DNA sequencing for cancer

Sequencing DNA was once a slow and expensive process carried out at a very small scale in research labs. The ambition of the human genome project and the subsequent development of fast, efficient and cheaper technology means that DNA sequencing is now a common feature of cancer research, diagnosis and treatment. This article will describe what DNA sequencing is and how it is used in studying and treating cancer.

What is gene sequencing?
dna double helix

What is DNA?

Every cell contains a set of instructions that can be thought of as the blueprints for your body. They are followed as you develop from a fertilised egg to a fully grown baby and throughout your life. They control what each cell makes and how it behaves. These instructions are not written in words, but in a code, held in that most iconic molecule, DNA.

DNA is an extremely long molecule shaped like a twisted ladder, called a helix. Every cell contains around 2 metres of DNA packed into 23 pairs of chromosomes of different sizes. Chromosomes are sometimes seen as X-shaped structures like these.

On the chromosomes are many small sections that we call genes and we have around twenty five thousand different genes. Each gene is the instructions for making one protein. These genes only make up 2% of our total DNA and are called the exome. The rest have several jobs, including controlling when these different genes are switched on to make their protein.

The rungs of the DNA ladder are made from chemicals called bases. There are four different bases that are used in DNA. These are given the letters A,T,C and G and there are 3.2 billion in every cell. It is the order of these bases that tells the cell what to make and when and this is what we are finding when we sequence DNA.

Reading the book of life – the human genome project

The story of DNA is littered with Nobel prize winning work, but the most important here is the work of Fred Sanger and his colleagues. They developed a way of reading the order of the bases. Initially only suitable for a few hundred bases at a time, but new technology was developed to speed up the process. In 1990 a global project was started to sequence the complete DNA of a human – the genome. This took 13 years and cost around £2.5 billion. A few years later in 2008 the first genome of a cancer was completed.

Today even more progress in technology has led to “Next Generation Sequencing” or NGS where the whole genome can be sequenced in a couple of days for a few hundred pounds.

What has sequencing got to do with cancer?

We all have differences, or variations in the DNA sequences of our genes, they are part of what creates the differences between individuals. Cancers develop when variations occur in the genes that make some cells behave in a way that is harmful to the rest of the body. These changes are usually called mutations. They can lead to cells producing too much of a protein, too little or a changed form which behaves differently to normal. The effect of these changed proteins can be that they drive cells to divide uncontrollably, leading to cancer.

Sometimes these mutations are inherited from your parents, they are present at birth and will be found in every cell of the body. This rare type of mutation makes getting certain cancers more likely. Most mutations happen to individual cells as a result of damage from the environment. Radiation from X-rays or natural sources such as sunlight or tiny amounts of radioactive elements in rocks and certain chemicals such as the ones in cigarette smoke or petrol can damage the DNA bases so they are missing, misread or changed for another one.

Sequencing some, or all of the DNA in cancer can answer many important questions about the disease.

We can identify if a cancer is inherited and if someone has inherited genes that increase the risk of getting that cancer. We can accurately diagnose a cancer and make predictions about how it will grow and spread. It allows us to find the most suitable treatments based on the particular mutations found and monitor how effective they are, something called precision, or personalised medicine. Sequencing can also find variations between individuals that affect the way that drugs are broken down and removed from the body which can affect the choice of treatments used.

Finally by comparing the DNA of cancer cells with normal cells we can discover new genes that are mutated in cancer which can be used to help develop new medicines to treat it.

How is DNA sequencing used in cancer?

Sequencing the whole genome is not quite yet affordable or feasible for all patients and it takes time to interpret the complex results. But sequencing smaller amounts of DNA, a single gene, or a panel of genes is a routine test used in diagnosing and treating many cancers. Whole tumour sequencing is sometimes used for certain cancers and there are many research projects where extensive sequencing is used to enhance our understanding of particular cancers.

Single gene tests – diagnosis risks and sensitivity.

There are many genes that we now know are mutated in cancer. Some are mutated commonly in many cancers, whilst others are strongly associated with particular cancers. The most well known of these are the two BRCA genes that are linked to breast cancer. Whilst the exact cause of most breast cancers is unknown, around 5-10% are linked to faults in two genes that are normally responsible for repairing DNA. These make it much more likely that someone will develop breast cancer, although it is not guaranteed as several other genetic changes also have to happen before cancer will develop. 

As the BRCA gene changes can be inherited, testing can be offered to family members to discover if they are more at risk of breast cancer. For other cancers a single gene sequence may be all that is needed to confirm a diagnosis or find whether a patient is likely to respond to a particular drug. In GIST, a rare tumour of the digestive system, a protein called KIT is often mutated. The drug, Glivec, can be used to treat cancers caused by KIT mutations if they are present, but the dose required is also affected by the exact type of mutation. In this case single gene sequencing is an essential to guide treatment.

Gene Panels

As many cancers have one or more of several gene mutations often associated with them, panel, or set of genes can be sequenced, again to get a confirmed diagnosis or to direct treatment. An example of this are cancers where several genes called NTRK can be mutated and if they are found specific drugs, called NTRK inhibitors can be used to treat them. These panels can be sequenced quickly as they are done using the fast, next generation sequencing technology.

Whole Genome Sequencing (WGS)

When the whole genome of a cancer is sequenced it is usually done together with normal DNA from the same person so that any mutations due to the cancer can be identified by comparing the two. Samples are taken of the tumour (often at surgery or biopsy) and normal tissue as a blood, cheek cell or skin sample. The sequences are compared to identify genes that may have been mutated.

There are several reasons why a whole genome sequence will be done. If the nature or origin of the cancer has not been identified or the cancer has not responded to other treatments it can give medical staff valuable information as to what the cancer or what drugs might be the best to use.

WGS is available in the NHS for several cancers including many paediatric (childrens) cancers, sarcomas and triple negative breast cancer.

Exome Sequencing

By sequencing the exome, researchers focus on the 2% of DNA that contains genes that produce proteins. By sequencing many cancer and normal genomes it was discovered that very few harmful mutations are found outside of these regions. So by sequencing the exome scientists can study cancer genes a little more quickly and cheaply than sequencing the whole genome. This is usually used for research rather than for cancer care.

DNA sequencing in research.

As we have become able to sequence huge amounts of DNA and the equipment to do so has become more available, whole genome sequencing to identify genes involved in cancer is being used by more research labs. Huge advances are being made in identifying genes that are most commonly mutated as well as unusual mutations in particular cancers. It is even possible to sequence the DNA of individual tumour cells which has revealed how complex tumours are and how they can change over time.

Another example of how sequencing and genetic analysis may improve cancer treatments in future is the DETERMINE trial. Patients with rare cancers are having their DNA sequenced to see if they share mutated genes with more common cancers where there is already a licenced treatment.
If this trial is successful it could allow medicines that are already available and well understood to be tested for their effectiveness in patients that have the same mutation, but a different cancer, increasing the effective treatment options for patients with rare cancers.

In conclusion

The last century has seen astonishing progress in our understanding of DNA, genes and how they relate to cancer. We now know to read the sequence of bases in DNA and this tells us a lot about the differences between the genes of normal cells and cancer cells. Increasingly sophisticated technology means we can sequence and interpret whole genomes in hours. This is opening up a wealth of possibilities for health screening and the treatment of diseases like cancer. In future routine genetic screening could be used to identify people at risk of cancer and other diseases. Patient monitoring and awareness of any increased risks will allow earlier diagnosis and thus, more effective treatment should cancer develop.

Whole genome sequencing is becoming fast, easy and economical. In future it may well become a standard part of the diagnosis, monitoring and treatment of cancer for all patients. Sequencing will help to ensure more patients get the best available treatment and that will deliver better outcomes for more people.