Features

As 2010 is the 10th anniversary of the Human Genome Project [HPG] we'll be running a series of articles to celebrate. In this post we look back at how far genome research has come in the last decade...

‘It’s hard to think back and remember how we worked then. We were scrabbling around in the dark,’ says Professor Mark McCarthy of the Oxford Centre for Diabetes, Endocrinology and Metabolism [OCDEM], recalling how research on the genetic causes of disease had to be carried out before the human genome was sequenced.

The first draft sequence of the human genome was announced at the White House 10 years ago this June by Bill Clinton, with the promise that it would lead to new ways to prevent, diagnose and treat disease.

Mark McCarthy, who is also at the Wellcome Trust Centre for Human Genetics [WTCHG], is the ideal person to explain what has happened since researchers got their hands on the DNA code and where we are now, 10 years on. Mark’s research aims to identify genes involved in diabetes and obesity, and he has been a leader in international collaborations to use the latest genotyping technology to advance our knowledge in this area.

Genetics of diabetes & obesity
One in ten people either has diabetes now or will get it in future, making it a global health challenge now and in the coming decades.

‘Not everyone exposed to our increasingly sedentary lifestyles becomes overweight,’ says Mark, ‘meaning obesity is the result of a combination of nature and nurture, the effects of genes and the environment.'

‘In diabetes we’ve found just short of 40 genes associated with an increased risk of the condition. For obesity, the number’s similar.’

He adds: ‘For diabetes, some of these genes are involved in cell cycle regulation and so may help in maintaining the cells in the pancreas that produce insulin. Perhaps some people are blessed with more or better islet cells in the pancreas.'

‘The evidence from the genes identified for obesity supports the involvement of the part of the brain involved with appetite and the feeling of satiety. It seems that subtle effects in the neural circuitry in the brain that controls what and how much we eat are involved here.’

For Mark, the importance of the human genome is clear: ‘We can trace all this progress back to the sequencing of the human genome. It was an overwhelmingly positive step which has stood the test of time.'

‘Genetics is one of the tools we can use to unlock the mysteries of disease. By identifying the bits of biological machinery involved, we can then use this to treat disease.’

Sequencing the genome
Before the Human Genome Project, researchers wanting to identify genes involved in disease processes would have to rely on laborious or haphazard techniques – ones that didn’t reveal much detail or ones that gave no sense of the bigger picture.

Researchers might select one or two candidates genes that, at best guess, might be involved in disease (‘many were looked at, many turned out not to be involved,’ says Mark). Or scientists could look at broad genetic markers and see how often they occurred in families – perhaps they were linked or often inherited alongside causative genes for disease.

The human genome gave scientists the data they needed to systematically search for, identify, and determine the roles of crucial genes.

‘The first human genome was a hugely influential and transformative step. It gave us a systematic way of looking at genes and heralded an era when genetics became 'big science' like astronomy and physics,’ says Mark.

Once that first human genome had been sequenced, an obvious next step was to understand the genetic origin of variation between people – to find the 1 per cent of the genome that differed between people and where it was located. This could now be attempted in a comprehensive, systematic way across the 3 billion letters in the human DNA code.

Two international collaborative efforts involving many hundreds of scientists, the SNP Consortium and the International HapMap Project, mapped the locations of common single-letter changes in the DNA code of different people.

With that powerful knowledge in hand, it became possible to see if any of these differences in individual genetic makeup could explain people’s predisposition to common diseases like cancer, heart disease and diabetes.

‘These individual differences were the logical place to start looking for differences in people’s DNA that can lead to disease,’ Mark explains.

‘Three things came together at the same time, creating a 'perfect storm',’ he says. ‘The HapMap project told us where common variation was; improvements in the accuracy and cost of genotyping technology meant we could look at hundreds of thousands of locations on the genome; and there was the realisation that a few hundred samples were not enough. We needed larger-scale studies of thousands of people, or to combine multiple studies to give us reliable results.’

Scanning for genes and disease
The result was a new industry of big, international studies that scanned the whole genome of thousands of people using the latest technology. The studies checked the large number of sites where individual differences were now known to occur, to see whether common genetic variations could be associated with a particular disease or condition. And this huge effort has been very successful.

‘Close to 1000 sites of genetic variation have now been associated with common diseases, such as diabetes, heart disease and cancer,’ Mark says. ‘That is way more than we might have expected and it has given us insights into many diseases.'

'At the same time, the results have also been surprising in that the variants we’ve identified don’t explain more than a minority of the genetic basis for disease, and it has proved harder than we imagined to translate the results of these studies rapidly into new biological insights.’

The fact that, after all these studies, most of the genetic basis for common diseases still remains unknown has led to the concept of ‘missing heritability’. For example, despite almost 40 genes having been connected to diabetes and another 40 to obesity, in both cases the identified gene regions account for only around 10 per cent of the known risk that is inherited of developing these conditions.

‘There has been a lot of discussion about the 'missing heritability', comparing it to dark matter in physics – something that we know must be there but haven’t discovered yet,’ says Mark. ‘There are many possibilities for what makes up that missing heritability.’

The most likely, he says, is that less common or rare variants in the DNA code – which would not arise often enough to be picked up in genome-wide screens – have big impacts. Although rare, some of these variants would be connected with a much greater increased risk of disease over those found so far, and help to account for that missing heritability. And the search is now on.

New technology, new studies
Advances in sequencing technology mean it now should be easier to look for these rare sites and test them systematically for association with common diseases - cancer, heart disease, or even schizophrenia, for example.

Rather than scan the genome as before, checking individual locations (albeit many thousands of them), the aim is now to sequence all of the DNA for thousands of people - with and without disease - and find genetic differences linked with various conditions.

The 1000 Genomes Project is already sequencing the genomes of different people to provide a more complete understanding of sequence variation between individuals than we have had so far. It’s sequenced around 300 people so far. But as the technology improves almost month by month, even larger projects become possible.

‘It took 10 years, $3 billion and many scientists around the world to sequence the first human genome,’ Mark explains. ‘Huge technological changes in the capacity to generate data means a handful of people can now generate a genome in a week for maybe $30-40,000. But these figures are almost out of date as soon as you write them down.'

‘New studies that compare whole genome sequences should be able to pick up common and rare variants in a way that has not been possible to date. There is optimism that this will nail the missing heritability. The first efforts to do this on a large scale are now beginning or being planned.’

Mark McCarthy is part of a new transatlantic consortium of researchers that is setting out to sequence the whole genomes of 3000 people: 1500 with diabetes and 1500 without.’

‘This will be a large effort. 3000 people is ten times the size of any dataset currently available,’ he says. ‘We calculate that the project will allow us to detect variants that are present in 1 in 100 people that are associated with diabetes.'

‘Previously, we’ve done very well at detecting variants present at a level of 1 in 10 people, but there will be many more variants present at lower frequencies that that.’ How soon this new knowledge will translate into new genetics-based medicines?'

‘That’s the big open-ended question. It is very easy to talk about possibilities for new treatments and underestimate the time it takes. But we can take hope where rare mutations causing diabetes have been identified – mutations that may be responsible for perhaps 2 per cent of diabetes cases. It has been possible to use that information to come up with new approaches for diagnosis and treatment for these rare types of diabetes.’

‘It is not out of bounds that we could do something similar with the information we obtain in these new sequencing studies,’ says Mark.

Images of the brain with various areas ‘lighting up’ in a rainbow of colours are now pretty familiar to many of us.

These come from studies in which people are given tasks to do inside MRI scanners, and the areas that light up show where there is increased brain activity as a result. And ‘functional’ MRI [fMRI] has been incredibly successful in revealing the way the brain is organised.

But this approach of mapping tasks onto different areas of the brain is always going to be constrained by the experiment design and the task set, prior assumptions about what you hope to test for, and what you set out to see.

This is the reason why researchers are now looking to a new technique called resting-state fMRI, which gets rid of any of the constraints or assumptions of task-based fMRI.

Resting-state fMRI is just as it sounds. People are asked to do precisely nothing in the scanner - just rest for 5 minutes or so. Yet the results consistently and reliably show connections between areas of the brain that are working together in networks. The result is a map of the functioning brain.

Oxford researchers at the Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB) have been at the forefront of these efforts. They are co-authors on a new paper in PNAS by an international group of researchers that sets out the potential of the technique.

Dr Steve Smith explains: ‘If you’re interested in a specific group of people or patients - say with Alzheimer’s for example - you want to find any differences in brain activity that might be of interest, not just those involved in a specific task. With resting-state fMRI, you don’t necessarily have to know what you’re looking for.’

The group at FMRIB, led by Dr Clare Mackay and Steve Smith, has already shown the value of the technique. Last year they found differences in young people’s brain activity using resting-state fMRI according to whether or not they had a gene variant that is linked to increased risk of Alzheimer’s. This difference in brain activity is decades before any symptoms of the disease would be apparent.

Clare said at the time: ‘We have shown that brain activity is different in people with this version of the gene decades before any memory problems might develop. We’ve also shown that this form of fMRI, where people just lie in the scanner doing nothing, is sensitive enough to pick up these changes. These are exciting first steps towards a tantalising prospect: a simple test that will be able to distinguish who will go on to develop Alzheimer’s.’

As well as the potential clinical relevance of this form of brain scanning, the hope is that resting-state fMRI could connect differences in people’s brain activity with factors like age, sex, genes, behaviour, or disease progression.

Another great advantage of resting-state fMRI is that everyone will be conducting their experiments in the same way. This means that data can be combined from groups all over the world to map out the functioning networks in the brain - essentially giving the complete wiring diagram of the brain.

This is what the new paper by the international collaboration set out in PNAS this week. They show how it is possible to combine data from over 1000 volunteers collected at 35 different centres across the world (including Oxford). With all the data, they show they find the same patterns of networks functioning in the brain and are able to begin to see differences between different groups of people by age and by sex.

The PNAS paper compares this approach to genomics. Indeed, the maps produced of connections in the brain are being called the ‘connectome’ in the same way that the genome is the map of all our genes.

Steve Smith does see the analogy with genomics, suggesting that mapping out the connections which determine how our brains work is similar in concept to decoding our genes to discover how our body works. And there is also the similarity in approach - big international consortiums gathering data to pinpoint variation between people to gain more understanding about disease.

However, he points out that the resolution of MRI still needs to be improved. With genomics, everyone reads out directly the same fundamental chemical DNA sequence but, with MRI scans, there is still a distance between what is seen in MRI signals and the individual neural circuits that are active in the brain. 

It's great to see that Oxford's Dorothy Hodgkin is honoured in a new set of Royal Mail stamps celebrating the 350th anniversary of the Royal Society.

The stamp celebrates advances in X-ray crystallography she made at Oxford University: she determined the molecular structures of penicillin, vitamin B12, and insulin.

In 1964 she received the Nobel Prize for Chemistry, becoming the only British woman scientist to win a Nobel so far.

Royal Mail say the idea was to choose ten significant scientific RS figures from the last 350 years, with one figure representing each 35-year period. Each stamp includes a portrait and imagery relevant to the scientist's greatest achievement.

Hodgkin is the only woman in an illustrious line-up that includes Isaac Newton, Ernest Rutherford, and Edward Jenner. You can find out more about how the stamps were put together in this BBC Online audio slideshow.

For her undergraduate degree Hodgkin studied chemistry at Somerville College and, after doing doctoral studies at Cambridge, she returned to Oxford in 1934 as a fellow at Somerville and set up her X-ray equipment in a shared laboratory in a basement corner of the University Museum. She would continue her research and teaching work at Oxford for the next 43 years.

Her crystallography work enabled her to deduce the structure of ever-larger and more complex molecules. One of her greatest achievements was, with the help of one of the first electronic computers, solving the 100-atom structure of the vitamin B12 in 1957, a feat Lawrence Bragg likened to ‘breaking the sound barrier’.

Georgina Ferry, the author of the definitive biography of Hodgkin, writes: 'In the case of each of the three projects for which she is best known - penicillin, vitamin B12, and insulin - Dorothy pushed the boundaries of what was possible with the techniques available.'

'Her distinction lay not in developing new approaches, but in a remarkable ability to envisage possibilities in three-dimensional structures, grounded in a profound understanding of the underlying chemistry.'

'While she did not consider it part of her role to explore the function of the molecules she studied, her results made it possible for others to increase their understanding of their biosynthesis and chemical interactions, and hence to develop improved therapies for disease.'

In 1976 Hodgkin became the first woman to receive the Royal Society's most prestigious award, the Copley medal.

Special thanks: Oxford DNB

Using genetics to render female Aedes aegypti mosquitoes flightless could halt dengue fever in its tracks.

The finding is reported in a paper in this week's PNAS on work led by Luke Alphey of Oxford University's Department of Zoology and Oxford spin-out firm Oxitec.

We've previously reported on how the Oxford team investigated inserting a 'dominant lethal' gene into mosquitoes that, when passed on by males, would see the larvae die before they could develop and spread the disease.

As reported in BBC News Online and elsewhere the team's new approach targets females - whose bite is what actually passes on the infection that affects millions of people a year. Their work suggests that male mozzies can be genetically altered to carry a gene that limits wing growth in their female offspring - rendering their daughters flightless.

Not only does it stop these females from infecting humans but, as the researchers write in the paper: 'Flightless females also are effectively sterile, being unable to attract and mate males as courtship and mating depend on the wing oscillations 'song''.

Luke told BBC Online: 'The technology is completely species-specific, as the released males will mate only with females of the same species.'

'Another attractive feature of this method is that it's egalitarian - all people in the treated areas are equally protected, regardless of their wealth, power or education.'

The researchers believe their approach could be extended to other species of mosquito that spread human disease.

The research is reported in a paper, entitled 'Female-specific flightless phenotype for mosquito control', published online in PNAS this week.

In the world of fossils it's usually befanged predators or their feathered bird-like cousins that steal the limelight.

So finding out about Bonnericthys, one of the unsung heroes of the Jurassic & Cretaceous - as part of working on this news story - has been an unexpected treat.

These giants were about as far from the flesh-eating inhabitants of Jurassic Park as you can get: 9m-long fish gliding around the prehistoric seas hoovering up plankton much like the benign basking sharks, whale sharks and blue & grey whales we know today.

Big & small fry
Making the video turned up a lot of fascinating detail and context that didn't make the final cut: like the fact that these large filter-feeders shared the ancient oceans with the ancestors of smaller fry living off the same resources, such as early herrings and anchovies.

'These familiar fishes survive to the present day, but the most striking difference between these suspension feeders and the extinct ones we've studied is size,' Matt Friedman, of Oxford University's Department of Earth Sciences, told me.

'The extinct fishes reaching lengths of 9m or more are giants on any scale, but they are particularly massive in comparison to living bony fishes that thrive on plankton.'

The awkward size and shape of some of the museum specimens is one reason why they were misidentified or ignored, but another factor is the peculiar anatomy of the giant plankton-eater:

'First is the enormous mouth, with long, slender jaws that bear no teeth whatsoever - a feature common to filter feeders,' Matt explained.

'Another important feature is the enormous gill skeleton: Fishes use gills to breathe, but suspension feeders have co-opted their gill arches to extract plankton from the water. They pull off this trick helped by structures called gill rakers, finger-like projections that extend off the front of the gill arches, which can assume elaborate shapes in suspension feeders.'

'As for the body of these animals, it would have been very streamlined, with a well-developed pair of fins just behind the head, and a massive, crescent-moon shaped fin at the back of the tail.'

Things fall apart
These specialised lightweight bodies, fine-tuned by evolution, contain skeletons with very little bone - so that they tend to fall apart after death, leaving only fragments of skull and flipper to sink to the ocean floor and be preserved.

It was a series of new finds from excavations around the world that helped unlock the story of Bonnericthys:

'The most important fossil specimens for our study came from rocks laid down in western Kansas near the end of the age of dinosaurs, about 80 million years ago. We've also got other pieces of this same fish from other parts of the US including New Jersey, South Dakota, Wyoming, and Alabama,' Matt told me.

'Other examples of this group of fishes that we report for the first time came from Kent and Dorset here in the UK, as well as from as far away as Japan.'

These giants proved to be quite the globe-trotters, but it is the longevity of their 100m-year-dynasty that marks them out as an evolutionary success story rather than just an interesting experiment, Matt comments:

'They cruised the oceans for at least 100 million years. To put this in context, that's longer than the giant baleen whales have been around, and longer than any of the groups of  massive filter-feeding sharks.'

'Another way to think about these fishes is by comparing them to mammals: mammals have been dominant on land for something like 65 million years, the time from the end of the age of dinosaurs up to today. I think we'd all agree that mammals are a pretty successful group.'

'Of course these giant fishes never achieved the diversity of mammals, but they were in the oceans for a longer period of time than mammals have been the dominant land vertebrates.'