Closing the gap between knowledge and clinical application: challenges for genomic translation

Bridging the gap between omics research and dental practice

AIM

The burgeoning field of omics research has witnessed exponential growth in both medicine and dentistry. However, despite more than a decade of advancements, clinical dentistry, particularly in Low- and Middle-Income Countries (LMICs), has seen limited progress in integrating omics-based approaches into routine practice. This review aims to provide a comprehensive overview of the integration of omics approaches in dentistry, focusing on the challenges and opportunities for translating research findings into clinical practice.

METHODS

we conducted a literature review using key databases to provide a brief overview of the history of genomics in dentistry. Additionally, we summarised recent breakthroughs in omics relevant to oral health practitioners, emphasising the inadequate translation of omics research into clinical practice.

RESULTS

Despite significant growth in omics research in both medicine and dentistry, its translation into routine clinical practice in dentistry remains limited. We summarise recent breakthroughs in omics and highlight the gap between research advancements and clinical implementation.

DISCUSSION AND CONCLUSION

The integration of omics approaches holds promise for enhancing diagnostics, personalised treatment strategies, and preventive measures in dental practice, ushering in a new era of precision oral healthcare. However, several challenges, including infrastructure limitations, cost-effectiveness, and education gaps, hinder the widespread adoption of omics-based approaches in clinical dentistry. A strong commitment to transforming dentistry is required to embrace this transition. This shift has the potential to revolutionise oral healthcare by advancing precision diagnostics and treatment strategies tailored to individual patient needs.

Exome and genome sequencing for rare genetic disease diagnosis: A scoping review and critical appraisal of clinical guidance documents produced by genetics professional organizations

PURPOSE

Exome and genome sequencing have rapidly transitioned from research methods to widely used clinical tests for diagnosing rare genetic diseases. We sought to synthesize the topics covered and appraise the development processes of clinical guidance documents generated by genetics professional organizations.

METHODS

We conducted a scoping review of guidance documents published since 2010, systematically identified in peer-reviewed and gray literature, using established methods and reporting guidelines. We coded verbatim recommendations by topic using content analysis and critically appraised documents using the Appraisal of Guidelines Research and Evaluation (AGREE) II tool.

RESULTS

We identified 30 guidance documents produced by 8 organizations (2012-2022), yielding 611 recommendations covering 21 topics. The most common topic related to findings beyond the primary testing indication. Mean AGREE II scores were low across all 6 quality domains; scores for items related to rigor of development were among the lowest. More recently published documents generally received higher scores.

CONCLUSION

Guidance documents included a broad range of recommendations but were of low quality, particularly in their rigor of development. Developers should consider using tools such as AGREE II and basing recommendations on living knowledge syntheses to improve guidance development in this evolving space.

Physicians' Perspectives on AI in Clinical Decision Support Systems: Interview Study of the CURATE.AI Personalized Dose Optimization Platform

BACKGROUND

Physicians play a key role in integrating new clinical technology into care practices through user feedback and growth propositions to developers of the technology. As physicians are stakeholders involved through the technology iteration process, understanding their roles as users can provide nuanced insights into the workings of these technologies that are being explored. Therefore, understanding physicians' perceptions can be critical toward clinical validation, implementation, and downstream adoption. Given the increasing prevalence of clinical decision support systems (CDSSs), there remains a need to gain an in-depth understanding of physicians' perceptions and expectations toward their downstream implementation. This paper explores physicians' perceptions of integrating CURATE.AI, a novel artificial intelligence (AI)-based and clinical stage personalized dosing CDSSs, into clinical practice.

OBJECTIVE

This study aims to understand physicians' perspectives of integrating CURATE.AI for clinical work and to gather insights on considerations of the implementation of AI-based CDSS tools.

METHODS

A total of 12 participants completed semistructured interviews examining their knowledge, experience, attitudes, risks, and future course of the personalized combination therapy dosing platform, CURATE.AI. Interviews were audio recorded, transcribed verbatim, and coded manually. The data were thematically analyzed.

RESULTS

Overall, 3 broad themes and 9 subthemes were identified through thematic analysis. The themes covered considerations that physicians perceived as significant across various stages of new technology development, including trial, clinical implementation, and mass adoption.

CONCLUSIONS

The study laid out the various ways physicians interpreted an AI-based personalized dosing CDSS, CURATE.AI, for their clinical practice. The research pointed out that physicians' expectations during the different stages of technology exploration can be nuanced and layered with expectations of implementation that are relevant for technology developers and researchers.

Determinants of targeted cancer therapy use in community oncology practice: a qualitative study using the Theoretical Domains Framework and Rummler-Brache process mapping

BACKGROUND

Precision medicine holds enormous potential to improve outcomes for cancer patients, offering improved rates of cancer control and quality of life. Not all patients who could benefit from targeted cancer therapy receive it, and some who may not benefit do receive targeted therapy. We sought to comprehensively identify determinants of targeted therapy use among community oncology programs, where most cancer patients receive their care.

METHODS

Guided by the Theoretical Domains Framework, we conducted semi-structured interviews with 24 community cancer care providers and mapped targeted therapy delivery across 11 cancer care delivery teams using a Rummler-Brache diagram. Transcripts were coded to the framework using template analysis, and inductive coding was used to identify key behaviors. Coding was revised until a consensus was reached.

RESULTS

Intention to deliver precision medicine was high across all participants interviewed, who also reported untenable knowledge demands. We identified distinctly different teams, processes, and determinants for (1) genomic test ordering and (2) delivery of targeted therapies. A key determinant of molecular testing was role alignment. The dominant expectation for oncologists to order and interpret genomic tests is at odds with their role as treatment decision-makers' and pathologists' typical role to stage tumors. Programs in which pathologists considered genomic test ordering as part of their staging responsibilities reported high and timely testing rates. Determinants of treatment delivery were contingent on resources and ability to offset delivery costs, which low- volume programs could not do. Rural programs faced additional treatment delivery challenges.

CONCLUSIONS

We identified novel determinants of targeted therapy delivery that potentially could be addressed through role re-alignment. Standardized, pathology-initiated genomic testing may prove fruitful in ensuring patients eligible for targeted therapy are identified, even if the care they need cannot be delivered at small and rural sites which may have distinct challenges in treatment delivery. Incorporating behavior specification and Rummler-Brache process mapping with determinant analysis may extend its usefulness beyond the identification of the need for contextual adaptation.

Pharmacists' Knowledge, and Insights in Implementing Pharmacogenomics in Saudi Arabia

BACKGROUND

Pharmacogenomics (PGx) and personalized medicine embrace the potential to optimize drug treatment and improve the patient's quality of life. Pharmacists' roles include contributing to genetic testing, patient counseling, and pharmacotherapies selection for superior treatment outcomes. The aim of this study is to assess the pharmacists' knowledge, insight, and self-confidence toward PGx testing, identify their future preferred education patterns, and determine the barriers to pharmacogenomic testing implementation.

METHOD

A cross-sectional study was conducted using a previously validated questionnaire among pharmacists working in the Kingdom of Saudi Arabia (KSA). The questionnaire was designed in seven major categories, consisting of 26 questions.

RESULTS

A total of 671 pharmacists participated in this survey. As for knowledge, only 29.8% of pharmacists had good knowledge regarding PGx, while 42.9% had poor knowledge levels. Respectable PGx knowledge was significantly higher among outpatient dispensing pharmacists (33.6%; p = 0.049) and among pharmacists who had completed PGx testing-related training or education (40.3%; p = 0.001). Considering perception, it was positive among 50% of pharmacists and negative among 19.8%. With regard to self-confidence, it was high among 39.2% of male pharmacists (p = 0.042), among 43% of clinical pharmacists (p = 0.006), and among 44.8% of pharmacists who had extra credentials (p = 0.001). The utmost favored continuing-education learning approaches were workshops or seminars. The barriers to the implementation of PGx testing included a lack of testing devices, clinical guidelines, training or education, and personnel.

CONCLUSION

The present study revealed that pharmacists in KSA had inadequate knowledge and understanding of PGx. Nevertheless, the majority established that PGx is a valuable tool for augmenting drug efficacy and safety.

Genetic and genomic learning needs of oncologists and oncology nurses in the era of precision medicine: a scoping review

Genetic and genomic data are increasingly guiding clinical care for cancer patients. To meet the growing demand for precision medicine, patient-facing oncology staff will be a part of leading the provision of genomic testing. A scoping review was undertaken to identify the range of genetic and genomic learning needs of oncologists and oncology nurses. Learning needs were reported relating to interpretation of genomic data, clinical decision-making, patient communication and counseling, and fundamentals of genetics and genomics. There was a lack of empirical research specific to oncology nurses and their learning needs in tumor sequencing. Our findings suggest that oncologists and oncology nurses need tailored support, education and training to improve their confidence and skills in adopting genomic testing into clinical practice.

The International Association for the Study of Lung Cancer Global Survey on Molecular Testing in Lung Cancer

INTRODUCTION

Access to targeted therapies for lung cancer depends on the accurate identification of patients' biomarkers through molecular testing. The International Association for the Study of Lung Cancer (IASLC) conducted an international survey to evaluate perceptions on current practice and barriers to implementation of molecular testing.

METHODS

We distributed the survey to IASLC members and other health care professionals around the world. The survey included a seven-question introduction for all respondents, who then answered according to one of three tracks: (1) requesting tests and treating patients, (2) performing and interpreting assays, or (3) tissue acquisition. Barriers to implementing molecular testing were provided in free-response fields. The chi-square test was used for regional comparisons.

RESULTS

A total of 2537 respondents from 102 countries participated. Most respondents who test and treat patients believe that less than 50% of patients with lung cancer in their country receive molecular testing, but reported higher rates within their own practice. Although many results varied by region, the five most frequent barriers cited in all regions were cost, quality and standards, access, awareness, and turnaround time. Many respondents expressed dissatisfaction with the current state of molecular testing for lung cancer, including 41% of those performing and interpreting assays. Issues identified included trouble understanding results (37%) and the quality of the samples (23% reported >10% rejection rate). Despite concerns regarding the quality of testing, 47% in the performing and interpreting track stated there is no policy or strategy to improve quality in their country. In addition, 33% of respondents who request tests and treat patients were unaware of the most recent College of American Pathologists, IASLC, and Association for Molecular Pathology guidelines for molecular testing.

CONCLUSIONS

Adoption of molecular testing for lung cancer is relatively low across the world. Barriers include cost, access, quality, turnaround time, and lack of awareness.

Knowledge Translation in Oncology: The Bumpy Ride From Bench to Bedside

OBJECTIVES

Knowledge translation (KT) is the dynamic process of mobilizing best-practice evidence to guide health care decisions.

METHODS

Using a PubMed search, challenges were identified and milestones defined.

RESULTS

Substantial challenges exist in integrating discoveries into patient care, including technical limitations related to genomic testing like turnaround time, standardization, reproducibility, and results interpretation. Other challenges include lack of proper training in genetic counseling for health care providers, clarity of scientific evidence, and ethical, legal and social considerations. In addition, most health care systems lack accessibility to genetic testing services. Moving forward, KT should be addressed at three main frontiers. The first is patients centered for proper understanding and decision making; the second is directed toward health care professionals, including clinical decision support and clarity of roles; and the third addresses resources of health care systems.

CONCLUSIONS

Implementing KT requires developing strategies to enhance awareness and promote behavioral changes congruent with research evidence, designing a systematic approach by health care providers and stakeholders to achieve patient-centered care.

Informing Integration of Genomic Medicine Into Primary Care: An Assessment of Current Practice, Attitudes, and Desired Resources

Introduction: Preparing primary care providers for genomic medicine (GM) first requires assessment of their educational needs in order to provide clear, purposeful direction and justify educational activities. More understanding is needed about primary care providers’ perspectives on their role in newer areas of GM and what resources would be helpful in practice. Our objective was to determine family physicians’ (FP) current involvement and confidence in GM, attitudes regarding its clinical value, suggestions for integration of GM into practice, and resources and education required.

Methods: A self-complete anonymous questionnaire was mailed to a random sample of 2,000 FPs in Ontario, Canada in September 2012.

Results: Adjusted response rate was 26% (361/1,365), mean age was 51, and 53% were male. FPs reported many aspects of traditional GM as part of current practice (eliciting family history: 93%; deciding who to refer to genetics: 94%; but few reported confidence (44%, 32% respectively). Newer areas of GM were not part of most FPs’ current practice and confidence was low (pharmacogenetics: 28% part of practice, 5% confident; direct-to-consumer genetic testing: 14%/2%; whole genome sequencing: 8%/2%). Attitudes were mixed with 59% agreeing that GM would improve patient health outcomes, 41% seeing benefits to genetic testing, but only 36% agreeing it was their responsibility to incorporate GM into practice. Few could identify useful sources of genetic information (22%) or find information about genetic tests (21%). Educational resources participants anticipated would be useful included contact information for local genetics clinics (89%), summaries of genetic disorders (86%), and genetic referral (85%) and testing (86%) criteria. About 58% were interested in learning about new genetic technologies. Most (76%) wanted to learn through in-person teaching (lectures, seminars etc.), 66% wanted contact with a local genetic counselor to answer questions, and 59% were interested in a genetics education website.

Conclusion: FPs lack confidence in GM skills needed for practice, particularly in emerging areas of GM. They see their role as making appropriate referrals, are somewhat optimistic about the contribution GM may make to patient care, but express caution about its current clinical benefits. There is a need for evidence-based educational resources integrated into primary care and improved communication with genetic specialists.

Implementation of a genomic medicine multi-disciplinary team approach for rare disease in the clinical setting: a prospective exome sequencing case series

BACKGROUND

A multi-disciplinary approach to promote engagement, inform decision-making and support clinicians and patients is increasingly advocated to realise the potential of genome-scale sequencing in the clinic for patient benefit. Here we describe the results of establishing a genomic medicine multi-disciplinary team (GM-MDT) for case selection, processing, interpretation and return of results.

METHODS

We report a consecutive case series of 132 patients (involving 10 medical specialties with 43.2% cases having a neurological disorder) undergoing exome sequencing over a 10-month period following the establishment of the GM-MDT in a UK NHS tertiary referral hospital. The costs of running the MDT are also reported.

RESULTS

In total 76 cases underwent exome sequencing following triage by the GM-MDT with a clinically reportable molecular diagnosis in 24 (31.6%). GM-MDT composition, operation and rationale for whether to proceed to sequencing are described, together with the health economics (cost per case for the GM-MDT was £399.61), the utility and informativeness of exome sequencing for molecular diagnosis in a range of traits, the impact of choice of sequencing strategy on molecular diagnostic rates and challenge of defining pathogenic variants. In 5 cases (6.6%), an alternative clinical diagnosis was indicated by sequencing results. Examples were also found where findings from initial genetic testing were reconsidered in the light of exome sequencing including TP63 and PRKAG2 (detection of a partial exon deletion and a mosaic missense pathogenic variant respectively); together with tissue-specific mosaicism involving a cytogenetic abnormality following a normal prenatal array comparative genomic hybridization.

CONCLUSIONS

This consecutive case series describes the results and experience of a multidisciplinary team format that was found to promote engagement across specialties and facilitate return of results to the responsible clinicians.

Qualitative study of system-level factors related to genomic implementation

PURPOSE

Research on genomic medicine integration has focused on applications at the individual level, with less attention paid to implementation within clinical settings. Therefore, we conducted a qualitative study using the Consolidated Framework for Implementation Research (CFIR) to identify system-level factors that played a role in implementation of genomic medicine within Implementing GeNomics In PracTicE (IGNITE) Network projects.

METHODS

Up to four study personnel, including principal investigators and study coordinators from each of six IGNITE projects, were interviewed using a semistructured interview guide that asked interviewees to describe study site(s), progress at each site, and factors facilitating or impeding project implementation. Interviews were coded following CFIR inner-setting constructs.

RESULTS

Key barriers included (1) limitations in integrating genomic data and clinical decision support tools into electronic health records, (2) physician reluctance toward genomic research participation and clinical implementation due to a limited evidence base, (3) inadequate reimbursement for genomic medicine, (4) communication among and between investigators and clinicians, and (5) lack of clinical and leadership engagement.

CONCLUSION

Implementation of genomic medicine is hindered by several system-level barriers to both research and practice. Addressing these barriers may serve as important facilitators for studying and implementing genomics in practice.

Assessing risk for Mendelian disorders in a Bronx population

Background

To identify variants likely responsible for Mendelian disorders among the three major ethnic groups in the Bronx that might be useful to include in genetic screening panels or whole exome sequencing filters and to estimate their likely prevalence in these populations.

Methods

Variants from a high‐density oligonucleotide screen of 192 members from each of the three ethnic‐national populations (African Americans, Puerto Ricans, and Dominicans) were evaluated for overlap with next generation sequencing data. Variants were curated manually for clinical validity and utility using the American College of Medical Genetics (ACMG) scoring system. Additional variants were identified through literature review.

Results

A panel of 75 variants displaying autosomal dominant, autosomal recessive, autosomal recessive/digenic recessive, X‐linked recessive, and X‐linked dominant inheritance patterns representing 39 Mendelian disorders were identified among these populations.

Conclusion

Screening for a broader range of disorders could offer the benefits of early or presymptomatic diagnosis and reproductive choice.

Damschroder L, Cooper-DeHoff RM, Denny JC, Ginsburg GS, Guan Y, Horowitz CR, Levy KD, Levy MA, Madden EB, Matheny ME, Pollin TI, Pratt VM, Rosenman M, Voils CI, W. Weitzel K, Wilke RA, Ryanne Wu R, Orlando LA. Challenges and strategies for implementing genomic services in diverse settings: experiences from the Implementing GeNomics In pracTicE (IGNITE) network

BACKGROUND

To realize potential public health benefits from genetic and genomic innovations, understanding how best to implement the innovations into clinical care is important. The objective of this study was to synthesize data on challenges identified by six diverse projects that are part of a National Human Genome Research Institute (NHGRI)-funded network focused on implementing genomics into practice and strategies to overcome these challenges.

METHODS

We used a multiple-case study approach with each project considered as a case and qualitative methods to elicit and describe themes related to implementation challenges and strategies. We describe challenges and strategies in an implementation framework and typology to enable consistent definitions and cross-case comparisons. Strategies were linked to challenges based on expert review and shared themes.

RESULTS

Three challenges were identified by all six projects, and strategies to address these challenges varied across the projects. One common challenge was to increase the relative priority of integrating genomics within the health system electronic health record (EHR). Four projects used data warehousing techniques to accomplish the integration. The second common challenge was to strengthen clinicians' knowledge and beliefs about genomic medicine. To overcome this challenge, all projects developed educational materials and conducted meetings and outreach focused on genomic education for clinicians. The third challenge was engaging patients in the genomic medicine projects. Strategies to overcome this challenge included use of mass media to spread the word, actively involving patients in implementation (e.g., a patient advisory board), and preparing patients to be active participants in their healthcare decisions.

CONCLUSIONS

This is the first collaborative evaluation focusing on the description of genomic medicine innovations implemented in multiple real-world clinical settings. Findings suggest that strategies to facilitate integration of genomic data within existing EHRs and educate stakeholders about the value of genomic services are considered important for effective implementation. Future work could build on these findings to evaluate which strategies are optimal under what conditions. This information will be useful for guiding translation of discoveries to clinical care, which, in turn, can provide data to inform continual improvement of genomic innovations and their applications.

The role of hospital pharmacists in the adoption and use of pharmacogenomics and precision medicine

Aim: Our aim was to assess the knowledge and attitudes of US hospital pharmacists about the implementation of clinical pharmacogenomics, and examine liability risks of adopting pharmacogenomics by pharmacists. Methods: We surveyed hospital pharmacists. Linear regression models of predictor variables for pharmacist adoption and use of pharmacogenomics were analyzed. Results: The survey was administered to 660 hospital pharmacists (23% response rate; n = 149). The majority of respondents (72%) favor implementing pharmacogenomics into pharmacy practice. However, only 25% are confident in their abilities to interpret pharmacogenomic test results. Conclusion: Pharmacists lack confidence in their abilities to interpret and use pharmacogenomic information in clinical care. These results raise potential liability risks that are pertinent to pharmacists.

Bermuda 2.0: reflections from Santa Cruz

In February 1996, the genome community met in Bermuda to formulate principles for circulating genomic data. Although it is now 20 years since the Bermuda Principles were formulated, they continue to play a central role in shaping genomic and data-sharing practices. However, since 1996, "openness" has become an increasingly complex issue. This commentary seeks to articulate three core challenges data-sharing faces today.

Ethical issues in pediatric genetic testing and screening

PURPOSE OF REVIEW

Developments in genetic test technologies enable a detailed analysis of the genomes of individuals across the range of human development from embryos to adults with increased precision and lower cost. These powerful technologies raise a number of ethical issues in pediatrics, primarily because of the frequent lack of clinical utility of genetic information, the generation of secondary results and questions over the proper scope of parental authority for testing.

RECENT FINDINGS

Several professional organizations in the fields of genetics and pediatrics have published new guidance on the ethical, legal, and policy issues relevant to genetic testing in children. The roles of predictive testing for adult-onset conditions, the management of secondary findings and the role of informed consent for newborn screening remain controversial. However, research and experience are not demonstrating serious adverse psychosocial impacts from genetic testing and screening in children. The use of these technologies is expanding with the notion that the personal utility of test results, rather than clinical utility, may be sufficient to justify testing.

SUMMARY

The use of microarray and genome sequencing technologies is expanding in the care of children. More deference to parental decision-making is evolving in contexts wherein information and counseling can be made readily available.

Patient safety in genomic medicine: an exploratory study

PURPOSE

Concerns about patient safety and the potential for medical error are largely unexplored for genetic testing, despite the expansion of test use. In this preliminary qualitative study, we sought the views of genetics professionals about error and patient safety concerns in genomic medicine and factors that might mitigate them.

METHODS

Twelve semistructured interviews with experienced genetics professionals were conducted. Transcripts were analyzed using selective coding for issues related to error definition, mitigation, and communication. Additional thematic analysis captured themes across content categories.

RESULTS

Key informants suggested that the potential for adverse events exists in all phases of genetic testing, from ordering to analysis, interpretation, and follow-up. A perceived contributor was lack of physician knowledge about genetics, resulting in errors in test ordering and interpretation. The limitations and uncertainty inherent to rapidly evolving technology were also seen as contributing factors. Strategies to prevent errors included physician education, availability of genetic experts for consultation, and enhanced communication such as improved test reports and electronic decision support.

CONCLUSION

Genetic testing poses concerns for patient safety due to errors and the limitations of current tests. As genomic tests are integrated into medical care, anticipating and addressing patient safety concerns identified by these key informants will be crucial.Genet Med 18 11, 1136-1142.

Genomic and clinical predictors for improving estimator precision in randomized trials of breast cancer treatments

Background

The hope that genomic biomarkers would dramatically and immediately improve care for common, complex diseases has been tempered by slow progress in their translation beyond bioinformatics. We propose a novel use of genomic information where the goal is to improve estimator precision in a randomized trial. We analyze the potential precision gains from the popular MammaPrint genomic signature and clinical variables in simulations of randomized trials analyzed using covariate adjustment.

Methods

We apply an estimator for the average treatment effect in the trial that adjusts for prognostic baseline variables to improve precision [1]. This precision gain can be translated directly into sample size reduction and corresponding cost savings. We conduct simulation studies based on resampling genomic and clinical data of breast cancer patients from four publicly available observational studies.

Results

Separate simulation studies were conducted based on each of the four data sets, with sample sizes ranging from 115 to 307. Adjusting only for clinical variables provided gains of −1%, 5%, 6%, 17%, compared to the unadjusted estimator. Adjusting only for the MammaPrint genomic signature provided gains of 2%, 4%, 4%, 5%. Simultaneously adjusting for clinical variables and the genomic signature provided gains of 2%, 6%, 7%, 16%. The differences between precision gains from adjusting for genomic plus clinical variables, versus only clinical variables, were −1%, 0%, 1%, 3%.

Conclusions

Adjusting only for clinical variables led to substantial precision gains (at least 5%) in three of the four data sets, with a 1% precision loss in the remaining data set. These gains were unchanged or increased when sample sizes were doubled in our simulations. The precision gains due to incorporating genomic information, beyond the gains from adjusting for clinical variables, were not substantial.

Challenges in Translating GWAS Results to Clinical Care

Clinical genetic testing for Mendelian disorders is standard of care in many cases; however, it is less clear to what extent and in which situations clinical genetic testing may improve preventive efforts, diagnosis and/or prognosis of complex disease. One challenge is that much of the reported research relies on tag single nucleotide polymorphisms (SNPs) to act as proxies for assumed underlying functional variants that are not yet known. Here we use coronary artery disease and melanoma as case studies to evaluate how well reported genetic risk variants tag surrounding variants across population samples in the 1000 Genomes Project Phase 3 data. We performed a simulation study where we randomly assigned a "functional" variant and evaluated how often this simulated functional variant was correctly tagged in diverse population samples. Our results indicate a relatively large error rate when generalizing increased genetic risk of complex disease across diverse population samples, even when generalizing within geographic regions. Our results further highlight the importance of including diverse populations in genome-wide association studies. Future work focused on identifying functional variants will eliminate the need for tag SNPs; however, until functional variants are known, caution should be used in the interpretation of genetic risk for complex disease using tag SNPs.

Prevention and Control of Antimicrobial Resistant Healthcare-Associated Infections: The Microbiology Laboratory Rocks!

In Europe, each year, more than four milion patients acquire a healthcare-associated infection (HAI) and almost 40 thousand die as a direct consequence of it. Regardless of many stategies to prevent and control HAIs, they remain an important cause of morbidity and mortality worldwide with a significant economic impact: a recent estimate places it at the ten billion dollars/year. The control of HAIs requires a prompt and efficient identification of the etiological agent and a rapid communication with the clinician. The Microbiology Laboratory has a significant role in the prevention and control of these infections and is a key element of any Infection Control Program. The work of the Microbiology Laboratory covers microbial isolation and identification, determination of antimicrobial susceptibility patterns, epidemiological surveillance and outbreak detection, education, and report of quality assured results. In this paper we address the role and importance of the Microbiology Laboratory in the prevention and control of HAI and in Antibiotic Stewardship Programs and how it can be leveraged when combined with the use of information systems. Additionally, we critically review some challenges that the Microbiology Laboratory has to deal with, including the selection of analytic methods and the proper use of communication channels with other healthcare services.

Recent Advances in Application of Pharmacogenomics for Biotherapeutics

Biotherapeutics (BTs), one of the fastest growing classes of drug molecules, offer several advantages over the traditional small molecule pharmaceuticals because of their relatively high specificity, low off-target effects, and biocompatible metabolism, in addition to legal and logistic advantages. However, their clinical utility is limited, among other things, by their high immunogenic potential and/or variable therapeutic efficacy in different patient populations. Both of these issues, also commonly experienced with small molecule drugs, have been addressed effectively in a number of cases by the successful application of pharmacogenomic tools and approaches. In this introductory article of the special issue, we review the current state of application of pharmacogenomics to BTs and offer suggestions for further expansion of the field.

Personal Genome Sequencing in Ostensibly Healthy Individuals and the PeopleSeq Consortium

Thousands of ostensibly healthy individuals have had their exome or genome sequenced, but a much smaller number of these individuals have received any personal genomic results from that sequencing. We term those projects in which ostensibly healthy participants can receive sequencing-derived genetic findings and may also have access to their genomic data as participatory predispositional personal genome sequencing (PPGS). Here we are focused on genome sequencing applied in a pre-symptomatic context and so define PPGS to exclude diagnostic genome sequencing intended to identify the molecular cause of suspected or diagnosed genetic disease. In this report we describe the design of completed and underway PPGS projects, briefly summarize the results reported to date and introduce the PeopleSeq Consortium, a newly formed collaboration of PPGS projects designed to collect much-needed longitudinal outcome data.

Sociocultural variation in attitudes toward use of genetic information and participation in genetic research by race in the United States: implications for precision medicine

Background “Precision medicine” (PM) requires researchers to identify actionable genetic risks and for clinicians to interpret genetic testing results to patients. Whether PM will equally benefit all populations or exacerbate existing disparities is uncertain.

Methods We ascertained attitudes toward genetic testing and genetic research by race in the United States using the online Amazon mTurk US workforce (n = 403 White; n = 56 African American (AA)). Generalized linear models were used to test differences in beliefs and preferences by race, adjusting for sociodemographics and prior genetic experience.

Results AA were less likely than White to believe that genetic tests should be promoted or made available. Further, AA were less likely to want genetic testing results or to participate in genetic research.

Conclusions Important dimensions that underlay PM are not universally accepted by all populations. Without clear attention to concerns, AA communities may not equally benefit from the rapidly-emerging trend in PM-centered research and clinical practice.

Improving Decision Making about Genetic Testing in the Clinic: An Overview of Effective Knowledge Translation Interventions

Background

Knowledge translation (KT) interventions are attempts to change behavior in keeping with scientific evidence. While genetic tests are increasingly available to healthcare consumers in the clinic, evidence about their benefits is unclear and decisions about genetic testing are thus difficult for all parties.

Objective

We sought to identify KT interventions that involved decisions about genetic testing in the clinical context and to assess their effectiveness for improving decision making in terms of behavior change, increased knowledge and wellbeing.

Methods

We searched for trials assessing KT interventions in the context of genetic testing up to March 2014 in all systematic reviews (n = 153) published by two Cochrane review groups: Effective Practice and Organisation of Care (EPOC) and Consumers and Communication.

Results

We retrieved 2473 unique trials of which we retained only 28 (1%). Two EPOC reviews yielded two trials of KT interventions: audit and feedback (n = 1) and educational outreach (n = 1). Both targeted health professionals and the KT intervention they assessed was found to be effective. Four Consumers and Communication reviews yielded 26 trials: decision aids (n = 15), communication of DNA-based disease risk estimates (n = 7), personalized risk communication (n = 3) and mobile phone messaging (n = 1). Among these, 25 trials targeted only health consumers or patients and the KT interventions were found to be effective in four trials, partly effective in seven, and ineffective in four. Lastly, only one trial targeted both physicians and patients and was found to be effective.

Conclusions

More research on the effectiveness of KT interventions regarding genetic testing in the clinical context may contribute to patients making informed value-based decisions and drawing the maximum benefit from clinical applications of genetic and genomic innovations.

Forward Individualized Medicine from Personal Genomes to Interactomes

When considering the variation in the genome, transcriptome, proteome and metabolome, and their interaction with the environment, every individual can be rightfully considered as a unique biological entity. Individualized medicine promises to take this uniqueness into account to optimize disease treatment and thereby improve health benefits for every patient. The success of individualized medicine relies on a precise understanding of the genotype-phenotype relationship. Although omics technologies advance rapidly, there are several challenges that need to be overcome: Next generation sequencing can efficiently decipher genomic sequences, epigenetic changes, and transcriptomic variation in patients, but it does not automatically indicate how or whether the identified variation will cause pathological changes. This is likely due to the inability to account for (1) the consequences of gene-gene and gene-environment interactions, and (2) (post)transcriptional as well as (post)translational processes that eventually determine the concentration of key metabolites. The technologies to accurately measure changes in these latter layers are still under development, and such measurements in humans are also mainly restricted to blood and circulating cells. Despite these challenges, it is already possible to track dynamic changes in the human interactome in healthy and diseased states by using the integration of multi-omics data. In this review, we evaluate the potential value of current major bioinformatics and systems biology-based approaches, including genome wide association studies, epigenetics, gene regulatory and protein-protein interaction networks, and genome-scale metabolic modeling. Moreover, we address the question whether integrative analysis of personal multi-omics data will help understanding of personal genotype-phenotype relationships.

Initiation of universal tumor screening for Lynch syndrome in colorectal cancer patients as a model for the implementation of genetic information into clinical oncology practice

BACKGROUND

Lynch syndrome confers a hereditary predisposition to colorectal and other cancers. Universal tumor screening (UTS) for Lynch syndrome is recommended by several professional societies, but the implementation can be complex. This article describes the evaluation, process development, and initiation of Lynch syndrome UTS at a tertiary referral cancer center.

METHODS

A multidisciplinary team developed the new process design. Issues in 5 themes were noted: timing, funding, second-opinion patients, result processing, and the role of genetics providers. A committee approach was used to examine each issue for process-improvement development.

RESULTS

The issues related to testing were addressed individually for the successful implementation of UTS at the institutional level. In the conventional-care period, 9 of 30 cases (30%) received Lynch syndrome screening, and 4 cases were referred to medical genetics. During the 6 months following the implementation of UTS, 32 of 44 patients (73%) received Lynch syndrome screening. The 13 unscreened patients all had identified reasons for nonscreening (eg, financial limitations). Ten patients were referred to medical genetics, which identified no new cases of Lynch syndrome, but a low-risk adenomatous polyposis coli (APC) variant was detected in 1 individual.

CONCLUSIONS

The implementation of effective Lynch syndrome UTS can feasibly alter practice at the institutional level. This experience with the assessment and management of issues relevant to the successful implementation of a new clinical care paradigm based on emerging technology has implications for the uptake of advances across molecular oncology into clinical practice, and this is highly relevant in the current era of rapidly evolving genomic technology.

Current directions in behavioral medicine research on genetic testing for disease susceptibility: introduction to the special section

The aim of this special section is to showcase research contributing to our understanding of factors influencing decisions to undergo genetic testing and the impact of the genetic testing process on health-related behaviors of tested individuals. The first two articles report studies investigating factors associated with interest in genetic testing and acceptance of test results (Sherman et al. in J Behav Med doi: 10.1007/s10865-015-9630-9 , 2015; Taber et al. in J Behav Med doi: 10.1007/s10865-015-9642-5 , 2015b). The next two papers address the unique contribution of genetic risk information to understanding risk beyond genetic counseling alone (Heiniger et al. in J Behav Med doi 10.1007/s10865-015-9632-7 , 2015; Taber et al. in J Behav Med doi: 10.1007/s10865-015-9648-z , 2015a). The final three articles investigate the effects of genetic risk information on beliefs about disease control and prevention (Aspinwall et al. in J Behav Med doi: 10.1007/s10865-015-9631-8 , 2015; Kelly et al. in J Behav Med doi 10.1007/s10865-014-9613-2 , 2014; Myers et al. in J Behav Med doi: 10.1007/s10865-015-9626-5 , 2015). Collectively, the special section of papers highlights the diverse ways in which behavioural medicine contributes to our understanding of genetic testing for disease risk, and points to the value of further research to better understand ways in which individuals perceive, interpret and respond to genetic risk information.