We know that a variety of factors play a part in how sick people become with COVID-19. But scientific research has shown that even when all these factors are taken into account, there is something else.
Project overview
Helping to solve the COVID puzzle
Genomics England worked in partnership with the GenOMICC consortium, led by the University of Edinburgh, to analyse the whole genome sequences of approximately 20,000 people who have been severely affected by COVID-19.
These cases, which were severe enough to require admission to intensive care, were then compared to 15,000 other genomes from people who were only mildly affected or had no symptoms at all.
Read on to find out more about this study.
Aims of the study
Decode the puzzle
Discover if there are genetic reasons why COVID-19 affects people of different, age, gender and ethnicity
Find genetic causes
Understand why some healthy people become seriously ill with COVID-19
Better patient care
Uncover answers to help improve treatments for everyone
Why study how COVID-19 affects people?
Some people become very severely ill with COVID-19 and end up in hospital, while others only experienced a mild illness.
We know that a variety of factors play a part in how sick people become; an existing medical condition, being overweight, their ethnicity, and deprivation. But scientific research has shown that even when all these factors are taken into account, there is something else.
This study aimed to discover those differences.
FAQs about the GenOMICC COVID-19 study
General questions about the study
A wide range of expert organisations were involved in developing this project:
The GenOMICC (Genetics of Mortality in Critical Care) consortium of ITUs, led by Dr Kenneth Baillie, Consultant in Critical Care Medicine, University of Edinburgh
Genomics England, with Sir Mark Caulfield as the scientific lead and Parker Moss as the Partnerships lead
Academic leads from the universities of Oxford, Kings College London, Liverpool, Edinburgh, Cambridge, Cardiff, Glasgow as well as the Wellcome Sanger Centre in Cambridge
Illumina Laboratory Services (ILS) in Cambridge
The human genome code is 3 billion letters long. 99.9% of it is the same, one human to another. The other 0.1% is the bit that makes each of us unique. Some of the differences between us are healthy ones while others are not, but we can’t say for sure which are harmful changes until we can compare thousands of genomes. Another issue is that a difference which might be healthy in one population – say of Indian heritage – could be harmful in another population. This is why having samples from as many ethnicities as possible is so important.
Together with the University of Edinburgh and the GenOMICC consortium, we matched the demographics of the patients recruited for mild comparison group with those brought in to the severe group through intensive care units.
Initial studies, such as the ‘Disparities in the risk and outcomes of COVID-19’ by Public Health England, have shown that ethnic minority groups are disproportionately affected by the coronavirus, so having more volunteers from ethnic minority backgrounds was incredibly important.
Another study, in which our former Chief Scientist Professor Sir Mark Caulfield was involved, suggested that many of the expected factors (such as socio-economic) are not enough to explain the disparities. This means must look at genomic differences for more answers, and we tried to match those severely affected with those who were only mildly affected.
Results
We expected to see some signals around genes involved in blood group determination (this has already been established). We then looked very carefully at immune system genes as this would be an obvious place for differences to be important. We also looked carefully at genes with instructions for the particular kind of cell docking bays that allow the virus to break into our cells.
Beyond that, we kept an open mind, and results are still forthcoming.
The first genomes from our severe volunteers came through in June 2020. By June 2021, interim findings from the study were published. With luck and the very hard work of our scientists, these findings have already helped doctors make better decisions when treating patients with COVID-19, resulting in better outcomes.
In addition, two therapeutic drug trials have also commenced.
The final findings from the study are anticipated to be published in early 2022.
Please note that our volunteers for both the severe and mild groups will not receive any individual, personalised results as this is not a clinical programme. However, what we discover through your help will be of value in the next wave of the pandemic. If you signed up for the study, you were given the option to consent to being told more about the outcomes from the research, later down the line.
Data security and access
Once our sequencing partner Illumina sequenced patients’ whole genomes, they sent this data to Genomics England. We then stripped identifiable, personal data from this, and the de-identified genomic data is stored in our secure database, the National Genomic Research Library. Only validated researchers with express permission are allowed to access the raw data.
This data is protected to the same high standards as the data collected from the 100,000 Genomes Project.
Consent to use genomic data was obtained from patients or their families, utilising the GenOMICC study’s existing network of research nurses and clinicians across the country.
Genomics England’s priority has always been to ensure that the data of all participants is protected. Any data that researchers can access has been de-identified. This data cannot be removed or copied by researchers. We are committed to full transparency about the use of people’s data. Read our full privacy notices for more information.
All participant data is stripped of any identifiable, personal details and the de-identified genomic data is stored in our secure cloud database.
Most of us use cloud services for things like storing photos and music on our mobile phones. Cloud services are actually high security warehouses filled with massive computing computer. Genome data is enormous, and we use a cloud service from Amazon Web Services (AWS) – based in the UK – to provide a secure cloud computing and storage infrastructure. We use another tech company called Lifebit to help researchers wrangle this huge quantity of data, using their unique technology platform.
We joined forces with AWS and Lifebit to ensure that all the data we look after is highly secure, while allowing researchers to do their analysis flexibly.
Any data that researchers can access has been de-identified.
Participants of the 100,000 Genomes Project were a key part of the jigsaw in the COVID-19 study. Many 100,000 Genomes Project participants who had severe COVID consented to be included in the study, and many who tested positive but had mild symptoms volunteered as well.
People’s genomes contain many changes which are normal and not associated with ill health. Because we have the health records and genomes of the people that took part in the 100,000 Genomes Project, we can use their data to help check whether changes we see in COVID-19 patients’ genomes are just healthy changes, or likely to be associated with a harmful response. Their data was of huge value in this programme.
We are very grateful to the participants in the 100,000 Genomes Project who have agreed to have their data used in this way.
Although many participants will have received a result at this stage, we are aware that there are still some participants who have not received anything yet. We have also promised to do reanalysis for all 100,000 Genomes Project participants, and additional findings for those who have asked for them. Unfortunately, this work was delayed due to our focus on COVID-19. Genomics England and NHS England have jointly written a letter to participants explaining the current situation and next steps.
General questions about the study
A wide range of expert organisations were involved in developing this project:
The GenOMICC (Genetics of Mortality in Critical Care) consortium of ITUs, led by Dr Kenneth Baillie, Consultant in Critical Care Medicine, University of Edinburgh
Genomics England, with Sir Mark Caulfield as the scientific lead and Parker Moss as the Partnerships lead
Academic leads from the universities of Oxford, Kings College London, Liverpool, Edinburgh, Cambridge, Cardiff, Glasgow as well as the Wellcome Sanger Centre in Cambridge
Illumina Laboratory Services (ILS) in Cambridge
The human genome code is 3 billion letters long. 99.9% of it is the same, one human to another. The other 0.1% is the bit that makes each of us unique. Some of the differences between us are healthy ones while others are not, but we can’t say for sure which are harmful changes until we can compare thousands of genomes. Another issue is that a difference which might be healthy in one population – say of Indian heritage – could be harmful in another population. This is why having samples from as many ethnicities as possible is so important.
Together with the University of Edinburgh and the GenOMICC consortium, we matched the demographics of the patients recruited for mild comparison group with those brought in to the severe group through intensive care units.
Initial studies, such as the ‘Disparities in the risk and outcomes of COVID-19’ by Public Health England, have shown that ethnic minority groups are disproportionately affected by the coronavirus, so having more volunteers from ethnic minority backgrounds was incredibly important.
Another study, in which our former Chief Scientist Professor Sir Mark Caulfield was involved, suggested that many of the expected factors (such as socio-economic) are not enough to explain the disparities. This means must look at genomic differences for more answers, and we tried to match those severely affected with those who were only mildly affected.
Results
We expected to see some signals around genes involved in blood group determination (this has already been established). We then looked very carefully at immune system genes as this would be an obvious place for differences to be important. We also looked carefully at genes with instructions for the particular kind of cell docking bays that allow the virus to break into our cells.
Beyond that, we kept an open mind, and results are still forthcoming.
The first genomes from our severe volunteers came through in June 2020. By June 2021, interim findings from the study were published. With luck and the very hard work of our scientists, these findings have already helped doctors make better decisions when treating patients with COVID-19, resulting in better outcomes.
In addition, two therapeutic drug trials have also commenced.
The final findings from the study are anticipated to be published in early 2022.
Please note that our volunteers for both the severe and mild groups will not receive any individual, personalised results as this is not a clinical programme. However, what we discover through your help will be of value in the next wave of the pandemic. If you signed up for the study, you were given the option to consent to being told more about the outcomes from the research, later down the line.
Data security and access
Once our sequencing partner Illumina sequenced patients’ whole genomes, they sent this data to Genomics England. We then stripped identifiable, personal data from this, and the de-identified genomic data is stored in our secure database, the National Genomic Research Library. Only validated researchers with express permission are allowed to access the raw data.
This data is protected to the same high standards as the data collected from the 100,000 Genomes Project.
Consent to use genomic data was obtained from patients or their families, utilising the GenOMICC study’s existing network of research nurses and clinicians across the country.
Genomics England’s priority has always been to ensure that the data of all participants is protected. Any data that researchers can access has been de-identified. This data cannot be removed or copied by researchers. We are committed to full transparency about the use of people’s data. Read our full privacy notices for more information.
All participant data is stripped of any identifiable, personal details and the de-identified genomic data is stored in our secure cloud database.
Most of us use cloud services for things like storing photos and music on our mobile phones. Cloud services are actually high security warehouses filled with massive computing computer. Genome data is enormous, and we use a cloud service from Amazon Web Services (AWS) – based in the UK – to provide a secure cloud computing and storage infrastructure. We use another tech company called Lifebit to help researchers wrangle this huge quantity of data, using their unique technology platform.
We joined forces with AWS and Lifebit to ensure that all the data we look after is highly secure, while allowing researchers to do their analysis flexibly.
Any data that researchers can access has been de-identified.
Participants of the 100,000 Genomes Project were a key part of the jigsaw in the COVID-19 study. Many 100,000 Genomes Project participants who had severe COVID consented to be included in the study, and many who tested positive but had mild symptoms volunteered as well.
People’s genomes contain many changes which are normal and not associated with ill health. Because we have the health records and genomes of the people that took part in the 100,000 Genomes Project, we can use their data to help check whether changes we see in COVID-19 patients’ genomes are just healthy changes, or likely to be associated with a harmful response. Their data was of huge value in this programme.
We are very grateful to the participants in the 100,000 Genomes Project who have agreed to have their data used in this way.
Although many participants will have received a result at this stage, we are aware that there are still some participants who have not received anything yet. We have also promised to do reanalysis for all 100,000 Genomes Project participants, and additional findings for those who have asked for them. Unfortunately, this work was delayed due to our focus on COVID-19. Genomics England and NHS England have jointly written a letter to participants explaining the current situation and next steps.
