The 100,000 Genome Project is a national project aiming to transform the way the NHS uses genomics in the treatment and care of patients. In September 2014, Manchester, along with 5 other centres, was asked to pilot this project. Around 600 patients took part from the Greater Manchester area.

There are now 13 “Genomic Medical Centres” (GMCs) recruiting to the main 100,000 Genomes Project, providing access to the project across the whole of England. In the main project, we are recruiting patients with rare diseases and cancer. We have recruited over 1,300 patients in Greater Manchester so far and we recruit about 100 families a month. Nationally, the project hopes to recruit 70,000 people with the aim of sequencing 100,000 genomes. Around 30,000 will be cancer patients where both the tumour cells and blood cells will be sequenced.

The aim of the project is to improve diagnosis and management of rare diseases and develop research opportunities for treatments. In the cancer part of the project, genomics is helping to deliver personalised treatments for cancer.

The human genome is made up of 3 billion letters which make up the DNA code. Sequencing involves reading the DNA code. Once the code has been sequenced, scientists need to analyse this code to look for differences or variations that may contribute to disease. We all carry differences in our DNA code – in fact, we have many thousands of differences.

The more genomes that are sequenced, the better the data will be. We can compare genome sequences to understand which differences are common and unlikely to be related to a rare disease, and which ones are unique to certain groups of patients.

Genome sequencing is a new technology. It has required the science, computers and experts to develop this technology for this project. This will leave a legacy for the NHS to deliver genome sequencing to patients in the future.

However, developing this has taken time but we are now starting to receive results and we expect to be receiving results at a faster rate now that the systems have been put into place.

Experts have developed panels of known genes relating to clinical conditions. For example, they have put together a group of all the genes identified so far that can cause seizures (epilepsy). This means that the genome sequence of a person affected by epilepsy will first be analysed using the panel of known genes to see if there is a sequence variation that can be recognised to cause their condition (“mutation”). These results will be fed back to the local Genomic Medical Centre for re-testing in an NHS lab (all research tests are “validated” in an NHS lab to make sure they are correct) and the results can then be given back to the family.

If the analysis of the sequence does not reveal a difference in a known gene that can be interpreted, then the sequences in the Main programme will be shared with the “Clinical Interpretation Partnerships” (GeCIPs) of national experts, researchers (and commercial companies such as pharmaceutical companies) to bring all the data together to try to discover new genes or new genome variants that might explain the condition in the family. This means that research will be on-going even if the first analysis does not find the answer.

In the pilot, patients and families were consented for the sequence to be analysed for known genes. In the main programme, patients and families have consented to share their data so that on-going analysis can be done within the GeCIPs. Patients were also given the option to have their sequence analysed for rare “secondary findings” such as genes that can increase the risk of certain types of cancer.

We divided into groups to discuss topics relating to the project. Firstly, we wanted some feedback for our clinical team as we prepare to deliver results back to families. We heard about patients’ experiences waiting for two years for results. We talked about how people might like to hear about their results – by phone or by letter. We talked about the word “negative” results and how we should use words like “inconclusive” so that families know testing is on-going even when the first analysis has not found the answer.

Secondly, we talked about the pilot project transferring to the main project. People had had mixed experiences in hearing about this transfer. Most people did not know about their options for receiving information about the secondary findings.

We will share with the clinical team the feedback from the participants to help us plan the best ways to contact and deliver the results. We are receiving increasing numbers of results from Genomics England. These are being tested in different ways using different types of computer program (as part of the process to understand what works best) so we do not necessarily know the order of the results that will be returned. However, we can see that more sequence data and results are arriving each week and we have the scientist and multidisciplinary team meetings set up each week to discuss these results in a timely way ready for the lab validation and clinicians to contact patients.

We have arranged discussions with Genomics England about the transfer from the pilot to the main study, as we have heard that patients need to know if they have transferred and how to opt out of the main programme or opt into secondary findings. As soon as we understand the best way to do this, we can inform all the pilot participants.

Secondary findings will not be analysed for some time. The analysis is focusing on the condition in the family in the first instance. Families will be able to opt in or out of the secondary findings at any time in the future.

Families fed back that the day had been helpful and they would like to have on-going information and opportunities for discussion. We can look at ways to do this, possible through newsletters. We do also have a website and we will aim to keep information and updates from Manchester on this website. The Genomics England website also has national updates and a lot of information.

We will also plan to organise another event in the Spring for the participants in the main programme to have a similar opportunity for discussion and feedback.

We anticipate there will be increasing media interest around the project as families start to hear their results. Please be assured that we are working on all results as swiftly as we can and we will let people know as soon as we have something to report back.

We have developed a Participant Ambassadors Group. This group keeps in touch by email as opportunities arise. Some participants have taken part in supporting education, sharing their experiences to help us teach doctors and healthcare professionals about the importance of genomics in the future. Other participants have given us feedback on written information, other associated research projects or attended project meetings as a patient representative. If you think you might be interested in joining this email group, please do contact Georgina.hall@mft.nhs.uk. There will be no commitment but you will hear about different opportunities when they arise.

Email: genetics.research@mft.nhs.uk
Call: 0161 701 0177