Most of the world is missing out on the genomics revolution: why this is bad for science

Yoonsu Cho, Bryony Hayes and Daniel Lawson

As we usher in the era of precision medicine – healthcare tailored to the individual – genetic information is being used to design drugs, tests and medical procedures. While this approach enables physicians to better predict the needs of patients and quickly adopt the most suitable treatment, it should be acknowledged that what is suitable for many, is not suitable for all. Appropriate medical care is linked with ancestry – for example, healthy people with African ancestry naturally exhale less air than reference samples of Europeans, leading to mis-diagnosis for Asthma. For people from Black and Minority Ethnicities, the potential impact of ethnicity is intensely debated in Cancer treatment. Research suggests that lack of BME participation in medical research will lead to poor medication choices, genetic tests being less useful, and any COVID-19 treatments being less well tested.

The World Health Organization has stated that “everyone should have a fair opportunity to attain their full health potential and that no one should be disadvantaged from achieving their potential”. However, systematic discrimination & socio-economic-related disadvantages such as lower education and difficulty accessing high quality jobs are overwhelmingly experienced by non-white people, with statistics showing that 80% of Black African and Caribbean communities are living in England’s most deprived areas (as defined by the Neighbourhood Renewal Fund). These factors contribute to people from those communities receiving worse medical care overall. Beyond this, poor representation in research now can only lead to systematically poorer healthcare in the years to come. In 2009, only 4% of genetic association studies used samples with non-European ancestry. Whilst this rose to almost 20% by 2016, this improvement was largely due to East Asian nations such as Korea, China and Japan initiating their own biobank projects, leaving many ethnicities under-represented. Hence, from a medical genetics perspective, “Black and Minority Ethnicity” (BME) is well defined as “ethnicities without a rich nation to back a representative genetic biobank” and includes African ancestry.

Improving participation of underrepresented populations in Biobanks should make science more useful for all.

Why does biobank representation matter?

Epidemiological comparisons – that is, comparing large numbers of people who develop disease and those that do not – often rely on genetics to infer which behaviours and conditions are causes and which are effects. These analyses use a technique called Mendelian Randomization (MR). MR  has demonstrated, for example, that alcohol consumption causally increases body mass and made it clear that even moderate alcohol intake has no beneficial effect on health outcomes. Causal hypotheses are a critical pathway to drug discovery and public health intervention, but are based almost entirely on European populations. Since there are many genes that affect most disease risk and these are of different importance across ancestries, we cannot be certain that the associations found apply to other populations. This urgently needs to be addressed in order to:

  • promote representative translational research that is relevant to all
  • reduce bias in the consideration of new health policies that may negatively impact minority populations.

Some populations have increased risk from specific diseases, and many people have ancestry from all over the world, making the categorisation of ‘race’ in medicine of some value but increasingly problematic. The IEU leads work on measuring this ancestry variation, which is important for individuals’ health. Getting at the cause of disease is key for understanding the effects of genes on disease risk and traits. Data on varied ethnicities is valuable for science, simply by showing us more variation. Traits such as height, weight and pre-inclination for education may not be directly related to ethnicity, but data from varied ancestries still helps to separate genetic cause from effect. Paradoxically, the least available data on African ancestry is particularly valuable scientifically, due to the lack of variation in the population that came out-of-africa around 50,000 years ago.

Science and the public improving representation together

Acknowledgement of this deficit is becoming more widespread, and the Black Lives Matter movement has refocused attention on representation in science, but the solution remains undetermined. How do we in the science and research community push for better diversity and representation in our resources? Biobanks operate on a consensual ‘opt in, opt out’ system and tend to favour certain groups. In 2016 the Financial Times generalised the participants of UK Biobank and “healthy, wealthy and white”, but why do so many more individuals from this demographic ‘opt in’? In 2018 Prictor et al theorised that BME groups may experience more barriers to participation such as location, cultural sensitivities around human tissue, and issues of literacy and language. However, given the history of the relationship between the research community and minority groups, seen in cases such as the Tuskegee Study, it is easy to see why BME populations might be less inclined to participate, if invited.

Although there is still need for considerable change, several recent developments will help, including the China Kadoori Biobank, the ancestrally diverse US-based Million Veterans program, and many others. However, given restrictions on privacy and reporting methods, these biobanks are hard to compare. Currently the IEU is part of a multi-national effort to develop tools to get the best science possible out of these comparisons, whilst simultaneously respecting privacy and data security issues. The IEU has been collaborating with various research groups across the world to make our research more reproducible. Building tools that work at scale is a challenge encompassing Mathematics, Statistics, Computer Science, Engineering, Genomics and Epidemiology, but this work is paving the way to promoting representative research that is inclusive and applicable for all.

 

 

What can genetics tell us about how sleep affects our health?

Deborah Lawlor, Professor of Epidemiology, Emma Anderson, MRC Research Fellow, Marcus Munafò, Professor of Experimental Psychology, Mark Gibson, PhD student, Rebecca Richmond, Vice Chancellor’s Research Fellow

Follow Deborah, Marcus, and Rebecca on Twitter

Association is not causation – are we fooled (confounded) when we see associations between sleep problems and disease?

Sleep is important for health. Observational studies show that people who report having sleep problems are more likely to be overweight, and have more health problems including heart disease, some cancers and mental health problems.

A major problem with conventional observational studies is that we cannot tell whether these associations are causal; does being overweight cause sleep problems, or do sleep problems cause people to become overweight? Alternatively, factors that influence how we sleep may also influence our health. For example, smoking might cause sleep problems as well as heart disease and so we are fooled (confounded) into thinking sleep problems cause heart disease when it is really all explained by smoking. In the green paper Advancing our Health: Prevention in the 2020s, the UK Government acknowledged that sleep has had little attention in policy, and that causality between sleep and health is likely to run in both directions.

But, how can we determine the direction of causality for sure? And, how do we make sure we are results are not confounded?

Randomly allocated genetic variation

Our genes are randomly allocated to us from our parents when we are conceived. They do not change across our lifespan, and cannot be changed by smoking, overweight or ill health.

Here at the MRC Integrative Epidemiology Unit we have developed a research method called Mendelian randomization, which uses this family-level random allocation of genes to explore causal effects. To find out more about Mendelian randomization take a look at this primer from the Director of the Unit (Prof George Davey Smith).

In the last two years, we and colleagues from the Universities of Manchester, Exeter and Harvard have identified large numbers of genetic variants that relate to different sleep characteristics. These include:

  • Insomnia symptoms
  • How long, on average, someone sleeps each night
  • Chronotype (whether someone is an ‘early bird’ or ‘lark’ and prefers mornings, or a ‘night owl’ and prefers evenings). Chronotype is thought to reflect variation in our body clock (known as circadian rhythms).

We can use these genetic variants in Mendelian randomization studies to get a better understanding of whether sleep characteristics affect health and disease.

What we did

In our initial studies we used Mendelian randomization to explore the effects of sleep duration, insomnia and chronotype on body mass index, coronary heart disease, mental health problems, Alzheimer’s disease, and breast cancer. We analysed whether the genetic traits that are related to sleep characteristics – rather than the sleep characteristics themselves – are associated with the health outcomes. We combined those results with the effect of the genetic variants on sleep traits which allows us to estimate a causal effect. Using genetic variants rather than participants’ reports of their sleep characteristics makes us much more certain that the effects we identify are not due to confounding or reverse causation.

Are you a night owl or a lark?

What we found

Our results show a mixed picture; different sleep characteristics have varying effects on a range of health outcomes.

What does this mean?

Having better research evidence about the effects of sleep traits on different health outcomes means that we can give better advice to people at risk of specific health problems. For example, developing effective programmes to alleviate insomnia may prevent coronary heart disease and depression in those at risk. It can also help reduce worry about sleep and health, by demonstrating that some associations that have been found in previous studies are not likely to reflect causality.

If you are worried about your own sleep, the NHS has some useful guidance and signposting to further support.

Want to find out more?

Contact the researchers

Deborah A Lawlor mailto:d.a.lawlor@bristol.ac.uk

Further reading

This research has been published in the following open access research papers:

Genome-wide association analyses of chronotype in 697,828 individuals provides insights into circadian rhythms. Nature Comms (2019) https://www.nature.com/articles/s41467-018-08259-7

Biological and clinical insights from genetics of insomnia symptoms.  Nature Gen. (2019) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6415688/

Genome-wide association study identifies genetic loci for self-reported habitual sleep duration supported by accelerometer-derived estimates. Nature Comms. (2019) https://www.nature.com/articles/s41467-019-08917-4

Investigating causal relations between sleep traits and risk of breast cancer in women: mendelian randomisation study. BMJ (2019) https://www.bmj.com/content/365/bmj.l2327

Is disrupted sleep a risk factor for Alzheimer’s disease? Evidence from a two-sample Mendelian randomization analysis. https://www.biorxiv.org/content/10.1101/609834v1 (open access pre-print)

Evidence for Genetic Correlations and Bidirectional, Causal Effects Between Smoking and Sleep Behaviors. Nicotine and Tobacco (2018) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6528151/