Nicholas Volker was not a healthy child. The doctors found that tiny holes opened on his skin. Worse still he had the same holes in his intestines, which spilled their contents into his abdomen. By the time he was three years old, he’d had over 100 surgeries. At the age of four, he weighed just seventeen pounds.
The medical team at the Children’s Hospital of Wisconsin were at their wits’ end. But they would not give up. Determined to get to the bottom of the problem they embarked upon an exercise that was, just ten years ago, long, uncertain and extremely expensive. They decided to sequence his DNA. They started by looking at individual genes known to be implicated in Crohn’s Disease and irritable bowel syndrome. They found no mutations.
So they expanded their search, to look at all the exons – the DNA strands that code for proteins. Single DNA reads are not entirely accurate, so to make sure they spotted any mutation they sequenced the DNA thirty-four times. Next they compared Nicholas’s DNA to the reference provided by the Human Genome Project. This threw up 16,000 variations. They trawled through these and eventually came to a gene called XIAP, which prevents the immune system from attacking the intestine. A single letter of its DNA was abnormal. Nicholas had an A (adenine) where others had a G (guanine).
Finally the doctors had the answer. Nicholas was given an umbilical cord blood transplant from an anonymous donor and has recovered to lead a reasonably normal life. Nobody born with Nicholas’s terrible illness could be called lucky. But he was fortunate that the doctors decided to devote the time, effort and dollars to sequence his DNA at a time when it was very expensive.
Gene sequencing is more than a promising new treatment. It’s a world changing, and investable, scientific breakthrough and it’s also set to change agriculture and farming.
The most important chart in genomics
To put this into context let us start back in 1977, when Sir Frederick Sanger invented the first method for reading DNA. Given the rapid advances in technology since then it is surprising that ‘Sanger Sequencing’ remained the standard method for thirty years.
But in 2005 Life Sciences (now part of Roche) launched its Genome Sequencer. Based upon ‘massively parallel’ sequencing this was able to read millions of fragments of DNA simultaneously – using the Sanger method the maximum was just 384. Post-Sanger technologies are collectively known as ‘Next Generation’ and although there are a number of different versions, they all use massive parallel sequencing.
The chart says it all:
Falling cost opens up new possibilities. Until now the cost of sequencing the entire genome of an organism has often been prohibitive. Instead, researchers have looked only at a specific region of interest. They have studied individual genes known to be related to disease, for example the BRCA1 and BRCA2 genes that are implicated in breast and ovarian cancer.
They have studied only the exons,(EXpressed regiONS) of the genome that collectively form the exome and, unlike the remaining 98.5% ‘junk’ DNA, code for proteins. This selective approach has uncovered some genetic causes of disease, especially in inherited ‘Mendelian’ diseases, and it has also been sufficient to transform forensics and bring criminals to justice. But we now understand that many diseases have many genetic triggers; that junk DNA may have a function after all; and that our genes are not so much a series of single transmitters but a network. So we want to see the whole genome, not just a part of it, and next generation sequencing makes this possible.
We are now seeing some ambitious projects. In England the University of Cambridge, Genomics England and ILLUMINA Inc have launched a three-year project to sequence the whole genome of 10,000 children and adults with rare genetic diseases. This marks the beginning of a national endeavour to sequence 100,000. In the USA Human Longevity Inc, backed by Craig Venter, intends to sequence up to 100,000 human genomes per year. This venture will also gather information on the microbiome (the microbes that live in and on the human body) and the metabolome (metabolites, biochemicals and lipids circulating throughout the human body). Armed with this mass of information the project aims to unravel the process of ageing and associated diseases like cancer, diabetes and dementia.
Eight things we’re learning from genetics science
The Venter and Cambridge studies will generate a torrent of data, spurring the development of bioinformatics, and should give a better understanding of the cause of disease. But advances in sequencing capability promise more than just these broad studies. Let me remind you of the applications of Next Generation Sequencing.
1) Defining rare disorders
Many diseases are thought to be caused by genetic flaws. In particular 80% of rare diseases have a genetic component and while each of these is uncommon, collectively there are some 6,000-8,000 rare diseases. One in seventeen of us will get a rare disease at some time in our lives and a survey in the USA has found that accurate diagnosis takes an average of 4.8 years.
Rare diseases that are inherited are known as Mendelian disorders, after the 19th century monk Gregor Mendel who established the principle of inheritance. The Online Mendelian Inheritance In Man (OMIM) website shows that we are able to pinpoint the molecular basis of an increasing number of inherited phenotypes (observable traits).
2) Describing cancer
Cancer is a major target of geneticists. All cancers are genetic and arise when genes within a normal cell are damaged or mutated, perhaps due to cigarette smoke or solar radiation. The key cancer genes are growth promoting genes (called proto-oncogenes); growth inhibiting genes (tumour suppressor genes) and genes whose function is to repair damaged DNA. And the number of mutations implicated in cancer has grown exponentially over the last two years.
However cancer is not the result of a single mutation. Multiple mutations in several key genes finally trigger uncontrolled cell growth and, since this takes time, it explains why cancer comes with old age. So researchers are increasingly looking for network effects as a number of specific genes interact. They are also sequencing the cancer cells themselves, a challenge complicated by the fact that tumours are not homogeneous and change over time.
3) Clinical trials & therapeutic selection
Next Generation Sequencing can be used to stratify patients for clinical trials. New drugs are approved on the basis first of safety and then efficacy. If a drug only works for one patient in ten it might not be approved. However if it works for one person in two, then it probably will be approved. For years researchers have been trying to achieve this outcome by improving drugs. However an easier route could be to identify only those patients likely to benefit. This is the basis of ‘stratified’ or ‘personalised’ medicine.
4) Carrier screening
Tay-Sachs is a debilitating neurological disease for which there is no known cure. It is an ‘autosomal recessive’ genetic disorder meaning that both parents can carry a particular genetic mutation without contracting the disease. However their child would have a 25% chance of contracting Tay-Sachs. Screening of the parent’s DNA can establish whether there is a risk, and inform the decision about childbirth or indeed whether to get married in the first place.
5) Pre-natal testing
Pre-Natal testing assesses whether babies are likely to be born with defects. Cells from the fetus are shed into the mother’s blood, and these can be captured for testing. At present tests are typically run only for high risk pregnancies and look for particular chromosomal disorders such as Down’s Syndrome, but as the cost of sequencing comes down these tests could be used more widely and reveal much more about both the appearance and the health risks of the new baby.
6) Microbial genomics
The ability to capture the DNA of pathogens, including bacteria, viruses, fungi, parasites and insect vectors of disease offers the best hope of tackling infectious diseases. For example China was able to deal with an outbreak of bird flu last year after sequencing the virus and making the results available to scientists around the world.
Reduced costs for DNA sequencing are likely to boost the nascent market for personal DNA testing. The leader in this market is 23andme, which looks for over 900,000 specific mutations from DNA extracted from a saliva sample. It has recently run into trouble with the FDA for making dubious claims about its ability to predict disease, and its website now promotes the service as a way of exploring your ancestry.
Sequencing is instrumental in screening plants and animals for preferred traits. Plants that can adapt to the environment and hardy animals that yield more meat and milk are being designed on the basis of genetic information.
Whether we are investigating pathogens, looking for the triggers of human disease, or re-engineering the living world the sequencing of DNA is vital. Next Generation Sequencing allows us to harvest genetic data on an unprecedented scale.