Personalised Genome: The Good, the Bad and the Ugly

As new age technology, such as high-throughput sequencing and nanopores, slashes both costs and time needed for genomic analysis, the age where commercialisation of individual one thousand pound gemones dawns. With its inevitable manifestation around the corner, it has never been more pressing to assess impacts, both social and clinical, so that we can truly be prepared for the changes in how the genetic world interacts with everyday life.


As 10,000 new germline mutations are identified annually, and 300 new inherited disease genes highlighted, personalised genomic sequencing could be used to locate, monitor and understand further disease-associated mutations, though this will only be possible if the data is in fact made public. Inheritance of disease will be better understood, which is a very exciting prospect for potential parents, as current prenatal tests only identify a fraction of potential defects. Currently personalised genome sequencing is used for prenatal and preimplantation genetic testing of conditions such as Turner’s syndrome and muscular dystrophy; however these tests are currently available only to high risk children. With the potential commercialisation of sequencing, testing may be readily available to everyone, undeniably changing the way in which these tests are implemented and as with most change, the line between it being positive and negative lies thin.

‘All creatures would agree that it was better to be healthy than sick… well fitted than ill fitted for their part in life; in short that it was better to be a good rather than a bad specimen of their kind’ – Galton

Global screening of embryos for disorders could lead to self directed human evolution, in other words, eugenics. The risk of profitable ‘designer babies’ could lead personal genomics to encounter ethical scrutiny, therefore a balance will have to be struck:

‘Given the power and the authority granted to parents to seek to improve or better their children… at least (by) some forms of genetic selection or alteration (it) seems equally ethically defensible if they are undertaken freely and do not disempower or disadvantage their children’ – Galton

Certain countries have banned inappropriate preimplantation diagnosis, such as that for sex selection in the UK.

After heart disease, cancer and stroke, adverse drug reaction is the fourth most common cause of death for americans, the fast growing field of pharmacogenetics will find genomic profiles vital in the production of personalised medication. Not only would personalised medication reduce deaths from undesirable reaction, but these tailor made gems would benefit both diagnosis as well as treatment efficiency. While focusing on disease, it must be said that it’s susceptibility is complex, often involving multiple genes, with a partial influence of environmental exposure to certain substances, such as carcinogens. Shedding light on perhaps a limitation of sequencing is the reality that it is not likely to have a great deal of predictive power; a study analysing over 53,000 pairs of monozygotic twins for the incidence of 24 diseases, ranging from autoimmune to obesity associated diseases and cancer, implied 2% of women undergoing whole genome sequencing would have mutations linked to ovarian cancer detected; at least a one in ten chance of developing ovarian cancer. However, the remaining 98% having found no mutations would still be at a 1.4% risk, that of the general public; it would be fair to say that the day when sequences produces infallible figures is a while away.

Unfortunately sequencing may also reveal to patients more than they were prepared to know, diagnosing age-onset, incurable diseases such as Alzheimer’s disease. And once the diagnosis has been confirmed, who else has the right to know? New guidelines issued by the UK GMC allow disclosure of patient information, given the diagnosis of a genetically heritable disease to family members if it is ‘justified in the public interest’. Genetic availability dawns a problematic issue as the UK lacks a counterpart to the USA Genetic Information Nondiscrimination Act.

There also remains the risk of people missing out on potentially life-saving intervention; as genomic sequencing enable quick, cost-efficient diagnosis and family history has long been collected as a means of assessing risk, individuals may not get tested in the fear of employment and insurance discrimination. Although comfort can be taken in the fact that the US Department of Energy and the National Institute of Health devotes 3-5% of their annual Human Genome Project budget towards studying the ethical, legal and social issues surrounding genetic availability, illustrating how research into the issue is currently active.

Sequencing potentials are astounding; from revolutionising diagnosis of disease to screening embryos for chromosomal abnormalities. Personal genomic sequencing allows useful deviations from the reference genome to be analysed. In turn, these incentivise an increase in the sophistication of modern technology. The ethical issues of pharmacogenetics, eugenics and social discrimination dawn as a result of personal genomic sequencing; although there is evidence that research is going towards investigating problematic issues, with rules and regulations already in place. As time progresses, so will our knowledge, all that remains is the hope that we are prepared for the double helix’s dormant revelations.

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Artificial organs – science fiction or reality?

Since the dawn of modern molecular biology and cell biology in the 1950s, many people have been dreaming of a day one can create organs in the laboratory from patients’ cell samples. Every year many patients die in hospitals due to malfunctioning or failing organs caused by various diseases or accidents. Organ transplantation from donors has many complications and remains risky due to the rejection of foreign tissues by the immune system.

Compatibility is often rare and researchers have been searching for a solution of this problem for a long time. In recent years there have been great advances in the new so-called field of tissue engineering, which focuses on the creation of human tissues and organs grown in the laboratory. One of the pioneering laboratories has been the Vacanti laboratory in Boston/ MA. The laboratory focuses on the interface between fundamental and translational research. Now, researchers at the Frauenhofer Institut in Stuttgart/ Germany have started to engineer human skin samples and aim to supply 5000 of these every month. Cambridge has just announced a meeting in October on musculoskeletal tissue engineering and Oxford even has a centre for tissue engineering actively involved in this research. The main advantage of the creation of tissues and organs from the laboratory is that they are virtually samples of one’s own body and will not face any rejection. Furthermore, such a technique could eliminate organ shortage, which costs so many lives every year.

However, the engineering of human tissues has been a great challenge for researchers. Until now successful applications in Europe have mainly been limited to the creation of new cartilage that can be transplanted.

Do we need to be afraid? Are all these laboratories fragments of our greatest nightmares stemming from science fiction movies and the fear of the unknown? Are we interfering with something better left alone?

These are all very valid ethical questions and need to be addressed before any such research is conducted. Furthermore, the public needs to know what people are doing and what public research money is spent on. I have been involved in biomedical research for a while now and am happy to comment on any of our readers’ comments.

What will organ transplantation look like in a decade from now? This is something that is likely to concern many of us in one way or another.

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The Dangers of Cloning – a Popular Myth?

The world of biology was relatively quiet and untainted, whereas other natural sciences such as physics and chemistry had suffered from some bad reputations. Nuclear physics is now associated with the tragedies of Chernobyl and Fukushima and chemistry has been associated with pesticides, dangerous drugs and horrible toxins. But the view on biology changed in 1996 when Dolly the Sheep was born, the first official clone of a mammal.

Suddenly the press went haywire, drawing scenarios of the doom of humanity. The scientists from Scotland were suddenly accused that they had been interfering with the essentials of life and created a monster. Was this the beginning of Frankenstein come true? Certainly not. The streets are still safe and there is no army of human clones trying to invade us as so beautifully demonstrated in Star Wars. But what is the truth about the myth of cloning? How does it affect our everyday lives and what are the biologists cooking next in their laboratories?

Dolly is dead now. She died from lung cancer in 2003 after enjoying only half the life span of a normal sheep of that breed. Since Dolly, many mammals have been cloned, including bulls and horses and none of those has hit the news as vigorously – or maybe the name Bull 86 just did not quite cut it. Why do we clone animals?

First of all, it is important to understand what is cloning. Cloning is a natural phenomenon, just as is nuclear energy. Many organisms in nature reproduce asexually, for example bacteria, some plants and some insects. By definition, two clones are organisms with exactly the same genetic make-up. If a bacteria divides for example, two clones are formed. There are approximately 40 million bacteria in one gram of soil, often from the same clone, and thus two grams of soil has potentially got more clones than Britain has people.

Cloning is a technique used routinely in laboratories and has been since the dawn of molecular biology. It is a tool absolutely necessary to study the fundamentals of life and study mechanisms in cells that ultimately help us understand many diseases. So, cloning seems to be a good word. But why do we need to clone mammals or potentially even humans, which is still illegal.

Interestingly, Dolly was not even a real clone. There are two pools of DNA in a mammalian cells, one the nucleus which is passed on from the father and the mother, and one in the mitochondria, the “power plants” of a cell, which is only passed on from the mother. The mitochondria were not replaced and thus Dolly was strictly speaking not a clone – neither is any of the other mammals that have been cloned since.

Many plants that we cultivate and finally eat are clones. With the technology available we can also use cloning to genetically modify plants in order to increase crops, yield and even taste. Again there is the question as to whether this is necessary.

Despite heated debates and many laws about stem cells, genetically modified food and cloning, once Pandora’s box is open, it usually doesn’t get closed again. Cloning is good and has helped our understanding of the mechanisms of the cell and helped guide the development of many drugs which help millions of people. The question is not as to whether one should use cloning, but rather what is the scientist’s conscience using such techniques. We live in a society with strict moral codes laid upon us, some of them maybe debatable. As society evolves, the moral code also changes. To me, a scientist conducting experiments is responsible for his/her actions. Politics is responsible for laws that try to lead the conscience of people. It surely is our responsibility to understand the needs of society as a whole and help guide scientists to make good decisions and use the knowledge they generate wisely.

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Revolution Through Competition: Unravelling the Archon Genomics X Prize with Dr Eugene Schuster

We truly are living in the age of technology, but not as we know it. Machines will no longer be developed through scientific knowledge; scientific knowledge will be developed through machines.

Dr Eugene Schuster
Functional Genomics of Aging
Genetics, Evolution and Environment
University College London




Science Writer Sumaya Anwar interviews Dr Eugene Schuster to find out more about the Archon Genomics X prize. The $10 million prize competition, which awaits a team capable of sequencing 100 genomes, at a cost of $1000 per genome, in 30 days or less with no more than 1 error in 1,000,000 bases!

It seems surprising to see head-to-head competition in the scientific world, is this something you have come across often or is the vision of scientists working fully together and sharing their findings more realistic?

There is a growing movement in the scientific community for this type of competition – another example is and shows that the crowdsourcing movement has entered into the scientific community. I think the impact of these types of competitions will be limited and focused to very particular research areas and will not greatly expand as a funding source for academic research. This is because research is very expensive to conduct and you need funding from the beginning. Only an extremely well funded lab or company could undertake such a project and most likely would already have funding in place to do this type of research – so winning the X prize would only be a bonus. However, I think it is much more likely that crowdfunding – when someone proposes to build or do something and ask the public for funds to accomplish the task – will become a bigger part of scientific funding in the future.

The 100 genomes to be sequenced have been donated from centenarians; as a researcher within the aging field how would this genomic database benefit you?

Although, my group studies ageing in a tiny worm called Caenorhabditis elegans, we are interested in identifying evolutionarily conserved mechanisms that can affect lifespans. We would clearly benefit by this research because when human genes are discovered that might help humans to live past 100 we can immediately test if the equivalent genes in worms also affect lifespan. For example, we study a gene called daf-16 in worms and almost 20 years ago the scientist Cynthia Kenyon discovered that this gene plays an important role in extending the lifespan of worms. In the past few years the equivalent gene in humans (called FOXO3A) has been implicated in helping humans to live past 100. We believe that by understanding the role of this gene in worms we can start to understand what it does in humans.

Which standard of the competition do you think is going to be most difficult to meet: 98% completeness of the sequences, the time restriction of 30 days or less, the cost restriction of $1,000 per genome or achieving complete haplotype phasing of the chromosomes?

Complete haplotype phasing will be the most difficult to achieve. It is very difficult to predict inheritance without sequencing the parents or related individuals. To do this probably requires the ability to sequence very long stretches of single strands of DNA with very little error – which is probably beyond current methods.

The process of aging is no doubt complex; research tends to be conducted on model organisms, would the development of genomic sequencing technology mean the end of model organism use?

No because having genomic information does not mean the end of experiments. Large sequencing studies in human will only provide weak evidence that a gene may be involved in a disease or the prevention of a disease. Experiments will have to be done to show a definitive link between the disease and the gene and it is much easier to test these links in model organisms. In worms, you can do an aging experiment in a few weeks. If I started a study in humans, it is likely that the study would out live me.

Steve Jobs had his genome sequenced for $100,000; $1,000 seems much more commercially viable for the general public. What does the current price stand at?

To get a high quality genome with very few errors it would cost about $10,000 today. Once the price gets near $1000 (approximately the cost of an MRI scan) then it can become reasonable for insurance companies or the NHS to sequence a genome if there is good reason to suspect that there is a genetic basis for a disease or symptom. However, this does not include the cost of making sense of that genome and including analysis and interpretation costs may significantly add to the price.

Which technologies are currently at the forefront in terms of cost-efficient sequencing and how do they achieve this?

Two companies that have recently announced low cost genome sequencing are Ion Torrent and Oxford Nanopore Technologies. Both companies will use a semiconductor based technology – Ion Torrent bases the technology on detecting ion charges during the sequencing process and Oxford Nanopore detects changes to the electrical current as a strand of DNA is passed through a nanopore. The major cost savings of these technologies is that they do not rely on optics (i.e. expensive lasers and scanners) nor on labelled samples (older technology typically relies on costly fluorescent labels to detect sequence).

This competition was first proposed in October 2006, what date would you estimate the commercialisation of the $1000 genome?

I would estimate that it will take 2 years before the first commercial $1000 genome (including the cost of interpretation) is available.

Look Younger Using Nutrigenomics

London Life Coach & Wellbeing Consultant Sloan Sheridan-Williams talks about Dr Perricone’s research into nutrigenomics. Follow Sloan on Twitter @SloanSW_London and check out Sloan’s website

Last year, you heard us talk about epigenetics which is the study of changes produced in gene expression caused by mechanisms other than changes in the underlying DNA.

Now we delve into a new and more specific niche – nutrigenomics. This field analyses both nutrition and genomics studying the relationship between what we eat and our gene expression, which begs the question on everyone’s lips – can we turn back time by changing what we eat and drink?

This niche area of scientific research questions what factors in food affect gene expression and in turn how the genes we possess react and utilise the nutrients we put into our body. If this research is proved to have any evidential value it could mean that by manipulating what we eat and when we eat it in addition to lifestyle, there is a possibility that we can change the way in which our genes are expressed and even influence the way information is transmitted.

It is commonly known amongst scientists that inflammation is present in conditions that we refer to as aging or age-related. Nutrigenomics and in particular gene expression allows us to find new ways to stop the genes responsible for inflammation by silencing them with specific stimuli.

Scientists will often discuss that genes can be upregulated (turned on) by transcription factors which translocate to the nucleus of the cell in question attaching to specific receptor sites on the genes themselves. Nutrigenomics research has shown us that although transcription factors play a very important role on gene expression,  that nutritents found in everyday foods can also affect gene expression in powerful and positive ways.

Dr Perricone’s research on nutrigenomics has revealed and claimed that his list of nutrients can result in:

  • Healthy body weight
  • Decreased incidence of cancer
  • Reduced cognitive decline
  • Maintenance of bone density
  • Optimal immune system functioning
  • Maintenance of muscle mass
  • Prevention of metabolic syndrome
  • Efficient functioning endocrine system
  • Reduction in aging

There have been many diets on the market which help aid in reversing the effects of time on your skin but Dr Perricone’s book Forever Young may have just hit the nail on the head.

Scientists working on the human genome project have for years been waxing lyrical about how genetic manipulation will transform our lives immeasurably. In the meantime the most successful diet for anti-aging so far seems to be the one that encourages a variety of colours and flavours into our diet also known as rainbow foods. The reason why this diet seems to have been working is that these foods unbeknownst to us have according to nutrigenomics been upregulating (turning on) the protective restorative genes while downregulating (turning off) the damaging ones.

For those of you wanting to add some of the superfoods that pack a powerful nutrigenomic punch when it comes to banishing aging, the next time you’re in the supermarket fill your trolley with:

  • Watercress
  • Cinnamon
  • Tumeric
  • Chocolate
  • Green tea

Watercress is useful as it contains active pharmaocophores. It is thought that these “super ingredients” control transcription factors and gene expression.  In fact, the American Journal of Clinical Nutrition suggested that not only do these pharmacophores reduce blood cell DNA damage but also help the blood cells prevent further DNA damage caused by free radicals.

If green tea is not your thing (its catechins are thought to suppress NF-KB) you could also try the following products which contain similar phytochemicals which also suppress NF-KB thereby purportingly keeping you looking younger for longer. These products include:

  • Basil
  • Rosemary
  • Blueberries
  • Cloves
  • Fennel
  • Coriander
  • Garlic
  • Ginger
  • Pomegranates
  • Red chillis

For those of you who jumped for joy reading that chocolate was a nutrigenomic favourite, make sure that you choose an extra dark chocolate with at least 70% cocoa content and where possible try to select non-Dutched cocoa. This type of chocolate not only affects brain chemistry, with particular reference to serotonin and dopamine making it a natural anti-depressant, but it also works on the cardiovascular system reducing the incidence of athelosclerosis.

If you would like to kick-start your anti-aging process I suggest you look into anti-inflammatory diets which claim a noticeable and visible improvement in your skin in as little as three days. Such diets consist of:

  • Proteins in the form of fish, poultry and tofu
  • Low glycemic index carbohydrates
  • Rainbow coloured fresh fruit and vegetables
  • Healthy fats as found in fish, nuts, seeds and olive oil
  • At least 8 glasses of water a day
  • Antioxidant rich beverages such as green tea

If three days seems too long and too much effort for a quick fix of radiance, EF MediSpas are offering DermaQuest glycolic acid resurfacing for as little as £70. For more details go to

For those of you who are a little braver, the Aesthetic Medical Clinic offers the RH Nutriboost treatment which uses acupunture-style needles to deliver homeopathic remedies, vitamins, nutrients and plant extracts to the mesoderm (middle layer of your skin) followed by rehydration of your skin and correction of collagen damage. These sessions cost £280. For more details call the clinic on 020 7636 1313.

If you have any further questions on nutrigenomics or if you have tried an anti-inflammatory diet and would like to share your experiences, I look forward to your comments below.

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Epigenetics in Cambridge – DNA May Not Be Your Destiny

Epigenetics is a newly emerging field in Biology and has invaded many news reports around the world over the past few years. But what exactly is epigenetics?

The term genetics describes the study of heritable changes involving DNA, which is the molecule carrying genetic information in our cells. When we reproduce, our genetic code recombines with that of our partner to create another fascinating individual. Sometimes our cells mutate and cause unwanted proliferation, which can lead to cancer. These are genetic changes, i.e. alterations in our actual genetic code. However, our bodies are not that simple and there are other changes which are heritable and do not include the change of the genetic sequence. Hence the term carries the prefix “epi” (Greek for besides, above). Factors such as the 3D-structure of our DNA, expression of genes, natural modifications such as methylations and so forth have a great influence on development and heritage. They can even be involved in the formation of diseases, which in return has drawn the attention of many pharmaceutical companies to this new field. So the good news is: we are not just the sum of our genes!

Cambridge as a place of world-class research is at the forefront of epigenetic research and the university has many outstanding research groups working in that field. The Cambridge Epigenetics Club, which meets regularly in Cambridge, has been set up for interested individuals of the university to share knowledge and bring people of the scientific field together.

Epigenetics will be hitting the news in the next few years and certainly there will be heavy debates about new strategies to tackle diseases. It is important to remember that the field aims to understand the fundamentals of life and the outcomes of the research can potentially be used to help people. Most likely there will be heavy debates on the subject. I my opinion, it is important to keep an open opinion and remember what scientist try to do. In this context, the word “Cloning” is a natural phenomenon seen in many species and only got a negative connotation when the news reported about “Dolly the Sheep” and “Designer Babies”. It is up to us as the public to decide where we want to lead society, what challenges we want to tackle in the future and how we want to use the invaluable wealth of knowledge science has to offer.

So we are not defined just by the sum of our genes. Who we are and what we are is determined by many other factors. What will be the next discovery?

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