Genomic medicine - our impact

Children’s rare diseases often require the identification of which cells, among the many types in the body, harbour the underlying rare condition. Identifying these cells allows the study of the impact of variations mutations, as well as their treatment. New technologies can now separate the genomes, transcriptomes and proteomes of single cells and assess their contribution to specific rare diseases. We have implemented and subsequently applied these technologies, developing experimental and computational pipelines that study individual cells for patients’ benefit.

One example of NIHR GOSH Biomedical Centre teams working in this area is the separation of leukemic stem cells from healthy ones in Chronic Myeloid Leukaemia and Acute Myeloid Leukaemia, identifying leukemic stem cells from their genetic variations and the expression of relevant markers (as transcripts or proteins). This opens the possibility to find new immunotherapy targets, e.g. surface markers that can be targeted with CAR-T treatment.

We use this deep understanding of cells to help develop new tissues. For example, we can encourage skin grafts to grow in the laboratory five times faster than usual, with single cell assessments determining if specific stems cells and other skin cells behave and are present as expected, even though we have sped up the growth. Further, we can track at individual cell levels any genetic variations that develop as the tissue grows. This ensures long-lasting self-renewal of skin grafts as well as their clinical safety to rapidly treat rare skin diseases.

These technologies also play a role when models of organs are required to understand or treat rare disease. In this case, we apply technologies that, while not yet at single cell resolution, preserve the tissue structure of the organ and, thus, the spatial distribution of small groups of neighbouring cells (1-10 cells per group). This allows us to test whether models of certain childhood brain diseases have the same properties in brain organoids as in a person's. These properties include the cell types present, their proportion, location and behaviour (e.g. which genes are expressed and how cells talk to each other), all features that are relevant to the ability of a model of a disease to be useful. These spatial techniques can be expanded to lab-grown full organs, e.g. the oesophagus. We assess the new organ’s capacity to replace a damaged one using these properties, and while still in animal models, it will eventually be an option to use such methods to treat rare oesophageal atresia (1 in 5,000 babies) where the upper and lower oesophagus are not connected.

NIHR GOSH Biomedical Research Centre funding allowed us to build early experimental and computational expertise through funding key UCL Genomics staff to develop these complex technologies. The pipelines developed for standard analyses have transitioned into genomics service for the wider benefit of GOSH and UCL researchers. Still, algorithms to answer the more complex questions regarding cells, tissues and organs for transplant remain an open health challenge.

Our genomes contain the code that determines our development, from our hair colour to what diseases we may have. Genome sequencing can examine the whole of our genetic code to identify the cause of rare conditions and cancer. Sequencing tests are now available in the NHS but they are very complicated and hard to describe to patients (children or adults) so that they can make informed decisions about whether or not to have these tests.

We worked with the GOSH Young Persons’ Advisory Group (YPAG) to see how they would like information on genomes and sequencing presented, and the best vocabulary to use. We took their ideas to local schools to get more opinions and used them to develop two short animations explaining how our DNA contains instructions to make our bodies work, likening it to computer codes used to control robots. 

My Genome Sequence animation explains:

- what is a genome?

- what is genomic variation?

- what is genome sequencing?

Sequencing My Genome animation describes:

- the limitations and uncertainties of genome sequencing

- what happens and what might be found when having genome sequencing

After watching these animations, knowledge and understanding of genomes and genome sequencing of 554 school pupils (11–15 years) increased significantly. Most found them “fun”, “easy to understand” and felt they understood the benefits, limitations and uncertainties of sequencing after watching.

Twelve young people, 14 parents and three health professionals taking part in the 100,000 Genomes Project also reported that the animation was clear and engaging, eased concerns about sequencing and empowered young people to take an active role in decision-making.

“It made it better because I actually knew what they were talking about….I’d have been thinking they were talking on another planet!” female age 11

Parents felt their child was “more at ease” with the process, making them “feel a bit more at ease about it”. Young people were more “positive” about sequencing after watching because it helped them understand that “you might get a result” and it could “help other people”.

These animations, voiced-over in English by a GOSH YPAG member, are available online, are translated into Turkish, Bengali, Chinese, used in educational sessions in Melbourne and Hong Kong, and have over 30,000 views on YouTube and 136,800 views on Chinese social media in a week of being posted.

To read more:

Development and mixed-methods evaluation of an online animation for young people about genome sequencing | European Journal of Human Genetics (nature.com)

Rare disease genome sequencing uncovers new diagnoses for patients | Great Ormond Street Hospital (gosh.nhs.uk)

When families want to know if their unborn baby has a genetic condition, because a parent is a carrier or they have a previous child with this serious genetic condition, we need to test the baby’s genetic material - their DNA. This is usually done by putting a needle into the womb to sample the placenta (chorionic villus sampling) or amniotic fluid (amniocentesis) - both have a small miscarriage risk.

But we know that a baby’s DNA is present in their mother’s blood from early pregnancy. Our researchers were among the first to develop maternal blood tests to detect genetic abnormalities in unborn babies by analysing this DNA in mothers’ blood. We helped the clinical laboratory establish the first accredited non-invasive prenatal diagnosis (NIPD) service for genetic conditions world-wide. NIPD results are available within five days, earlier than standard invasive testing.

Initially these tests were limited to conditions we knew were not inherited from the mother. This is because if she does not carry the faulty gene and it is detected in the test then we can be sure it belongs to the baby. However, we have now developed NIPD tests for conditions where the baby needs to inherit the genetic abnormality from both parents – these are known as recessive conditions. In these situations, the mother’s faulty gene also circulates in the blood so we use highly sensitive counting methods to compare the amounts of the faulty gene to regular gene – this is higher if the baby carriers two copies of the faulty gene. The team have also developed ‘bespoke’ testing for 138 families with very rare conditions where a sibling or the father has the gene.

We know parents welcome this safer testing. Previously we did 2-3 invasive tests annually for cystic fibrosis. Now we do around 20 NIPDs, a much higher uptake as parents can find out about their baby’s health without the invasive test risks. At GOSH we have done more than 2100 NIPDs for nearly 2000 families and 190 conditions and are exploring new methods to expand the NIPD service to more conditions (like sickle cell anaemia) to meet parents’ wishes.

NIPD is now included in the NHS National Genomic Test Directory so all families can access it, with GOSH and Birmingham Children’s hospital hosting the two laboratories offering this national service. As most countries do not offer NIPD for genetic conditions, we also take referrals from around the world.

To read more:

Noninvasive Prenatal Diagnosis for Cystic Fibrosis: Implementation, Uptake, Outcome, and Implications | Clinical Chemistry | Oxford Academic (oup.com)

Delivering an accredited non-invasive prenatal diagnosis service for monogenic disorders and recommendations for best practice - PubMed (nih.gov)

Genomes contain the code of life inside all living organisms and make us what we are. From people, flies to viruses, we all have our own individual genomes, which are different to each other. Modern genomic sequencing now allows us to examine genomes and identify changes, known as mutations, which may be associated with different features, for example, how dangerous a virus is to humans.

During the COVID-19 pandemic, we used our expertise at GOSH to quickly develop fast methods to sequence the whole SARS-CoV-2 viral genome – the virus responsible for COVID-19. This allowed us to lead the identification of mutations in the SARS-CoV-2 genome in London as part of a UK-wide collaborative study (COG-UK). This information informed and changed the way the Government managed the pandemic. By tracking mutations in the viral genome, we showed that the spread of the infection across the UK can be monitored, and the rise of dangerous mutations in new viral strains quickly identified, showing how viral sequencing can be used to inform decisions on the control of epidemics and pandemics.

Through COG-UK, we also led the national ‘Urgent Public Health’ Hospital Onset COVID Infection study to find out whether rapid genomic sequencing of SARS-CoV-2 could be used to reduce the spread of infection in hospitals. This study showed that the Alpha strain was a risk factor for more severe disease in hospitalised women. It also provided information on the best ways to use viral or bacterial genomic sequencing for management of hospital transmission. We showed how sequencing may be delivered in practice, its health benefits, how much it costs and how much money it can save.

Using sophisticated sequencing and analysis we also studied patients with more than one infection and monitored how they responded to various treatments. We changed the way viral infections are managed – particularly for RNA viruses like SARS-CoV-2. We showed how a drug called Favipiravir works against a range of common yet serious viruses including SARS-CoV-2, Influenza, Respiratory Syncytial Virus and Norovirus. We also demonstrated the benefits of using more than one drug simultaneously to treat these viruses. Using these methods we were able to treat 35 seriously sick children more effectively, supporting them until their immune system recovered, potentially saving lives.

To read more:

Surveillance for COVID-19-associated pulmonary aspergillosis - The Lancet Microbe

Mutagenesis in Norovirus in Response to Favipiravir Treatment | NEJM