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Whole Genome Sequencing is a very hot topic and its going to get hotter. There has been recent press coverage about delays in WGS not just for brain cancer, but for other cancers. So this is the beginning of a conversation about which you’ll be hearing so much more. Conversations are growing around what it is, why it is important in decision making, what the current issues are and what’s being done to resolve the challenges. The purpose of this feature is to familiarise you with the key points: we’ll expand on these over the coming weeks.

 

What is WGS?

Whole-genome sequencing (WGS) is the analysis of the entire genomic DNA sequence of a cell at a single time, providing the most comprehensive characterisation of the genome.

 

Why is it important?

WGS has revolutionised bioscience and has proven to be essential and invaluable to the identification of gene functions and their involvement in disease. It explores a much larger sequence in comparison to targeted approaches and therefore generates much more information about communities.

 

Why does it matter to people living with a brain tumour?

A Glioblastoma brain tumour is the most aggressive type of brain tumour. It is described as being heterogeneous which means it is made of various cells which are different. This means that there is more than one mutation of the cancer cell which causes the tumour to grow.  Treatments are targeted to the different types of mutations to stop growth, such as IDH1. We know though that over time cells find workarounds to the treatments and mutate, so that the tumour grows again (called progression). If we can map these mutations in detail it gives researchers the opportunity to develop therapies which can target the cancer cells and what causes them to mutate.

 

What does this mean?

Bottom line? It means that it isn’t going to be one treatment that is needed. We are going to need multiple treatments to target the different mutations. But we need to know what these mutations are and we need to look at cohorts of these tumours as well as individuals so that therapies can be personalised.

 

What are the challenges?

It’s a complex landscape and the challenges are varied.

In 2018 the Government set a high bar by promising that WGS would be available to all people with rare cancers. Then COVID caused a pivot; key resources were diverted so this has not been achieved.

We know that people diagnosed with a GBM can wait for over 400 days for WGS; this is too long to wait when you are diagnosed with a life limiting cancer.  The information given by WGS at this point is out of date and of little use to the person with the GBM.

There isn’t parity of access to tissue frozen – this is key for the detailed analysis needed. Some tissue is put into paraffin blocks which is less stable. You can read more about this here.

Delays in WGS are in part due to poorly performing IT systems, which still require the use of staff filling out paper test forms to operate.

There has been a lack of attention to the infrastructure to deliver what was promised. There is a lack of human resource, so there is now a backlog.

 

What are we doing to address this?

Nobody wants anyone to wait over 400 days for WGS to be done. Clinicians are as frustrated as the person with the brain tumour. It is acknowledged that the NHS Genomic Medicine Service is at the vanguard of Whole Genome Sequencing – it is world leading. There is a recovery plan and the mindset is focused on sorting out the problem – that’s a good start.

 

At brainstrust we know that we are none of us smart as all of us. It will need collective intelligence to transform the WGS landscape so we are working with the National Cancer Research Institute, with the British Neuro-Oncology Society and also with the Tessa Jowell Brain Cancer Mission to address these challenges. There are examples where WGS can be done efficiently; the work at Cambridge, supported by the Mindaroo Foundation is one such example. We know too that patients and caregivers have a voice in this conversation but that we need to understand what’s at play. This is why we are going to be expanding on this in the next few weeks.

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Introduction

The Brain Tumour Data Dashboard lets you explore up -to-date, population level data about the brain tumours diagnosed in England between 2013 and 2015. Using the drop down menus on the left you can select different groups of patients to view in the charts below. In these charts the number of patients for every 100 diagnoses is displayed as images of people. Patients have been grouped by date of diagnosis, type of tumour, age, gender, and region in England.

For each group of patients you can explore the different routes to diagnosis, the proportion of those who received chemotherapy or radiotherapy, as well as the survival of the patients within each group. For more information about what these metrics mean please see the glossary.

How to use

  1. Select the year of diagnosis using the drop down menu.
  2. Select your patient group of interest from the four drop down menus in the following order:
    1. Tumour group
    2. Age at diagnosis
    3. Region of England
    4. Gender of patient
  3. To view a second chart to compare different groups of patients, click the ‘compare’ button.The second chart will appear below the first chart.

*Note that the tool is best used on a laptop or tablet rather than a mobile phone*

Unavailable data

Some of the data in these charts is not available.There are two main reasons for this:

  1. How the data has been grouped

If you cannot select a patient group from the drop down menus, the data is unavailable because of how the data has been organised.

Public Health England has grouped the data like a branching tree. The bottom of the tree contains all the patients with brain tumours, and then each branch divides the data by a certain characteristics, like age, or location of tumour. But the data is divided in an order, starting with location of the tumour (endocrine or brain), then by age, region, and gender. Age is at the start because it makes a bigger difference to survival rates and treatment rates than gender or region. Sometimes, after the data has been split by type of tumour and age, there is not enough data to be split again. This is because to protect patient confidentiality groups cannot contain less than 100 patients. Because some groups cannot be split further, you cannot create ‘totals’ for everyone by region or gender. For example, you cannot see results for all ages by region, or all brain tumours by gender. If these totals were calculated and released, it might be possible to identify patients, which is why Public Health England cannot release this data.

  1. Statistical reasons and data availability

If you can select a patient group from the chart menus, but the chart does not display, the data is unavailable for one of several reasons:

  1. Data is not yet available for the selected year from Public Health England.
  2. Data is not available because the data quality is too poor to release this statistic.
  3. Data is not available as the statistic is not appropriate for this group.
  4. Data is not available because the standard error of the estimate was greater than 20% and so the estimate has been supressed.

Up to date brain tumour data

Brain tumour data may influence the decisions you make about your care. Data also helps you understand the bigger picture, or landscape, in which you find yourself.

Brain tumour data and statistics influence the focus, and work of organisations like brainstrust. The information helps us to understand the scale and impact of the problems we are setting out to solve.

This tool helps you understand the landscape in which you find yourself having been diagnosed with a brain tumour. This landscape can be particularly tricky to navigate as there are many different types of brain tumour, all of which have a different impact.

The information you see represents the most up-to-date, official, population level brain tumour data available for England. Over time we will be adding to the brain tumour data available and publishing reports, with recommendations, as a result of what we learn from this data.

The data behind this content has come from Public Health England’s National Cancer Registration and Analysis Service (NCRAS) and is a direct result of the ‘Get Data Out’ project.

This project provides anonymised population level brain tumour data for public use in the form of standard output tables, accessible here: http://cancerdata.nhs.uk/standardoutput

Incidence

The number or rate (per head of population) of new cases of a disease diagnosed in a given population during a specified time period (usually a calendar year). The crude rate is the total number of cases divided by the mid-year population, usually expressed per 100,000 population.

Malignant

Malignant tumours which grow by invasion into surrounding tissues and have the ability to metastasise to distant sites

Mortality

The number or rate (per head of population) of deaths in a given population during a specified time period (usually a calendar year). The crude rate is the total number of deaths divided by the mid-year population, usually expressed per 100,000 population.

Non-malignant

Not cancerous. Non-malignant tumours may grow larger but do not spread to other parts of the body.

Survival

The length of time from the date of diagnosis for a disease, such as cancer, that patients diagnosed with the disease are still alive. In a clinical trial, measuring the survival is one way to see how well a new treatment works. Also called ‘overall survival’ or ‘OS’.

Routes to Diagnosis

Under the ‘Routes to Diagnosis’ tab in the Brain Tumour Data Dashboard, you can explore the ways patients have been diagnosed with brain tumours. There are many ways, or routes, for cancers to be diagnosed in the NHS. A ‘route to diagnosis’ is the series of events between a patient and the healthcare system that leads to a diagnosis of cancer. The routes include:

  1. Two Week Wait

Patients are urgently referred by their GP for suspected cancer via the Two Week Wait system and are seen by a specialist within 2 weeks where they are diagnosed.

  1. GP referral

Diagnosis via a GP referral includes routine and urgent referrals where the patient was not referred under the Two Week Wait system.

  1. Emergency Presentation

Cancers can be diagnosed via emergency situations such as via A&E, emergency GP referral, emergency transfer or emergency admission.

  1. Outpatient

Outpatient cancer diagnoses include diagnoses via an elective route which started with an outpatient appointment that is either a self-referral or consultant to consultant referral. (It does not include those under the Two Week Wait referral system).

  1. Inpatient elective

Diagnosis via an inpatient elective route is where diagnosis occurs after the patient has been admitted into secondary care from a waiting list, or where the admission is booked or planned.

  1. Death Certificate Only

Diagnoses made by Death Certificate Only are made where there is no more information about the cancer diagnosis other than the cancer related death notifications. The date of diagnosis is the same as that of the date of death.

  1. Unknown

For some patients with a cancer diagnosis, there is no relevant data available to understand the route to diagnosis.

 

More information

If any of the statistical terms in this section of the brainstrust website are hard to understand, we recommend looking them up here:

Cancer Research UK’s Cancer Statistics Explained

http://www.cancerresearchuk.org/health-professional/cancer-statistics/cancer-stats-explained/statistics-terminology-explained#heading-Seven

If you are looking for help understanding terms relating specifically to brain tumours, and treatment, then the brainstrust glossary is available here:

https://www.brainstrust.org.uk/advice-glossary.php