we assessed TMB on a cohort of FFPE research samples including lung, colon, and melanoma tumors to discover the biologically relevant range of TMB values., Conclusions: These results show that the TML assay targeting a 1.7-Mb genomic footprint can accurately predict TMB values that are comparable to the WES. The TML assay workflow incorporates a simple workflow using the Ion GeneStudio S5 System. Further, the AmpliSeq chemistry allows the use of low input DNA to estimate mutational burden from FFPE samples. This TMB assay enables scalable, robust research into immuno-oncology biomarkers with scarce samples., Competing Interests: Conflicts of Interest: Employees of Thermo Fisher Scientific: R Chaudhary, D Cyanam, V Mittal, W Tom, J Au-Young, S Sadis, F Hyland. The other authors have no conflicts of interest to declare.

Pre-service teacher stress is an understudied research area, with the majority of research focusing on subjective reports of stress. The present study sought to examine the influence of stress-reduction techniques on both subjective and objective indicators of stress during microteaching in preservice teachers. A sample of 44 preservice teachers were randomly assigned to one of three intervention groups; biofeedback, relaxation, or control. Participants in the biofeedback group received relaxation-assisted biofeedback training designed to teach participants the physiological signs of the stress response using HeartMath monitor, along with the HeartMath Quick Coherence® technique. Those in the relaxation group were given training in the HeartMath Quick Coherence relaxation technique, with no biofeedback training. Finally, those in the control group did not receive any relaxation or biofeedback training. Using a repeated-measures design, both psychological and physiological indices of stress were measured before and after students engaged in microteaching approaches. Examination of the psychological ratings identified that feelings of calm increased across time; this showed that participants were more comfortable with the microteaching situation with repeated practice. However, none of the physiological interventions were effective in reducing stress. The present study highlights practice as a useful strategy to reduce stress in microteaching situations and points to the importance of employing evidence-based interventions when attempting to reduce stress.

A national workgroup convened by the Centers for Disease Control and Prevention identified principles and made recommendations for standardizing the description of sequence data contained within the variant file generated during the course of clinical next-generation sequence analysis for diagnosing human heritable conditions. The specifications for variant files were initially developed to be flexible with regard to content representation to support a variety of research applications. This flexibility permits variation with regard to how sequence findings are described and this depends, in part, on the conventions used. For clinical laboratory testing, this poses a problem because these differences can compromise the capability to compare sequence findings among laboratories to confirm results and to query databases to identify clinically relevant variants. To provide for a more consistent representation of sequence findings described within variant files, the workgroup made several recommendations that considered alignment to a common reference sequence, variant caller settings, use of genomic coordinates, and gene and variant naming conventions. These recommendations were considered with regard to the existing variant file specifications presently used in the clinical setting. Adoption of these recommendations is anticipated to reduce the potential for ambiguity in describing sequence findings and facilitate the sharing of genomic data among clinical laboratories and other entities., (Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.)

The Genome in a Bottle Consortium, hosted by the National Institute of Standards and Technology (NIST) is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. Here, we describe a large, diverse set of sequencing data for seven human genomes; five are current or candidate NIST Reference Materials. The pilot genome, NA12878, has been released as NIST RM 8398. We also describe data from two Personal Genome Project trios, one of Ashkenazim Jewish ancestry and one of Chinese ancestry. The data come from 12 technologies: BioNano Genomics, Complete Genomics paired-end and LFR, Ion Proton exome, Oxford Nanopore, Pacific Biosciences, SOLiD, 10X Genomics GemCode WGS, and Illumina exome and WGS paired-end, mate-pair, and synthetic long reads. Cell lines, DNA, and data from these individuals are publicly available. Therefore, we expect these data to be useful for revealing novel information about the human genome and improving sequencing technologies, SNP, indel, and structural variant calling, and de novo assembly.

Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers and companies with the specialty expertise and infrastructure required to identify and prioritize actionable variants. Such approaches are not scalable, preventing widespread adoption. Likewise, most targeted NGS approaches fail to assess key relevant genomic alteration classes. To address these challenges, we predefined the catalog of relevant solid tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics analysis of >700,000 samples. To detect these variants, we developed the Oncomine Comprehensive Panel (OCP), an integrative NGS-based assay [compatible with <20 ng of DNA/RNA from formalin-fixed paraffin-embedded (FFPE) tissues], coupled with an informatics pipeline to specifically identify relevant predefined variants and created a knowledge base of related potential treatments, current practice guidelines, and open clinical trials. We validated OCP using molecular standards and more than 300 FFPE tumor samples, achieving >95% accuracy for KRAS, epidermal growth factor receptor, and BRAF mutation detection as well as for ALK and TMPRSS2:ERG gene fusions. Associating positive variants with potential targeted treatments demonstrated that 6% to 42% of profiled samples (depending on cancer type) harbored alterations beyond routine molecular testing that were associated with approved or guideline-referenced therapies. As a translational research tool, OCP identified adaptive CTNNB1 amplifications/mutations in treated prostate cancers. Through predefining somatic variants in solid tumors and compiling associated potential treatment strategies, OCP represents a simplified, broadly applicable targeted NGS system with the potential to advance precision oncology efforts., (Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.)

The potential value of SNPs for individual identification has been recognized by many researchers and different panels have been proposed. Here we present a new interface in the ALFRED database to access compendia of allele frequencies for several published panels of markers for forensic uses. One of those is our panel of individual identification SNPs (IISNPs) based on samples of 44 populations originating from many parts of the world. Here we also present additional data and additional statistical analyses that continue to support the value of our panel of IISNPs as a universal panel. We also describe initial developments of multiplex methods and various robustness analyses for our 45 marker IISNP panel., (Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.)

A class of genes, known as drug metabolism enzymes (DMEs) are responsible for the metabolism and transport of drugs and other xenobiotics. Variation in DME genes most likely accounts for a proportion of the variability in drug response in humans, and may contribute to complex diseases such as cancer (Nebert DW, Dieter MZ. Pharmacology 2000;61:124-135). To date, assessing the extent of this variation has proven difficult, especially because of sequence paralogy issues that cause difficulty when attempting to genotype polymorphisms in very closely-related gene families (Murphy MP. Pharmacogenomics 2000;1:115-123; Ingelman-Sundberg M. Drug Metab Rev 1999;31:449-459). We have developed and genotyped a panel of N=2,325 individual TaqMan genotyping assays for polymorphisms in >200 DME genes; many of the variants in the panel are single nucleotide polymorphisms (SNPs) that are of known or putative function (e.g., missense, nonsense or frameshift). Using these assays, we have examined genetic variation among several groups of populations, including: 1) the two SNP500 Cancer population panels (http://snp500cancer.nci.nih.gov; last accessed: 11 December 2007); and 2) the panel used in the International HapMap Project panel (www.hapmap.org; last accessed: 11 December 2007). We have developed a comprehensive validation strategy to ensure reproducibility and accuracy of the assays and estimated minor allele frequencies. Here, we present the results of these analyses, which strongly suggest that this panel of DME assays are of extremely high quality and produce robust, accurate, and reproducible results.

Background: DNA microarrays are rapidly becoming a fundamental tool in discovery-based genomic and biomedical research. However, the reliability of the microarray results is being challenged due to the existence of different technologies and non-standard methods of data analysis and interpretation. In the absence of a "gold standard"/"reference method" for the gene expression measurements, studies evaluating and comparing the performance of various microarray platforms have often yielded subjective and conflicting conclusions. To address this issue we have conducted a large scale TaqMan Gene Expression Assay based real-time PCR experiment and used this data set as the reference to evaluate the performance of two representative commercial microarray platforms., Results: In this study, we analyzed the gene expression profiles of three human tissues: brain, lung, liver and one universal human reference sample (UHR) using two representative commercial long-oligonucleotide microarray platforms: (1) Applied Biosystems Human Genome Survey Microarrays (based on single-color detection); (2) Agilent Whole Human Genome Oligo Microarrays (based on two-color detection). 1,375 genes represented by both microarray platforms and spanning a wide dynamic range in gene expression levels, were selected for TaqMan Gene Expression Assay based real-time PCR validation. For each platform, four technical replicates were performed on the same total RNA samples according to each manufacturer's standard protocols. For Agilent arrays, comparative hybridization was performed using incorporation of Cy5 for brain/lung/liver RNA and Cy3 for UHR RNA (common reference). Using the TaqMan Gene Expression Assay based real-time PCR data set as the reference set, the performance of the two microarray platforms was evaluated focusing on the following criteria: (1) Sensitivity and accuracy in detection of expression; (2) Fold change correlation with real-time PCR data in pair-wise tissues as well as in gene expression profiles determined across all tissues; (3) Sensitivity and accuracy in detection of differential expression., Conclusion: Our study provides one of the largest "reference" data set of gene expression measurements using TaqMan Gene Expression Assay based real-time PCR technology. This data set allowed us to use an alternative gene expression technology to evaluate the performance of different microarray platforms. We conclude that microarrays are indeed invaluable discovery tools with acceptable reliability for genome-wide gene expression screening, though validation of putative changes in gene expression remains advisable. Our study also characterizes the limitations of microarrays; understanding these limitations will enable researchers to more effectively evaluate microarray results in a more cautious and appropriate manner.

Objectives: The aim of this study was to explore the relationship between risk factors for coronary heart disease (CHD) and perceived stress, adjusted for socio-economic position., Design: Cross-sectional analysis of CHD risk factors, perceived stress and socio-economic position., Method: A cohort of employed Scottish men (N = 5848) and women (N = 984) completed a questionnaire and attended a physical examination., Results: Higher socio-economic groups registered higher perceived stress scores. Perceived stress was associated with the following CHD risk factors in the expected direction: high plasma cholesterol, little recreational exercise, cigarette smoking, and high alcohol consumption. Contrary to expectations, stress was related negatively to high diastolic blood pressure, body mass index (BMI) and low forced expiratory volume. Correction for socio-economic position tended to abolish the associations between stress and physiological risk factors; the associations between stress and behavioural risk factors withstood such correction. The residual patterns of associations between perceived stress and CHD risk were broadly similar for men and women. A lower BMI, a greater number of cigarettes smoked, and greater alcohol consumption were associated with higher levels of perceived stress for both sexes. Lower levels of recreational exercise were associated with higher levels of stress for men only., Conclusions: Self-reported stress is related to health-related behaviours and to physiological CHD risk factors. The direction of the association with physiological risk was often contrary to expectation and appeared to be largely due to confounding by socio-economic position. In contrast, the association with health-related behaviours was in the expected direction and was largely independent of such confounding.