Alongside an initial focus on Rare Disease patients, the BioResource will be including volunteers from our Eating Disorders Genetics Initiative (EDGI) UK cohort and the Genes & Cognition Study (a large scale study of volunteers that aims to investigate brain function and cognitive decline) in the LRS project.
Rare Diseases and the LRS project
Between 2013-2018, the Rare Diseases BioResource conducted a Whole Genome Sequencing Study, which sequenced the DNA of around 8,000 participants with Rare Diseases and their family members. As a result, we were able to provide a genetic diagnosis for an average of 20% of the participating Rare Disease patients, which depended on the current research knowledge of that Rare Disease. This resulted in some patients' treatment being adjusted, whereas others found comfort in finally having a diagnosis.
There are an estimated 7,000 different Rare Diseases, of which most are inherited. Although they are rare, collectively over 3.5 million people in the UK alone will be affected by a Rare Disease at some point in their lifetime.
The journey that a patient undergoes to receive a diagnosis can be very long, often taking several years and may involve visiting many departments within a hospital. This process can be distressing, overwhelming and can have a profound effect upon the patient’s wellbeing as well as their families. We hope that by carrying out this research, the road to diagnosis will become shorter and provide more treatment options.
Over the last few decades, we have seen many advances in DNA sequencing technologies. Earlier methods were able to generate lots of small sections of DNA, which are put together so that we could look for variations. However, that is like doing a very big, complicated jigsaw with billions of pieces.
For this project, we are going to use the latest technology, which is called Long Read Sequencing. This method generates much bigger sections of DNA, whereby, very similar looking sections can be put together in the right place.
This makes piecing together the enormous jigsaw much simpler. We hope that this will enable us to identify variations in the DNA, that might have been missed when analysing sequences produced using the older sequencing methods.
It is hoped that this study will lead to:
- further improved diagnosis for Rare Disease patients
- the development of new treatments
- potential new research avenues
The Rare Diseases that we are currently recruiting to the Long Read Sequencing project are:
- Arthrogryposis
- Bleeding, Thrombotic and Platelet Disorders
- Ciliopathies – Bardet-Biedl and Alstrom Syndrome
- Rare Inherited Neurological Disorders
- Inherited Optic Neuropathies
- Inherited Retinal Dystrophy
- Ocular Maldevelopment: Microphthalmia, Anophthalmia and Ocular Coloboma
- Multiple Primary Malignant Tumours
- Neurofibromatosis Type 1
- Neurofibromatosis Type 2
- Primary Immunodeficiency
- Paediatric Neurodevelopmental Disorders
- Systemic Autoinflammatory Disorder – AODS and uSAID
- Stem Cell and Myeloid Disorders
- Septo-optic Dysplasia
The full list of Rare Disease projects at the NIHR BioResource, including those involved in the LRS project, can be found on our Rare Disease projects webpage.
Dr Kathy Stirrups – NIHR BioResource Samples Team Lead said:
“The NIHR Rare Diseases BioResource is aiming to build upon the experience from the Whole Genome Sequencing Project by undertaking the Long Read Sequencing Project. This is a cutting-edge new technology, and we are very excited to be involved in testing its utility for diagnosis or discovery of new causes across our Rare Disease studies.
"Many people and their families are affected by rare genetic diseases and we are committed to enhancing the knowledge base available for researchers and reducing the diagnostic odyssey for the patients.”
Participation in the Long Read Sequencing project
What happens if my clinician asks me to participate?
Your clinical team will approach you if you meet the inclusion criteria for the project. You would be asked to consent and join the NIHR BioResource Rare Diseases study and donate a 15 ml (~1 tablespoon) blood sample. From this blood sample, we will isolate, analyse and store your DNA and other components from the donation for use in medical research. We will also store your personal data on secure servers, this information can only be accessed by staff should their job role require them to do so. More details can be found on our privacy information pages.
I have a Rare Disease, can I help?
Currently, we are aiming for up to 3,000 patients with one of the listed Rare Disease conditions to participate until March 2025 (there is a possibility to extend). Clinicians are required to make an application for their Rare Disease to be a part of this project. Unfortunately, patients cannot refer themselves to participate in this study. The NIHR BioResource intends to continue expanding its recruitment to other Rare Disease conditions. Please look at our list of already adopted Rare Disease projects.
What happens to my information?
For further information, please see our privacy information pages.
DNA (deoxyribonucleic acid) is your genetic code; it is present in almost every cell in your body and contains the instructions to be able to make every part of you. However, although it is present in almost all cells, most of it does not need to be ‘read’. Your brain cells, for example, will just need to ‘read’ and express the parts of the DNA that are important for the brain cells to function. It will not ‘read’ or use (or express) parts of the DNA that are unique to, for example, skin cells.
Genetics: the study of single genes and how they are inherited. Genetic tests can identify a specific gene or variation in a family.
Genomics: the study of all the genes (also called the genome) at once, as well as the interaction of those genes with each other and any environmental influence on these genes. A genomic test can compare more than one gene at a time and in some cases all the DNA (Whole Genome Sequencing).
Whole Genome Sequencing gives a ‘read out’ of all your DNA – your genome, which for humans is 3 billion bases (or letters). Your DNA sequence is unique to you, however, some of it is shared with your relatives. By comparing your genome and understanding how it is similar or different from others, it is possible to learn more about why diseases may occur and how they may affect you.
There have been vast improvements in sequencing technology over the past decades that now enable whole human genomes to be sequenced in days.
The original next generation technology (now referred to as short read sequencing) produced lots of chunks of sequences of 150 bases, these could then be aligned to the reference genome (a representative human sequence that is used to compare data from new samples), essentially it is like doing a jigsaw with millions of tiny pieces and using the picture on the box to help put them in the right places.
The most recent technology, Long Read Sequencing (LRS) can generate much longer chunks of sequence often with an average of 10,000 to 20,000 bases long. This makes the jigsaw much simpler and will help align the pieces to the right location.
Some Rare Diseases may be due to variations in highly repetitive regions of the genome or in places where there has been a rearrangement of the DNA compared to the reference and so improving the accuracy of the mapping of the pieces and variant identification may enable a diagnosis. Long Read Sequencing can also look at methylation of the bases, which is a way cells use to turn on or off or regulate how much a gene is being used in certain situations which could be a different mechanism causing the Rare Disease.
So, it is possible these technological improvements may enable a diagnosis in some patients that have previously had short read sequencing or add more detail to the data available and allow discovery of new genes or mechanisms causing the Rare Disease which can then be used to improve treatments.
If you decide to join and participate in the study, you will be asked to attend an appointment to donate your blood (this technology requires DNA extracted from blood as this gives the most accurate data; DNA extracted from saliva may contain DNA from bacteria or food) and to sign the consent forms. The clinic team will go through the consent process with you and take your sample. The sample will be assigned a unique identifier so that you cannot be identified. The sample will be sent to the laboratory for processing.
Once the sample has been received in the laboratory it will undergo processing to extract the DNA, we will also bank other components such as plasma and serum from the sample.
The extracted DNA will be received into the specialized sequencing laboratory where we undertake very careful quality control processes that fragments and profiles the DNA so that we can decide the best protocol and obtain the best fragment sizes for the sequencing. We don’t want to over fragment the DNA as this will reduce the power of the Long Read technology, however, having too much very long DNA is detrimental and can reduce the amount of data obtained so we might not get full genome coverage.
After the quality checks have been completed, the DNA is prepared for sequencing, using a process called library preparation. The resultant libraries are then loaded onto the sequencing machine and for the next 72 hours the machine is continuously sequencing the fragments and collecting data. This data is transferred to our high-performance computing facility, where the sequence fragments are aligned against the human reference genome. Then specialists will analyse the data to look for potentially causative variations.
Long read sequencing generates a lot of data, the raw data generated can be over 1 Terabyte, which aligned against the reference genome and the variations annotated to make a much smaller file. This data is then analysed by bioinformaticians (computer scientists that specialise in looking at biological data) including detailed checks on the quality of the data.
When we have data from many individuals with the same Rare Disease we can look to see if there are similarities or patterns appearing in the sequences, which may be associated with the Rare Disease.
For some Rare Diseases there are known genes associated with the disease, the bioinformaticians can look at the variation within these genes and determine if these could be responsible for causing the disease. We work closely with the clinical teams to report and explain any research findings, so that these can be confirmed by the NHS Genomic Medicine service where appropriate. This enables the results to be used in a patient’s clinical care, e.g. to provide a genetic diagnosis, support treatment options, or to help inform a patient’s reproductive choices.