Genomics in routine clinical care: what does this mean for primary care?

Embedding genomics across the NHS: a primary care perspective

Primary care remains the point of access to the NHS as well as having key roles in care coordination and prescribing. Therefore, embedding of genomic medicine in the NHS relies on successful implementation into the primary care landscape. Primary care is currently facing considerable challenges, including increasing numbers of patients and consultations per GP, multiple health conditions and polypharmacy, all contributing to increasing workload within a resource-constrained system. Although genomic medicine has enormous potential to benefit patients, its successful implementation demands alignment with existing skills and working practices, development of underpinning informatics infrastructure, integration into care pathways with consideration of commissioning and leadership. Here, we set out current initiatives and future strategies to support primary care colleagues in the delivery of genomic medicine, covering issues of workforce development and education, primary care leadership, and data and digital considerations.

The utilisation of primary health care system concepts positively impacts the assistance of patients with rare diseases despite limited knowledge and experience by health care professionals: A qualitative synopsis of the evidence including approximately 78 000 individuals

Background

Individuals with rare diseases (RD) have been historically understudied. Previous publications reported that existing primary health care (PHC) workforces and associated infrastructure had been shown to improve their access and health-related outcomes in low- and middle-income countries (LMICs). As current evidence about the impact of PHC on patients diagnosed with RD is yet highly dispersed, this scoping review aimed to collate available evidence of the impact of PHC on patients with RD and summarize published information from multiple stakeholders about the perceived usefulness and barriers to effective use of the PHC system.

Methods

We searched Embase, Health System Evidence, PubMed, LILACS / BVS, and The Cochrane Library, from inception to September 1, 2022, for publications providing clear expert- or experience-based insights or data from patients living with RD at the PHC level of care. We included publications highlighting barriers to integrated care of patients with RD, reported by multiple social actors involved in caring for patients with RD. Two investigators screened publications, extracted data, and clustered information among records deemed eligible for inclusion. Data synthesis was performed using narrative and thematic-based analysis. Major findings identified and coded through a semantic-driven analysis were processed in vosViewer software and reported using descriptive statistics.

Findings

Eighty publications were included in this review. Quali-quantitative analyses evidenced that the PHC level is essential for approaching patients with RD, mainly due to its longitudinal, multidisciplinary, and coordinated care delivery. In addition, several publications highlighted that the medical curriculum is inappropriate for preparing health care providers to deal with patients presenting unusual signs and symptoms and being diagnosed with RD. PHC teams are essential in orienting patients and families on emergency events. Technology-related concepts were reported in 19 publications, emphasizing their effectiveness on early diagnosis, optimal treatment definition, improvement of quality of life, and long-lasting follow-up.

Conclusions

We provided valuable information on the effectiveness of the PHC in fostering a creative, integrative, and supportive environment for patients living with RD. Our results can be helpful to several stakeholders in deciding what actions are still pending to achieve a solid and positive experience for patients with RD in the PHC.

Registration

PROSPERO (CRD42022332347).

External validation of models for predicting risk of colorectal cancer using the China Kadoorie Biobank

BACKGROUND

In China, colorectal cancer (CRC) incidence and mortality have been steadily increasing over the last decades. Risk models to predict incident CRC have been developed in various populations, but they have not been systematically externally validated in a Chinese population.  This study aimed to assess the performance of risk scores in predicting CRC using the China Kadoorie Biobank (CKB), one of the largest and geographically diverse prospective cohort studies in China.

METHODS

Nine models were externally validated in 512,415 participants in CKB and included 2976 cases of CRC. Model discrimination was assessed, overall and by sex, age, site, and geographic location, using the area under the receiver operating characteristic curve (AUC). Model discrimination of these nine models was compared to a model using age alone. Calibration was assessed for five models, and they were re-calibrated in CKB.

RESULTS

The three models with the highest discrimination (Ma (Cox model) AUC 0.70 [95% CI 0.69-0.71]; Aleksandrova 0.70 [0.69-0.71]; Hong 0.69 [0.67-0.71]) included the variables age, smoking, and alcohol. These models performed significantly better than using a model based on age alone (AUC of 0.65 [95% CI 0.64-0.66]). Model discrimination was generally higher in younger participants, males, urban environments, and for colon cancer. The two models (Guo and Chen) developed in Chinese populations did not perform better than the others. Among the 10% of participants with the highest risk, the three best performing models identified 24-26% of participants that went on to develop CRC.

CONCLUSIONS

Several risk models based on easily obtainable demographic and modifiable lifestyle factor have good discrimination in a Chinese population. The three best performing models have a higher discrimination than using a model based on age alone.

Introducing genetic testing with case finding for familial hypercholesterolaemia in primary care: qualitative study of patient and health professional experience

BACKGROUND

Familial hypercholesterolaemia (FH) is a common inherited condition causing elevated cholesterol, premature heart disease, and early death. Although FH can be effectively treated, over 80% of people with FH remain undetected.

AIM

To explore patient and health professional experiences of introducing genetic testing with case finding for FH in primary care.

DESIGN AND SETTING

Qualitative study in UK general practice.

METHOD

Semi-structured interviews with a purposeful sample of 41 participants (24 patients and 17 health professionals) from eight practices, using an electronic case-finding tool (FAMCAT) to identify patients with higher likelihood of having FH and who were then offered diagnostic genetic testing in primary care. Data were analysed thematically.

RESULTS

While prior awareness of FH was low, patients were unsurprised to be identified as being at risk, and positive about being offered genetic testing by their practice. Patients not found to have FH were relieved, although some felt frustrated that their high cholesterol lacked a clear cause. Those confirmed to have FH largely expected and accepted this outcome. Practitioners saw detection of FH as an important new opportunity for preventive care. They found the case-finding tool easy to apply and noted patients' high uptake of genetic testing. While they were comfortable referring appropriate patients for further specialist management, GPs sought clearer definition about responsibility for identification and long- term care of FH in future care pathways.

CONCLUSION

Introducing genetic testing with electronic case finding for FH in primary care was positively experienced by patients and practitioners. Further development of this approach could help improve detection of FH in the general population.

Making a case for genomics in chiropractic education

OBJECTIVE

To determine if an existing course in genetics should be revised to refocus on the topic of genomics and its impact on health and primary care, a survey of chiropractors was conducted regarding genomics and patient care.

METHODS

A short survey was designed to ascertain chiropractors' knowledge and use of genomics in their practices, particularly regarding direct to consumer genetic testing. Nine closed-ended questions and 2 open-ended questions were included. Pearson correlation was used to evaluate relationships between close-ended responses. Content analysis was conducted on the final open-ended question that queried respondents for further comments.

RESULTS

There were 181 completed surveys returned. Patients do ask chiropractors about their own direct to consumer genetic testing results-42% indicated that they are approached by patients 1-3 times per month to discuss genetics/genomics. Knowledge of genomics varies among chiropractors, yet 51% feel that teaching genomics is moderately (31%) or extremely (20%) important.

CONCLUSION

An introductory course in clinical genomics is necessary to prepare a chiropractor for patient care.

How practice setting affects family physicians' views on genetic screening: a qualitative study

BACKGROUND

Genetic screening (GS), defined as the clinical testing of a population to identify asymptomatic individuals with the aim of providing those identified as high risk with prevention, early treatment, or reproductive options. Genetic screening (GS) improves patient outcomes and is accessible to the community. Family physicians (FPs) are ideally placed to offer GS. There is a need for FPs to adopt GS to address anticipated genetic specialist shortages.

OBJECTIVE

To explore FP attitudes, perceived roles, motivators and barriers, towards GS; and explore similarities and differences between private and public sector FPs.

METHODS

We developed a semi-structured interview guide using existing literature. We interviewed private and public sector FPs recruited by purposive, convenience and snowballing strategies, by telephone or video to theme saturation. All sessions were audio-recorded, transcribed and coded for themes by two independent researchers with an adjudicator.

RESULTS

Thirty FPs were interviewed (15 private, 15 public). Theme saturation was reached for each group. A total of 12 themes (6 common, 3 from private-practice participants, 3 public-employed participants) emerged. Six common major themes emerged: personal lack of training and experience, roles and relevance of GS to family medicine, reluctance and resistance to adding GS to practice, FP motivations for adoption, patient factors as barrier, and potential solutions. Three themes (all facilitators) were unique to the private group: strong rapport with patients, high practice autonomy, and high patient literacy. Three themes (all barriers) were unique to the public group: lack of control, patients' lower socioeconomic status, and rigid administrative infrastructure.

CONCLUSION

FPs are motivated to incorporate GS but need support for implementation. Policy-makers should consider the practice setting when introducing new screening functions. Strategies to change FP behaviours should be sensitive to their sense of autonomy, and the external factors (either as facilitators or as barriers) shaping FP practices in a given clinical setting.

A decade of toxicological trends: what the papers say

Here we look at popular trends and concepts in toxicology over the decade 2009-2019. The top 10 concepts included methodological approaches such as zebrafish and genomics as well as broader concepts such as personalized medicine and adverse outcome pathways. The total number and rank order for each of the top 10 were tracked year by year via PubMed with >9500 papers contributing to the analysis. The data revealed a slow upward trend in the number of papers across all the concepts from 260 in 2009 to >1700 in 2019. Zebrafish, genomics and personalized medicine remained in the top four slots since 2009 with zebrafish dominating the rankings over the entire decade. Genomics was a strong second until 2013 when it was displaced first by the microbiome in 2014 and secondly by personalized medicine in 2015. Other notable trends were the ascendancy of the microbiome and adverse outcome pathways and the descendancy of hormesis and the 3Rs (replacement, reduction and refinement of animals in testing). The observation that the top four slots have been static over the past 4 years suggests that new ideas are introduced and increase in popularity until they find their place in scientific culture. This may suggest that relatively new concepts such as artificial intelligence and microphysiological systems have yet to find their steady state in the rankings. Similarly, as a relatively new player in toxicology, the full impact of the human microbiome on drug efficacy and safety remains to be seen.

A Genomic Test for Colorectal Cancer Risk: Is This Acceptable and Feasible in Primary Care?

INTRODUCTION

Genomic tests can predict risk and tailor screening recommendations for colorectal cancer (CRC). Primary care could be suitable for their widespread implementation.

OBJECTIVE

We aimed to assess the feasibility and acceptability of administering a CRC genomic test in primary care.

METHODS

Participants aged 45-74 years recruited from 4 Australian general practices were offered a genomic CRC risk test. Participants received brief verbal information about the test comprising 45 CRC-associated single-nucleotide polymorphisms, before choosing whether to undertake the test. Personalized risks were given to testers. Uptake and knowledge of the genomic test, cancer-specific anxiety (Cancer Worry Scale), psychosocial impact (Multidimensional Impact of Cancer Risk Assessment [MICRA] score), and impact on CRC screening behaviour within 6 months were measured.

RESULTS

In 150 participants, test uptake was high (126, 84%), with 125 (83%) having good knowledge of the genomic test. Moderate risk participants were impacted more by the test (MICRA mean: 15.9) than average risk participants (mean: 9.5, difference in means: 6.4, 95% confidence interval (CI): 1.5, 11.2, p = 0.01), but all scores were low. Average risk participants' cancer-specific anxiety decreased (mean differences from baseline: 1 month -0.5, 95% CI: -1.0, -0.1, p = 0.03; 6 months -0.6, 95% CI: -1.0, -0.2, p = 0.01). We found limited evidence for genomic testers being more likely to complete the risk-appropriate CRC screening than non-testers (41 vs. 17%, odds ratio = 3.4, 95% CI: 0.6, 34.8, p = 0.19), but some mediators of screening behaviour were altered in genomic testers.

CONCLUSIONS

Genomic testing for CRC risk in primary care is acceptable and likely feasible. Further development of the risk assessment intervention could strengthen the impact on screening behaviour.

The implementation of pharmacogenomics into UK general practice: a qualitative study exploring barriers, challenges and opportunities

Pharmacogenomics describes interpatient genetic variability in drug responses. Information based on whole genome sequencing will soon open up the field of pharmacogenomics and facilitate the use of genomic information relating to drug metabolism and drug responses. We undertook a qualitative study, aiming to explore the potential barriers, opportunities and challenges facing the implementation of pharmacogenomics into primary care. Semi-structured interviews were undertaken with 18 clinical participants (16 GPs and 2 other clinicians). All interviews were recorded and transcribed verbatim. Using a thematic analysis approach, data items were coded, ordered and themes constructed. Most participants were aged 55–60 years and worked as part-time clinical GPs with other clearly defined roles. The emerging themes covered several areas of concern, including the following: the utility of pharmacogenomics and the value of introducing such testing into primary care; how to educate the primary care workforce and ‘mainstream’ pharmacogenomics; the ethical, legal and social aspects of pharmacogenomics and its impact on patients; and potential impacts on the healthcare system particularly around economics and informatics. Most participants had concerns about pharmacogenomics and felt that there were a number of barriers and challenges to its implementation into routine primary care. Most striking were their concerns around the cost-effectiveness of using pharmacogenomics in primary care. At the same time most recognised the increasing availability of direct-to-consumer testing, and felt that this would drive the need to understand the ethical and social implications of using genomic information in primary care. This study has raised important issues that need to be considered when planning the implementation of pharmacogenomics into clinical practice. Prior to the implementation of genomic testing into day-to-day practice in UK primary care, it is important that considerations around education, cost-effectiveness and informatics are addressed, as well as the impact on patients.

How genomic information is accessed in clinical practice: an electronic survey of UK general practitioners

Genomic technologies are having an increasing impact across medicine, including primary care. To enable their wider adoption and realize their potential, education of primary health-care practitioners will be required. To enable the development of such resources, understanding where GPs currently access genomic information is needed. One-hundred fifty-nine UK GPs completed the survey in response to an open invitation, between September 2017 and September 2018. Questions were in response to 4 clinical genomic scenarios, with further questions exploring resources used for rare disease patients, direct-to-consumer genetic testing and collecting a family history. Respondents were most commonly GP principals (independent GPs who own their clinic) (64.8%), aged 35-49 years (54%), worked as a GP for more than 15 years (44%) and practiced within suburban locations (typically wealthier) (50.3%). The most popular 'just in time' education source for all clinical genomic scenarios were online primary care focussed resources with general Internet search engines also popular. For genomic continuous medical education, over 70% of respondents preferred online learning. Considering specific scenarios, local guidelines were a popular resource for the familial breast cancer scenario. A large proportion (41%) had not heard of Genomics England's 100,000 genome project. Few respondents (4%) would access rare disease specific Internet resources (Orphanet, OMIM). Twenty-five percent of respondents were unsure how to respond to a direct-to-consumer commercial genetic test query, with 41% forwarding such queries to local genetic services. GPs require concise, relevant, primary care focussed resources in trusted and familiar online repositories of information. Inadequate genetic education of GPs could increase burden on local genetic services.

The role of primary care in management of rare diseases in Ireland

Background

‘Slaintecare’ aims to address complex patient care needs in an integrated fashion with an emphasis on patient-centred, patient-empowered community care.Currently there is a lack of knowledge of the impact of rare disease management in primary care and of the information tools required by general practitioners to deliver integrated care for rare disease patients.

Aims

To complete a pilot survey to estimate the general practice clinical workload attributable to selected rare diseases and assess the use of relevant information sources.

Methods

A retrospective cross-sectional survey was carried out of general practice consultations (2013–2017) for patients with 22 commonly recognised rare diseases.

Results

Around 31 general practitioners from 10 Irish practices completed information on 171 patients with rare diseases over 3707 consultations. General practice-specific coding systems were inadequate for rare disease patient identification. Over 139 (81.3%) patients were adult, and 32 (18.7%) were children. Management of care was hospital and not primary care based in 63%. Those eligible for state-reimbursed care had a significantly higher median number of consultations (23 consultations, IQR = 13–37, or 5.8 consultations/year) than those who paid privately (10 consultations, IQR = 4–19, or 2.5 consultations/year) (p < 0.005).General practitioners had access to public information resources on rare diseases but few had knowledge of (35.5%), or had ever used (12.9%) Orphanet, the international rare disease information portal.

Conclusions

Both specific rare disease-specific coding and use of the relevant rare disease information sources are lacking in general practice in Ireland.

A pediatric perspective on genomics and prevention in the twenty-first century

We present evidence from diverse disciplines and populations to identify the current and emerging role of genomics in prevention from both medical and public health perspectives as well as key challenges and potential untoward consequences of increasing the role of genomics in these endeavors. We begin by comparing screening in healthy populations (newborn screening), with testing in symptomatic populations, which may incidentally identify secondary findings and at-risk relatives. Emerging evidence suggests that variants in genes subject to the reporting of secondary findings are more common than expected in patients who otherwise would not meet the criteria for testing and population testing for variants in these genes may more precisely identify discrete populations to target for various prevention strategies starting in childhood. Conversely, despite its theoretical promise, recent studies attempting to demonstrate benefits of next-generation sequencing for newborn screening have instead demonstrated numerous barriers and pitfalls to this approach. We also examine the special cases of pharmacogenomics and polygenic risk scores as examples of ways genomics can contribute to prevention amongst a broader population than that affected by rare Mendelian disease. We conclude with unresolved questions which will benefit from future investigations of the role of genomics in disease prevention.

GP attitudes to and expectations for providing personal genomic risk information to the public: a qualitative study

Background

As part of a pilot randomised controlled trial examining the impact of personal melanoma genomic risk information on behavioural and psychosocial outcomes, GPs were sent a booklet containing their patient’s genomic risk of melanoma.

Aim

Using this booklet as an example of genomic risk information that might be offered on a population-level in the future, this study explored GP attitudes towards communicating genomic risk information and resources needed to support this process.

Design & setting

Semi-structured interviews were conducted with 22 Australian GPs.

Method

The interviews were recorded and transcribed, and data were analysed thematically.

Results

GPs in this sample believed that communicating genomic risk may become a responsibility within primary care and they recommended a shared decisionmaking approach to guide the testing process. Factors were identified that may influence how and when GPs communicate genomic risk information. GPs view genomics-based risk as one of many disease risk factors and feel that this type of information could be applied in practice in the context of overall risk assessment for diseases for which prevention and early detection strategies are available. They believe it is important to ensure that patients understand their genomic risk and do not experience long-term adverse psychological responses. GPs desire clinical practice guidelines that specify recommendations for genomic risk assessment and patient management, point-of-care resources, and risk prediction tools that include genomic and traditional risk factors.

Conclusion

These findings will inform the development of resources for preparing GPs to manage and implement genomic risk information in practice.

Beyond the Helix: Ethical, Legal, and Social Implications in Genomics

OBJECTIVE

To review ethical, legal, and social implications of genomics, a ground-breaking science that when applied improves cancer care outcomes.

DATA SOURCES

PubMed, Cumulative Index to Nursing and Allied Health (CINAHL), Cochrane Library, consensus statements, and professional guidelines.

CONCLUSION

Ethical, legal, and social domains of genomics are not fully delineated. Areas needing further discussion and policies include return of findings, informed consent, electronic health records, and data resources and sharing.

IMPLICATIONS FOR NURSING PRACTICE

All nurses need a basic understanding of the ethical, legal, and social implications of genomics.

External validation of risk prediction models for incident colorectal cancer using UK Biobank

BACKGROUND

This study aimed to compare and externally validate risk scores developed to predict incident colorectal cancer (CRC) that include variables routinely available or easily obtainable via self-completed questionnaire.

METHODS

External validation of fourteen risk models from a previous systematic review in 373 112 men and women within the UK Biobank cohort with 5-year follow-up, no prior history of CRC and data for incidence of CRC through linkage to national cancer registries.

RESULTS

There were 1719 (0.46%) cases of incident CRC. The performance of the risk models varied substantially. In men, the QCancer10 model and models by Tao, Driver and Ma all had an area under the receiver operating characteristic curve (AUC) between 0.67 and 0.70. Discrimination was lower in women: the QCancer10, Wells, Tao, Guesmi and Ma models were the best performing with AUCs between 0.63 and 0.66. Assessment of calibration was possible for six models in men and women. All would require country-specific recalibration if estimates of absolute risks were to be given to individuals.

CONCLUSIONS

Several risk models based on easily obtainable data have relatively good discrimination in a UK population. Modelling studies are now required to estimate the potential health benefits and cost-effectiveness of implementing stratified risk-based CRC screening.