The more feasible than ever to implement genomic technologies

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Last updated: October 24, 2019

The science of genomics with next-generation sequencing (NGS) and computational biology technologies has been and is continuing to advance at an unprecedented scale (1,2). Findings from sequencing research efforts allowed to improve our insight and understanding of human DNA, and this is set to grow with more than 500,000 genomes sequenced already (3). Therefore, it is becoming more feasible than ever to implement genomic technologies and testing into mainstream clinical settings. More and more genetic laboratories are taking advantage of affordable and fast output genomics data, especially as more evidence is being generated about their efficacy for diagnostic and prognostic use (1,2). Large-scale massively parallel sequencing facilitates the analysis of an individual’s whole exome or genome in different areas of clinical medicine. For example, it provides screening tools for the identification of the genetic carrier status or certain diseases predisposition (4), it is used for diagnosis of rare diseases (5), it is also used in infectious diseases for evaluation of species, identification of disease outbreaks to name a few (6,7). Moreover, it is also very applicable in oncology for identifying various biomarkers such as prognostic (e.

g BRCA1/BRCA for breast cancer), predictive (patient screening and selection for targeted therapy response), monitoring, tumour classification (8-10) as well as in pharmacogenomics for identification of genotype drug interactions (9). Adoption of genomics testing increases the amount of data that we can sequence, it allows for testing not only more patients but also more of the genomic targets providing increased diagnostic yield at a reduced rate. With the use of genomics we can improve and speed up cancer and rare disease diagnosis and select the best and most effective treatments, it provides a scope for personalised medicine(2). Findings from sequencing projects like HapMap, Human Genome or various GWAS have already provided a new insight into human genetics and certain diseases ethology as well as helped to discover new pathways to treatment, with some results having an effect on improved drug safety and efficacy (11). In addition, they provide an economic healthcare advantages and savings in the treatment costs (12). Department of Health is recognising the benefits of application of sequencing technologies in different areas of medicine with the aim of improving patient’s care.

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 For this reason, they have commissioned the 100,000 Genomes Project as means for the NHS transformation, paving the way for genomics implementation into everyday medical practice (13) with an ultimate aim of providing a personalised treatment at the individual level. There are many advantages that genomics can bring to healthcare practice as listed above. However, it is also vital to remember about limitations of these new next generation technologies. For example the fact that genomic testing it still relatively new and their clinical utility is not yet fully validated and demonstrated (14). Whole genome sequencing is generating an enormous amount of data including many genomic variations of unknown significance or false positives leading to increased testing and uncertainty not only in the interpretation of the test results, but also in assessing prognosis for the patient or the recurrence risk in the family (15). Furthermore, application of genomics raises some legal and ethical concerns for example issues surrounding gender selection, designer babies, promotion of eugenics concepts or even possible genetic discrimination in employment or insurance (16-19). Moreover, the validity of true informed consent or data privacy, security, release and storage is also challenging (20,21). Lack of unified genomic testing processing guidelines or technical standards for interpretative pipelines prevents the reproducibility of findings across different laboratories locally and worldwide (14,22,23).

Additionally, limited education and understanding of genomic technologies amongst patients and healthcare professional alike also impedes the on the implementation of these new technologies in the mainstream NHS (24,25). This essay will mainly concentrate on difficulties in managing and communicating of the genomic test results for the clinical staff and its implications for the practice and the patient. In the following sections some of the reasons which could impede on this communication will be explored as well as the skills and interventions that are needed to overcome these limitations. However, firstly  it is important to be familiar with the genetic issues that should be discussed during the consent process before the testing is undertaken as per recommendation by the UK’s Joint Committee on Medical Genetics please see Figure 1 below.Figure 1(19) (adapted from page 475)   In addition, those receiving consent must be properly trained and follow well established ethics principles and guidelines including unconditional positive regard, non-directive approach, empathy and others (26,27).

This is effect may help to reach goals of genetic counselling which are to educate and  explain all of the above aspects without giving direct advice, so that the patient can process all the available information and give their informed consent autonomysly, with emotional and practical support offered where possible regardless of their choices (28).Understanding genomic results and concept In regards to the potential difficulties that frontline clinicians face when managing and communicating genomics results in the clinical setting it is necessary to start with the level of understanding and expertise in the field. There are concerns that majority of frontline clinicians do not feel fully equipped with knowledge around genomic and report on lack of confidence in implementing genomic results in their clinical decision making (25,29). This includes not only insufficient awareness and education in regards to genomics concepts but what is important for the scope of this essay lack of their preparation in counselling and health communication skills in regards to genomics results.

Therefore, they would prefer to relay on genetics communication experts to not only prepare patients for genomic testing but also provide feedback and follow up (30). Unfortunately, the number of clinical geneticists and genetic counsellors is limited and sometimes even they are puzzled with genetic reports (19). However, with Department of Health far reaching aim of implementing genomics medicine into routine medical practice health professional need to be prepared to communicate genomic results to patients across many specialities (13).

This requires rising awareness and comprehension of genomics but also educating clinical staff in counselling skills because communication of these type of results proves difficult especially if provided by non-genetics (30). Expertise, timing and consistency is important and in ideal world scenario we would have patients and health professionals that understand the concept of genomics and are able to discuss and explore the implications, consequences and management together during consultation (28,31). This would allow patients to be much more empowered in their healthcare decision making in line with the published Department of Health Guidance 2010 on patient-centred approach in the NHS (32).

Researchers report that patient engagement approach provides many benefits (33).  However, the reality especially in the field of genomics is rather different because of limited knowledge that patients and clinicians have which prevents effective communication. Recent survey in the UK carried out by Welcome Trust reported that only 12 % of population admit to have a good understanding of the term genome (24). In addition, research findings also suggested lack of awareness and interest in genomics amongst health professionals (23,29,34). Therefore, engagement and raising knowledge of genomics through educational programmes for public and clinical staff, is vital (35-37). One of these initiatives is “Socialising the genome project” which is exploring different creative ways of explaining and engaging public into genomics concepts (36).  Moreover, NHS Health Education England is also investing in various genomics courses and awareness events for multi-disciplinary teams to equip them with better understanding and skills needed to deal with the interpretation and delivery of the genomics output data (38). Unfortunately, test results from WGS and WES might prove very difficult to interpret because of the sheer volume of data that they produce, incidental findings, uncertainty of rare de novo variants and lack of full understanding or validation (39,40).

In addition, many conditions are multifactorial and are caused by combination of intergenetic, environmental and other factors please see Figure 2 below. Figure 2.(41) Therefore, the diagnosis for some conditions may be uncertain or even wrong which in effect can have dangerous consequences and may lead to causing harm for the patient on many levels. Please see Figure 3 below for list of reported examples based on uncertainties surrounding genomics results. Figure 3. (39) Unfortunately, currently there is not a one centrally expert maintained and regularly updated data repository of all reported rare and disease-associated variants (15) where clinicians could refer to which doesn’t help in increasing their understanding.

Therefore, clinicians need to work closely together with geneticists and wider MDT whilst confirming the diagnosis for individual patients in line with standardised guidelines on variant interpretation (42). It is also important to have a healthy scepticism and sensitivity for the error in regards to possible diagnostics limitations. In addition, our knowledge on epigenetics and the assessment of disease risks is growing and changing rapidly and with this fast moving genomic data there are also challenges of reassessing and following up patient’s NGS results and currently no processes or line of responsibility for that to happen exist (23). Therefore, establishing clinical utility and predicting recurrence risk and prognosis for patient and their family based on the specific genomic variant still proves challenging for counselling and clinical follow-up decision. Risk estimationAnother challenge is estimating and communicating the information about the genetic risk for potential conditions following the test results. It is difficult because genomics rarely produces an absolute yes or no answers and is more based on likelihoods and chances (29,41).

Many clinicians and patients might find it difficult to accept as it is much easier to deal with definite conclusions. In addition, risk perception is different amongst individuals and there is also no consistency in practice when it comes to communicating genetic risks (41). For example the likelihoods might be explained as risk in percentages 25% or number odds of 1 in 4 chances as in the case of autosomal recessive or 50% chance and 1 in 2 chances in autosomal dominant conditions. On the other hand the approach might have to be adapted to individual patients as some might not understand or be confused with the idea of one or another. Hence, it is important to establish best way of explaining these risks for example with the help of situation scenarios (e.

g. room with 200 people you are one of them there is 1 in 200 chance that you could be affected), visual aids or multimedia (43,44). Furthermore, patients need to be reassured and understand that there is no right or wrong decisions, it will all depend on their individual situations at that moment in time.  Even if the clinician has a confirmed molecular diagnosis and estimated an accurate risk associated with a given condition it will count for noting if he is not able to successfully communicate this to the patient or a family that they are seeing. This needs to be done in a non-directive way, so that they understand the risk as well as long and short term consequences that may result from their decision and are facilitated to reach the conclusion by themselves in non-judgmental and autonomous way (28,31,45,46). Dealing with feelings and decision makingBoth the referral testing and delivery of results requires support in a form of genomic counselling so that patients’ feelings can be explored and they are in position to formulate their own answers (45). This could involve parents deciding whether to subject their child who had been screened for a rare condition to the series of diagnostic assessments, reaching agreement on prenatal diagnosis in regards to risk of serious inherited disorder but also associated choice for pregnancy termination.

Moreover, considering on predictive tests for cancer predisposition or late onset condition for themselves or their children, sharing the results with wider family and other issues associated with genomic testing.  Communication and empathy is very important in this process as patients need to be aware of consequences and implications of testing or results for them and their families and counselling can help with exploring accompanying emotions and finding their own solutions (31,45,46). Making a decision regarding potential genetic testing or dealing with results is not easy by any means and non-geneticists may not be prepared for outbursts of feelings. Majority of health professional are used to and comfortable in just treating sick patients and not use to dealing with the emotional aspects thus, they might be set in their ways and resistant to change their current practices. Therefore, it is vital to make sure that counselling and health communication training skills are crucial part of the training for current and new generations of health professionals so that they are prepared for genomic results and the associated psychological aspects. This should enable them to facilitate the exploration of reasons for and against the testing or outcomes as well as discussion of the associated decision consequences. Figure 4 below lists some examples of potential reasons, benefits, risks, and limitations of genetic testing for BRCA1/2.   When patients or parents of affected children are faced with certain diagnosis/no diagnosis or disease risk information there is a lot of potential for various feelings for exmple disappointment, blame, guilt, shame, unmet expectations, anxiety and others.

Level of their distress and their decision making will be depended on how they may perceive the risk as explained above, it will also be influenced by their level of understanding, the specificity of the diagnosed condition and the availability of preventive and treatment possibilities (44,46,48).  Risk level and feelings of confusion and anxiety will be significantly increased if patients are faced with uncertain findings from genomics testing which they don’t fully understand, especially if their clinician also feels inadequately prepared to communicate the information as explained earlier. In addition, some misleading and contradicting information available on the internet might also have an impact especially if patients need to wait a long time for their counselling visit. Therefore, delivery of results or discussion and exploration of feelings regarding potential testing as well as patient decision making in this area is a complex subject and might prove especially challenging for non-geneticists. Research suggests that using visual aids, appropriate multimedia or internet resources as well as utilising the support of other families with similar condition could help in giving a meaning and managing patients’ feelings and expectations and help them with decision making (43,44). This may prove more effective in cases on monogenic disorders or well identified genetic condition but will not be as useful in the case of rare de novo or variable condition with different spectrums of the phenotype or variants on unknown significance (41,48) .

Currently there are number of support organisations and groups for many rare genetic conditions for example Rare Disease UK and Genetic Alliance (49,50). This also includes SWAN support network for patients with syndrome without the name (51). All these organisations are the best point of contact as they provide most up to date and valid information as well as support for affected patients and families.  Whatever the case the additional clinic time is a key for expert health professionals whilst delivering the genetic results, this allows not only for a meaningful discussion but also exploration of patient’s feelings, active listening, empathy and support (44). Researchers report that majority of issues and concerns that families bring to the consultation regarding testing are very similar (41).

Therefore, communication techniques and psychological principles (44) used in genetic counselling should be utilised to address these problems. Exploration of feelings and facilitation of individual’s decision making as well as offer of support following the decision made may help patients to cope better even with uncertain findings. However, is it feasible and practical to explore the associated psychological aspect when it comes to the interpretation of the genetic results from the whole genome sequencing? The challenge is that the results could include 100 potential genetic risk on average and it has been reported by experts that it could take up to 5 hours of clinical time to communicate these risks (15). Yet, many of these risks have low or moderate risk therefore expert guidance is needed in regards to clinical utility and actionability of variants for reporting as patients and clinicians alike might be overwhelmed with data which could prove counterproductive.

Therefore, clarity is needed in this area. Whatever the case it has been reported that counselling reduces stress level and promotes autonomous decision making by giving a personal meaning to the results (28). However, this requires time, sensitivity and change to practice unfortunately, mainstream NHS is already under many threats and cost cutting pressures which have an impact on patient’s care (52). Therefore, the focus tends to be on providing complex genetic information without consideration for psychological aspect of its consequences, which has been a long standing issue in the field of genetics (15,41,44).

Summary As described above there are many challenges for clinicians in regards to managing and communicating the NGS results. However, at the same time genomic testing is becoming wide spread and is entering a mainstream NHS enabling clinical innovation and treatment breakthroughs for many conditions. Therefore, it is vital for Department of Health to provide support and training not just in genomics but also in health communication theory in order to equip clinicians with very much needed skills. This will help heath professional to explain genomic complexity of sequenced results (where possible) with associated risks, long and short term consequences and any possible interventions in a non-directive way so that patient is able to make their own autonomous decision. Furthermore, clinicians should work together in order to provide consistent information for individuals or families undergoing testing.

Therefore, further scientific investigation is needed for de novo and VUS so that the novel syndromes are defined better. Genetic counselling should become a fundamental part of healthcare practice when it comes to genomics and training is essential to explore and assess associated psychological aspect and support patients in their decision making. This preparation may help in gaining benefits from this new technology, while keeping the harms to a minimum, but it is for policy makers to realise this and support clinicians with the very much needed consultation time.  

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