Glasgow, UK: The informed consent process in biomedical research is biased towards people who can meet with clinical study staff during the working day. For those who have the availability to have a consent conversation, the time burden can be off-putting. Professor Eric Vilain, from the Department of Paediatrics, University of California, Irvine, USA, will tell the European Society of Human Genetics annual conference today (Tuesday 13 June) how results from his team’s study of the use of a chatbot (GIA – ‘Genetics Information Assistant’ developed by Invitae Corporation) in the consent process show that it encourages inclusivity, and leads to faster completion and high levels of understanding. Since such consent is the cornerstone of all research studies, finding ways of cutting the time spent on it while continuing to make sure that participants’ understanding is not lessened is something clinicians have aimed for some time.
Working with their institutional review board (IRB), Prof Vilain’s team from across University of California Irvine, Children’s National Hospital, and Invitae Corporation designed a script for the GIA chatbot to transform the trial consent form and protocol into a logic flow and script. Unlike conventional methods of obtaining consent, the bot was able to quiz participants to assess the knowledge they had attained. It could also be accessed at any time, allowing individuals with less free time to use it outside normal business hours. “We saw that more than half of our participants interacted with the bot at these times, and this shows its utility in decreasing the barriers to entry to research. Currently, most people who participate in biomedical research have time to do so as well as the knowledge that studies exist,” says Prof Vilain
The researchers involved 72 families in the consent process during a six-month time period as part of the US national GREGoR consortium, a National Institutes of Health initiative to advance rare disease research. A total of 37 families completed consent using the traditional process, while 35 used the chatbot. The researchers found that the median length of the consent conversation was shorter for those using the bot, at 44 rather than 76 minutes, and the time from referral to the study to consent completion was also faster, at five as opposed to 16 days. The level of understanding of those who had used the bot was assessed with a 10-question quiz that 96% of participants passed, and a request for feedback showed that 86% thought that they had had a positive experience.
“I was surprised and pleased that a significant number of people would feel comfortable communicating with a chatbot,” says Prof Vilain. “But we worked hard with our IRB to ensure that it didn’t ‘hallucinate’ (make mistakes) and to ensure that knowledge was conveyed correctly. When the bot was unable to answer a question, it encouraged the participant to speak with a member of the study team.”
While it is not possible to give an accurate account of cost saving, the time savings of staff were substantial, the researchers say. Because people can pause the chatbot consent process at any time, it can be completed much more quickly – for example, four participants completed in 24 hours. Of the consent conversations that were quick (less than an hour), 83% of them were with the chatbot. The consent conversations that were longer (between one and two hours), were with a study staff member (66%).
“But it’s far from being just about speed,” says Prof Vilain. The traditional method of consenting does not have a mechanism to verify understanding objectively. It is based on the conviction of the study staff member hosting the conversation that the consent has been informed properly and the individual understands what they are consenting to. The chat-based method can test comprehension more objectively. It does not allow users who do not show understanding to give consent, and puts them in touch with a genetic counsellor to figure out why knowledge transmission did not occur.
“We believe that our work has made an important contribution to the obtention of properly-informed consent, and would now like to see it used in different languages to reach global populations,” he concludes.
Professor Alexandre Reymond, chair of the conference, said: “The keystone to informed consent should be that it is by definition ‘informed’, and we should explore all possibilities to ensure this in the future.”
The research was funded by the NHGRI GREGoR Consortium, grant number U01HG011745.
Abstract no. C28.3: Development and Implementation of Novel Chatbot-based Genomic Research Consent
Glasgow, UK: Xeroderma pigmentosum (XP) is a rare and devastating genetic disorder characterised by an inability to repair skin damage caused by ultraviolet (UV) light. As a result, patients with XP develop skin cancers, usually in childhood. Once diagnosed, they can be protected by avoiding sunlight (hence sometimes being called ‘children of the night’), wearing special clothing and sunglasses, and using sunscreen. But some will also develop neurodegenerative conditions such as hearing loss, loss of intellectual function, poor co-ordination and seizures. Finding out why this is, and which patients are likely to develop such conditions, is a priority for XP researchers.
Dr Sophie Momen, a consultant dermatologist at Guy’s and St Thomas’ NHS Foundation Trust, London, UK and a researcher in Professor Serena Nik-Zainal’s lab at the University of Cambridge, will tell the annual conference of the European Society of Human Genetics today (Monday) of her team’s work in the development of an early detection algorithm to predict which patients may develop such neurodegeneration. Until now there has been little research in this area, partly because XP is a rare condition, affecting one person in a million, and because the brain, being an inaccessible organ in live patients, is very difficult to perform research on.
The researchers took blood samples from patients with XP with and without neurodegeneration, and from family members without XP, and turned these samples into pluripotent stem cells (cells that can be groomed into different cell types). The researchers were then able to identify the stem cells that would become brain cells (neurons). “We carried out various experiments on these neurons using multi-omic1 technologies to try to understand why some XP patients developed neurodegeneration and some did not. From this we were able to develop our algorithm. This will be useful if we can offer something to patients to try to slow down or halt the onset of neurodegeneration. Our research has revealed possible drug targets, which may do just that in the future,” says Dr Momen.
The researchers were fortunate, they say, in having access to a large group of patients from the national XP clinic at Guy’s and St Thomas’, where all British-resident patients with the condition are cared for by the same clinical team. “Having such a clinic means that patients with rare diseases can be followed up long-term in one place, and this facilitates investigations such as ours,” Dr Momen says. “This is the first time that so many patients with XP have been studied and their neurons have been characterised in such depth.”
Since the clinic came into being in 2010 , patients in the UK have been well-informed about photoprotection and about early detection of skin cancers, and as a result they are living long lives. “None of our patients has died from skin cancer,” says Dr Momen. “It is often said that patients with XP die in their 20s and 30s, either due to skin cancers or neurodegeneration, but this is not always the case. It is important to recognise that there are some patients with XP who do not develop neurodegeneration and mainly develop skin cancers, against which they can take protective measures at an early stage.”
The results may also be useful in understanding why otherwise healthy people develop neurodegeneration as they age. Over the past few years, the study of patients with XP has helped scientists to understand why some otherwise healthy people develop skin cancers after exposure to UV light. “We can now extrapolate the findings in our study to the understanding of why the faulty DNA repair pathway involved in XP is involved in brain health and this may, in turn, help us understand why some people develop neurodegeneration as they age.”
Further validation studies of the early detection algorithm will be necessary before it can be used as a predictive tool in clinical practice. Clinical trials will also be needed to see which, if any, medications may be useful in halting or delaying neurodegeneration in patients identified as being at risk.
“ I did not expect that we would be able to characterise the neurons derived from those patients with and without neurodegeneration so clearly. When we used proteomics, the results allowed us to see clearly whether patients had neurodegeneration or not,” says Dr Momen. “This is very encouraging and, we hope, a further step along the road to effective treatment of this distressing condition.”
Professor Alexandre Reymond, chair of the conference, said: “Our ability to personalise treatments will translate into a more effective health system. To reach this goal, we need new approaches to recognise those in the population who are more at risk.”
1.Multiomics is an approach to biological analysis that combines various ‘ome’ datasets, for example genome, proteome, transcriptome, epigenome, metabolome, and micobiome.
The research was funded by The Wellcome Trust, and Cancer Research UK.
Abstract no. 3869 Functional multi-omic studies unveil ER stress and proteasomal dysfunction in early-onset neurodegeneration in XP
Glasgow, UK: Rates of colorectal cancer are high despite widespread adoption of screening programmes in many high-income European countries. Such programmes tend to use a one-size-fits-all approach where most people are screened starting from the same age, and no individual factors are considered in organised population screening. Now, based on one of the largest genomics studies on the topic to date, researchers from Finland have outlined how common genetic factors could be used to identify individuals at high risk of developing the disease and hence improve current colorectal screening strategies.
Max Tamlander, MD at the Institute for Molecular Medicine Finland (FIMM) of the University of Helsinki, will present to the annual conference of the European Society of Human Genetics today (Monday 12 June) his team’s work on the development of a polygenic risk score (PRS) specifically for colorectal cancer. A PRS summarises the combined impact of an individual’s genetic risk factors for a disease into a single score. This allows an estimation of an individual’s likely disease risk and the identification of those who might benefit from earlier screening.
The researchers used data from the FinnGen study, a collection of health and genome data from more than 400,000 Finnish individuals, for which they calculated a genome-wide PRS for colorectal cancer. “A challenge of many prior PRS studies is that they have been performed in smaller datasets that are not representative of the general population, but in this study we used epidemiological and statistical approaches to calibrate our estimates with that population,” Dr Tamlander explains.
Most cases of colorectal cancer occur in individuals who do not have a family history of the disease or any other known strong risk factors. PRSs offer a new way of assessing risk in these individuals, which until now has been based on attained age alone. The researchers’ results also show that a PRS could be useful in the assessment of future colorectal cancer risk after a colonoscopy, the current gold-standard screening method, and identify those individuals who would potentially benefit from more frequent surveillance.
In Finland, screening for colorectal cancer in the general population currently starts at age 60; in some other European countries it starts earlier, from 50. The researchers found that, based on the current screening age 60 in Finland, individuals with a high PRS as compared to those with a low PRS could start screening at up to 16 years apart. For example, women and men at the top 1% of the PRS already had equivalent risks at ages 48.7 and 49.8, respectively. “This indicates that a colorectal cancer-specific PRS would be able to define more appropriate ages to start screening for individuals based on their genetic risk,” says Dr Tamlander.
As the cost of genotyping continues to fall, PRS-based approaches may become a feasible way to guide population-wide screening. “Millions of individuals already have their genomes available in large-scale biobanking initiatives,” says Dr Tamlander. “For example, the FinnGen biobank study already contains the genomic data of over 7% of all Finns, and this will soon increase to around 10%. One very useful aspect of PRSs is that genetic data extracted from a single sample can be used over the course of life to calculate risk scores for many common diseases, including the most common cancers.”
Further clinical studies as well as data on cost-effectiveness and the effective communication of risk information will be needed before large-scale implementation of the colorectal PRS, say the researchers. Another problem is that, to date, PRSs have been mainly developed in individuals of European descent, and therefore may not be valid for people of other ancestries.
“However, our findings are well in line with other studies on PRSs in breast cancer, another common cancer with organised population-level screening. For breast cancer, large clinical trials are currently underway to evaluate the performance of personalised breast cancer screening, and their results will help us to understand the implications of genome-guided, risk-based screening for colorectal cancer, as well as other diseases.”, Dr Tamlander continues.
“In the future, risk-based approaches considering genetic factors alongside other relevant risk factors have potential for personalising recommendations regarding how we could most effectively screen for colorectal cancer,” Dr Tamlander will conclude.
Professor Alexandre Reymond, chair of the conference, said: “Recognising the individuals who are at risk is fundamental if our health systems want to truly embrace personalised health in the future.”
The research was funded by the Academy of Finland, Horizon 2020 (EU), and the Sigrid Jusélius Foundation.
Abstract no. C20.2 Genome-wide polygenic risk scores substantially impact colorectal neoplasm risk with implications for stratified screening
Glasgow, UK: Genetic counselling is essential when dealing with individuals who are affected by, or at risk of, inherited disease. Although it is known to be useful in helping patients cope with test results and deal with uncertainty, there have been very few randomised controlled trials (RCTs) of its effectiveness. Dr Andrada Ciuca, a post-doctoral researcher at Babes-Bolyai University, Cluj-Napoca, Romania, will tell the annual conference today (Sunday 11 June) that the results of the first RCT of genetic counselling in familial colorectal cancer (fCRC) show that it provided significant improvements in patients’ feelings of empowerment, as well as other states of mind such as depression and emotional distress.
Genetic counselling involves the process of helping individuals and families affected by or at risk of genetic disorders to understand and adapt to the medical, psychological and familial implications of the genetic contribution to their disease. In recent years, with the advent of genomic medicine, such counselling has taken on a new importance.
The researchers recruited 82 individuals who were at risk for various types of fCRC from a Romanian oncology clinic, and randomised them to either standard care or standard care plus genetic counselling. Their average age was 44.81 years old, and 52.4% of the participants were female. They saw a significant effect on empowerment and depression scores in the group that received genetic counselling as compared to the control group, and further analysis showed that the counselling group also had improvements in knowledge, anxiety, and emotional distress.
“We found that lower emotional distress benefited more in terms of empowerment,” says Dr Ciuca. “Empowerment is particularly important for these patients, since not only does it help them feel they can make real, informed choices, but it also aids their ability to manage their feelings and make plans for the future. An interesting finding was that the more anxiety decreased after their counselling session, the greater the impact was on their empowerment. This highlights the importance of addressing emotional distress during genetic counselling.”
The researchers hope that their results will inform further investigations in genetic counselling, as well as clinical practice. Since it is a fairly young discipline, building a robust evidence base of its effectiveness is important, they say. In the meantime, their study should underline the need for more support for the further development of genetic counselling from healthcare systems and policy makers.
“Because genetic counselling is relatively new, it is perhaps unsurprising that there are so few RCTs of its use in inherited cancers. There have been trials looking at different counselling strategies in fCRC, but this is the first to look at the effect of counselling vs. no counselling. However, there is a strong evidence-based ethos in our discipline, and I would expect that more trials for other conditions will follow,” Dr Ciuca will conclude.
Professor Alexandre Reymond, chair of the conference, said: “We should empower patients to make informed choices. This is only possible if we are fully committed to help them understand the medical information we provide.”
Abstract no. C12.2 The efficacy of genetic counselling for familial colorectal cancer: findings from a randomised controlled trial
Glasgow, UK: Being to identify people at high risk of chronic disease means that they can be targeted with prevention measures before they become sick. Polygenic risk scores, where genomic information alone is used to assess the risk of developing diseases, have been receiving a lot of attention recently, but research to be presented at the annual conference of the European Society of Human Genetics today (Saturday 10 June) suggests that combining blood biomarkers with genomic information gives more accurate, cost-effective results.
Dr Jeffrey Barrett, Chief Scientific Officer, Nightingale Health, Helsinki, Finland, will describe how his team measured over 200 biomarkers in blood samples from 300,000 participants in the UK Biobank, and 200,000 in the Estonian biobank. “This is the biggest dataset of its kind that has ever been collected,” he says. The researchers used machine learning to build predictive models for individuals’ future risks of nine common diseases, based on their genetic information and the biomarkers that they measured. The diseases studied were ischaemic heart disease, stroke, lung cancer, diabetes, chronic obstructive pulmonary disease, Alzheimer’s and other dementias, depression, liver disease, and colon cancer. These are the top sources of “disability adjusted life years” in the European region, according to the WHO, and thus the biggest sources of suffering and health care costs, and the most important in terms of prevention.
“We found that in all the diseases, both genetics and biomarkers could provide useful information about disease risk, even ten years into the future. And the blood biomarkers provided better prediction in nearly all cases – for example, the 10% of individuals with the highest risk of lung cancer based on the biomarkers had four times the risk of an average person, whereas the top 10% based on genetics had only 1.8 times the risk,” says Dr Barrett. “And for liver disease the same numbers are 10 times and two times respectively.”
The team also found that the prediction using blood biomarkers was sometimes even stronger for near-term risk (for example in two or four years), which they believe may reflect direct links between some of what the biomarkers measure and the pre-symptomatic phase of the disease. At a time when healthcare systems are running out of money, in large part because ageing populations have increasing levels of lifestyle diseases like the ones studied, they believe that their work shows how easy-to-measure blood tests can be used in population preventive health. “It means that it is relatively easy to find the individuals at greatest risk of many diseases and offer them ways to reduce their risk, keeping them healthier and at the same time reducing the financial burden on healthcare systems,” says Dr Barrett.
“I was surprised by the breadth of the applicability of our approach – the way in which the data capture many core metabolic functions in one blood test could provide so much information across different areas of human health. We were able to show that our predictions were highly consistent across multiple biobanks, whereas many other studies have access to just one. This suggests that these biomarker scores are not a narrow research finding, and could be used effectively in general practice,” Dr Barrett concludes.
Professor Alexandre Reymond, chair of the conference, said: “While more work to assess the robustness of these predictions is warranted, it is tantalising to see the first steps of genomic preventive medicine.”
The research was entirely funded by Nightingale Health, a preventive health company based in Helsinki
Abstract no. C02.6 Early prevention for 9 common diseases via combined genomic and metabolomic prediction
Glasgow, UK: Inherited retinal diseases (IRDs), single-gene disorders affecting the retina, are very difficult to diagnose since they are uncommon and involve changes in one of many candidate genes. Outside specialist centres, there are few experts who have adequate knowledge of these diseases, and this makes it difficult for patients to access proper testing and diagnosis. But now, researchers from the UK and Germany have used artificial intelligence (AI) to develop a system that they believe will enable more widespread provision of testing, together with improved efficiency.
Dr Nikolas Pontikos, a group leader at the UCL Institute of Ophthalmology and Moorfields Eye Hospital, London, UK will tell the annual conference of the European Society of Human Genetics today (Saturday 10 June) about his team’s development of Eye2Gene, an AI system capable of identifying the genetic cause of IRDs from retinal scans. “Identifying the causative gene from a retinal scan is considered extremely challenging, even by experts. However, the AI is able to achieve this to a higher level of accuracy than most human experts,” says Dr Pontikos.
The researchers were able to utilise Moorfields Hospital’s vast database of information on IRDs, covering over 30 years of research. Over 4000 patients have received a genetic diagnosis as well as detailed retinal imaging at Moorfields, making it the largest single centre dataset of patients with both retinal and genetic data.
Identification of the gene involved in a retinal disease is often guided by using the patient’s phenotype defined using the Human Phenotype Ontology (HPO). The HPO involves the use of standardised and structured descriptions of medical terms of a patient’s phenotype, which are observable characteristics of an individual resulting from the expression of genes, to allow scientists and doctors to communicate more effectively. “However, HPO terms are often imperfect descriptions of retinal imaging phenotypes, and the promise of Eye2Gene is that is can provide a much richer source of information than HPO terms alone by working directly from the retinal imaging,” says Dr Pontikos.
The team benchmarked Eye2Gene on 130 IRD cases with a known gene diagnosis for which whole exome/genome, retinal scans, and detailed HPO descriptions were available, and compared their HPO gene scores with the Eye2Gene gene scores. They found Eye2Gene provided a rank for the correct gene higher or equal to the HPO-only score in over 70% of cases.
In the future, Eye2Gene could be easily incorporated into standard retinal examination, first as an assistant in specialist hospitals in order to get a second opinion, and eventually as a "synthetic expert” where such a person is not available. “Ideally, Eye2Gene software would be embedded into the retinal imaging device,” says Dr Pontikos.
Before its use becomes more widespread, the system will need to go through regulatory approvals to demonstrate safety and efficacy. This future use of AI has the potential to become a more effective, less invasive and more widely accessible approach to diagnosing patients, and to improve their management and treatment. “We need further evaluation of Eye2Gene in order to assess its performance for different types of IRD patients from different ethnicities, different types of imaging devices, and in different types of settings, for example primary vs secondary care. Clinical trials will be required before our system can be deployed in clinics as medical device software,” says Dr Pontikos.
“We all know that a picture is worth a thousand words, so we had some expectation that retinal scans interpreted by AI could out-perform HPO terms only. But we were still pleasantly surprised to see that, even when quite specific HPO terms were used, Eye2Gene could still do as well or better than an HPO-only approach. We hope that AI will help patients and their families by making specialist care more efficient, accessible, and equitable,” he will conclude.
Professor Alexandre Reymond, chair of the conference, said: “While real life experts are essential, the use of AI will help in mitigating biases and will allow diagnoses for all in the future.”
The research was funded by the National Institute of Health AI Award in the UK, with preliminary work funded by Moorfields Eye Charity.
Abstract no. PL3.6 Eye2Gene: a novel AI algorithm enables phenotype-driven gene prioritisation directly from retinal scans in inherited retinal diseases