In the news

  • Newsletter Edition
The PHG Foundation monthly newsletter features news and views about genetics and genetics research, from a public health perspective. The newsletter is written by staff of the PHG Foundation.

Opinion

Opinion   |   By Dr Philippa Brice   |   Published 3 May 2012

Genetic research is shedding light on how apparently very different diseases may be more closely related than previously supposed.

 

Determining the genetic causes and contributions to different diseases is important for understanding how diseases arise, and how it may be possible to prevent or treat them. Since the completion of the first human genome sequence, and with rapid advances in sequencing technology, there is a veritable explosion in genetic data about all kinds of diseases and conditions.

 

One unexpected development in recent years is the emergence of hitherto unsuspected genetic connections between different diseases. It has been known for some years that mutations in certain key genes such as p53 and KRAS are a common feature of different cancers. Most recently, research has suggested that breast cancer may effectively be ten separate diseases based on the underlying genetic mutations (see previous news), which could mean that an entirely new approach to diagnosis and treatment is indicated. Similarly, research into chronic fatigue syndrome has suggested that genetic differences may define seven different subtypes of disease (see previous news).

 

However, genetic links are also being found between very different diseases; for example, type 2 diabetes and Crohn's disease; type 1 diabetes, lupus and rheumatoid arthritis. By using a systems biology approach, which considers the complex interactions between DNA, RNA and proteins in living systems, researchers are trying to make sense of genetic and related links between diseases.

 

Comment: Although the complexity of interactions examined in systems biology is daunting – requiring new developments in computing to handle the volumes of data – this is an important area of research. As our conceptual understanding of a disease previously considered as a single entity, such a breast cancer, evolves, we can see how our whole approach to medicine may be in some senses flawed. Diseases that seem logically to share a common basis may not do so; apparently disparate diseases may eventually prove to be related.

These preliminary results suggest that our current concept of genomic medicine – exciting as it is - may actually evolve much further in the coming years. Although this is likely to remain largely a research question for the foreseeable future, oncologists and certain other specialties such as rheumatology are already taking on board new approaches based on genomic insights; other specialties may follow. 


In the news

News story   |   By Simon Leese   |   Published 30 May 2012

The world’s largest set of whole genome data on childhood cancers has been released with the aim of speeding up development of new treatments.

The release from the privately funded US Pediatric Cancer Genome Project (PCGP) effectively doubles the amount of whole genome data currently available. It was accompanied by an article from the project’s lead researchers in Nature Genetics outlining the PCGP’s aims and progress so far. The $65 million project has recently completed the second of its scheduled three years.

The data consists of 520 matched sequences of normal and tumour tissue from 260 young people with cancers that currently have the poorest outcomes. By analysing the differences between each individual’s normal and cancerous cells researchers aim to uncover genetic links to cancers. The larger the pool of genomes available, the more readily significant associations can theoretically be identified. The PCGP intends to have sequenced the matched genomes of 600 patients by the time of its completion next year.

The project has already suggested previously unknown associations for some of the most common and aggressive childhood cancers, including the eye cancer retinoblastoma. The genome sequences are potentially valuable for studying the genetic basis for other diseases as well as cancer. Project leader Dr James Downing said: "By sharing the information even before we analyse it ourselves, we're hoping that other researchers can use this rich resource for insights into many other types of diseases in children and adults”.

The sequence information is being made freely available by PCGP on the condition that it is used only for biomedical research and that researchers observe a nine month moratorium on presentation of work that makes use of it. The data can be accessed at The European Genome-phenome Archive website.


News story   |   By Simon Leese   |   Published 24 May 2012

New draft guidelines for fertility treatment on the NHS have been released by the National Institute for Health and Clinical Excellence (NICE).

The new guidance, currently open for consultation, proposes that the eligibility criteria for free IVF and other fertility treatments set out in 2004 be extended to encompass a number of new groups including:

  • Women aged 40-42, provided there is no chance of them conceiving naturally and they have not previously had IVF treatment.
  • Same-sex couples.
  • People unable to conceive naturally due to a physical or psychological impediment.
  • People due to undergo cancer treatment likely to make them infertile.

The proposed updates reflect both an expansion in the range of people requesting fertility treatment and improvements in technology over the past few years.

Some have questioned whether Primary Care Trusts (PCTs) will be able to afford treatment for those who fall under the new eligibility criteria, but others have pointed out that the actual numerical increase is likely to be small in the short term. In addition, eligibility for free treatment is not a guarantee of receiving it: approval is at the discretion of the local PCT, given budgetary constraints and likelihood of effectiveness. Current overall success rates for the proposed new category of women aged 40-42 for example, are under 15%.

The draft also proposes a number of changes in both advice and procedures given to those trying to conceive, including updated advice for people carrying infectious diseases such as HIV, and standardising the transfer of just a single embryo during the first IVF cycle rather than the current guidance of ‘no more than two embryos’.

The Deputy Executive of NICE, Dr Gill Leng, said "The aim of these new and updated recommendations is to ensure that everyone who has problems with fertility has access to the best levels of help. We are now consulting on this draft guideline and we welcome comments from interested parties". The full draft guidelines are available on the NICE website.


News story   |   By Simon Leese   |   Published 18 May 2012

The heads of research councils from nearly fifty countries have established the Global Research Council (GRC) with the aim of fostering international cooperation and consensus between national funding bodies.

At an inaugural summit and press conference this week hosted by US federal funding agency the National Science Foundation (NSF), the GRC issued a statement of six principles setting out the criteria by which funders should assess and select the most worthwhile projects. The six principles are: Expert Assessment, Transparency, Impartiality, Appropriateness, Confidentiality, and Integrity & Ethical Considerations.

The principles are intended both to help established funding agencies hone their practices and to provide a framework for developing nations. NSF Director Subra Suresh, whose idea the Council was, said that this was “the first step toward a more unified approach to the scientific process”. The GRC will act not as a funding body itself at this stage, but as a forum for strategic discussion and examining issues of general policy. It will be governed by a board comprised of equal numbers drawn from developed and developing nations.

The GRC intends to look at a succession of issues that affect funding bodies around the world. Problems and ideas will be worked through at regional meetings and the conclusions presented after an annual meet-up to be held at a different site each year. Next year’s gathering will be in Germany where the discussion will focus on research integrity and ways to promote open access to research results.



News story   |   By Simon Leese   |   Published 10 May 2012

The Minister for Universities and Science, David Willets, has announced that publicly-funded research in the UK will be made accessible free of charge to all and that Wikipedia co-founder Jimmy Wales has been enlisted as an unpaid advisor to help realise this goal.

The central idea of open accessibility is that researchers pay a fee to publish their work and that it is free for anyone to read, as opposed to the prevalent current system of readers paying fees to access research articles. The movement towards a policy of open access for UK research has gained momentum since a boycott of one of the leading scientific journal publishers Elsevier was organised by Professor Tim Gowers of the University of Cambridge at the beginning of this year.

The leading funders of biomedical research in the UK - Research Councils UK (RCUK) and the Wellcome Trust – already have open access policies in place for the work that they fund, but compliance by researchers is low. Both institutions are planning to expand the terms of their policies, and to introduce measures intended to increase adherence to those already in place: these include rejection of publishers’ embargo terms and withholding activation of researchers’ new grants until their previous work has been made open access. Competition from Wellcome Trust’s own recently announced open access journal eLife (see last month’s PHG news) is likely to further drive the shift towards the new publishing paradigm.

The latest announcements are not without their critics amongst academics: Professor of Classics Mary Beard has expressed reservations about a ‘one size fits all’ approach to open access, and particularly to the involvement of Jimmy Wales, while Professors John Bynner and Harvey Goldstein have argued in a blog post that open access will discriminate against researchers without the funds to cover  the cost (typically £1K-£2K per article) of publishing their work.


News story   |   By Dr Philippa Brice   |   Published 7 May 2012

New results suggest that a new genetic screening test for embryos could significantly improve IVF success rates.

 

The test from Cambridge-based company Blue Gnome examined chromosomes from IVF embryos using an arrayCGH-based method, 24Sure.

 

Published in Molecular Cytogenetics, the new screening method was compared with current approaches (visual inspection of embryos) for ‘good prognosis’ women (under 35 with no history of miscarriage) having first-time IVF. Both the initial and ongoing (20 weeks) pregnancy rates were higher for the Blue Gnome approach (70.9% and 69.1%) than for the normal procedures (45.8% and 41.7%).

 

IVF experts have commended the approach, saying it can boost the number of healthy pregnancies resulting from transfer of single embryos. Single embryo transfer during IVF is preferable to avoid the much higher-risk multiple births, but when success rates are low and treatments are expensive, there is pressure to implant more than one.

 

Blue Gnome chief executive Nick Haan cautioned that further research was needed, but said the results were exciting because it suggested that: “24-chromosome screening and single-embryo transfer has the potential to become the default standard of care for all IVF cycles worldwide".

Comment: The genetic screening of the embryos appeared to not only significantly improve overall conception rates but also reduce the proportion of early pregnancy losses among the IVF patients, making it a highly promising approach. In theory, it might perform even better among poorer prognosis patients (older women and those with a history of miscarriage) relative to current methods, as chromosomal abnormalities probably underlie a fair proportion of failed IVF and pregnancy loss in these groups. However, more research will be needed to find out. 


News story   |   By Rebecca Bazeley   |   Published 4 May 2012

Attempts to lose weight may be more successful when complemented with longer periods of sleep, according to new research.

Whilst other research has suggested that too much sleep can promote obesity, a new study suggests that gene expression that promotes obesity may be influenced by the amount of sleep we get.

Looking at 1,088 pairs of identical and non-identical twins, researchers found that in those sleeping less than seven hours at a time, genetic influences accounted for 70 percent of the differences in body mass index (BMI). For twins averaging more than nine hours of sleep, genetic factors contributed to just 32 percent of weight variation.  Thus, the lifestyle effect of more sleep appeared to reduce the impact of genetic predisposition to obesity.

The results suggest that shorter sleep provides a more permissive environment for the expression of obesity related genes,” said principal investigator Nathaniel Watson, MD, MSc, of the University of Washington. “Or it may be that extended sleep is protective by suppressing expression of obesity genes.”

The study is published in the journal Sleep.



News story   |   By Dr Philippa Brice   |   Published 2 May 2012

UK researchers have published data in the journal Cancer Research showing a strong link between an epigenetic modification of a gene in white blood cells and the risk of breast cancer.

 

The Breast Cancer Campaign funded scientists examined methylation levels in the ATM gene among 1380 women, of whom 640 went on to develop breast cancer. The highest levels of ATM gene methylation were associated with a two-fold increase in breast cancer risk.

 

Lead researcher Dr James Flanagan of Imperial College London said that, in addition to the contribution of genetic variation to disease risk: "With this new study we can now also say that epigenetic variation, or differences in how genes are modified, also has a role”. This may be a key genetic mechanism by which environmental influences influence disease risk.

Comment: The hope is that epigenetic data such as this might eventually be used alongside data about DNA sequence variation and other medical and lifestyle information in models to predict more precisely individuals’ future risk of cancer and improve screening and prevention


News story   |   By Rebecca Bazeley   |   Published 1 May 2012

Health professionals working in the field of congenital disorders can now benefit from six new topics published today in the PHG Foundation’s Health Needs Assessment Toolkit for Congenital Disorders.

The new Toolkit topics are Congenital Heart Disease, Congenital Hypothyroidism, Sickle Cell Disease, Thalassemias, Rhesus Haemolytic Disease, and Glucose-6-Phosphate Dehydrogenase Deficiency.

Congenital disorders, more commonly called birth defects, is an umbrella term for a group of serious disorders present from birth, the effects of which can be devastating - for the life chances of newborns and for the wellbeing of their families. The web-based Toolkit provides users - particularly in low- and middle-income countries - with a roadmap to implementing essential services to reduce this suffering.

The Toolkit is completely free to use, and is accessible online here

The Toolkit now has resources on the following topics:

  • Congenital Heart Disease
  • Congenital Hypothyroidism
  • Sickle Cell Disease
  • Thalassemias
  • Rhesus Haemolytic Disease
  • Glucose-6-Phosphate Dehydrogenase  Deficiency
  • Down's Syndrome
  • Neural tube defects
  • Orofacial clefts
  • Health services
  • Preconception care and screening  
  • Prenatal services  
  • Newborn screening    

Forthcoming topics to be released are Fetal Alcohol Spectrum Disorder, Teratogens, Congenital Rubella, and Congenital Syphilis. 

Keywords : DSthalassaemia

Research articles

Research article   |   By Simon Leese   |   Published 29 May 2012

Two studies published earlier this month in Science suggest that the vast majority of genetic variants that influence disease risk in humans are rare and as yet uncharacterised.

The large-scale studies used deep sequencing to uncover rare sequence variations within individuals. Rare variants are defined as being carried by less than 0.5% of the population.

One study sequenced over 15,000 genes in 2,440 people of European and African ancestry and found that of more than half a million variants identified, 86% were rare. A separate study sequenced 202 drug target genes in 14,002 people and determined that 95% of variants were rare, many being carried by only one person in the sample. In addition, the rare variants were predicted to be more likely than more common ones to have functional effects with consequences for health.

In both studies rare variants were found to be geographically localised, suggesting that they are the result of post-agricultural human population growth that natural selection has not yet had time to work upon. The full extent of rare variation had not been revealed by earlier sequencing studies because the sample sizes have not been sufficiently large.

These findings have potentially significant and troublesome implications for the quest to find associations between common genetic variants and disease. They suggest that the predictive value of profiling the common variants carried by an individual is limited, and that many thousands of people’s genomes will need to be studied in order to provide enough data to connect a given rare variant with a particular disease risk.


Research article   |   By Simon Leese   |   Published 22 May 2012

Research published in PLoS One suggests that Parkinson’s disease patients with a particular gene variant are likely to experience faster decline in motor function.

Parkinson’s disease is characterised by progressive deterioration of motor skills, but the rate and the degree of functional decline vary widely between patients. Clinicians currently use factors such as posture and gait to predict how an individual will progress. There has so far not been a reliable genetic predictive test available.

This study looked the SNCA gene which has a well established association both with risk of developing Parkinson’s disease in the first place, and with severity of symptoms. Two sequence variations at separate regions of the gene were investigated; it is possible for an individual to have either or both variants.

A cohort of 233 patients were assessed over a period of five years for changes in their motor function using the Unified Parkinson’s Disease Rating Scale. Patients with the SNCA promoter sequence REP1 were four times more likely to have experienced rapid decline of motor function than those without. The other sequence variation tested also showed some association with likelihood of faster decline, but to a much lesser extent. The risk was greatest for those who possessed both variants together.

The immediate significance of this study is as a proof of principle, in that it demonstrates SNCA variants can be effective predictors of rapid motor decline in Parkinson’s disease. This could aid identification of those patients most likely to benefit most from early interventions, as well as offering the possibility of selecting subjects for trials of new therapies that would return quicker results regarding their effectiveness.

It is likely that a number of other variants and genes influence the rate of motor function loss in Parkinson’s disease. Further large-scale studies should help both to identify those and to confirm the results of this study.


Research article   |   By Simon Leese   |   Published 16 May 2012

A study published in Proceedings of the National Academy of Sciences has identified a gene that influences both the capacity to form memories and an individual’s susceptibility to post-traumatic stress disorder (PTSD).

PTSD can be highly debilitating: symptoms may include repeatedly re-experiencing the traumatising event via flashbacks or nightmares, aversion to stimuli associated with the event and a heightened state of stress that can affect the sufferer’s ability to work, sleep and control their emotions.

The gene examined by the study is PRKCA which encodes an enzyme that had already been implicated as having a role in the formation of emotional memories. The gene comes in two variants or alleles known as A and G.

The study comprised three stages: In the first stage the PRKCA genes of 700 healthy volunteers were sequenced.  The volunteers were then shown a series of emotionally affecting images that they were later asked to describe. Those with two copies of the A variant of PRKCA were able to recall the most detail about the pictures, those with two G variants the least, and those with one copy of each variant a medium amount.

In the second stage of the study a further 394 participants performed the same task whilst undergoing brain imaging, revealing that possessors of A alleles had higher levels of prefrontal cortex activity during memory formation.

In the third stage the distribution of A alleles was analysed within a group of 347 refugees from the 1994 Rwandan genocide, all of whom had experienced traumatic events and 134 of whom had been diagnosed with PTSD. Those with the A allele had approximately double the incidence of PTSD.

The results of this study reinforce the widely accepted notion that emotional intensity strengthens memory formation and retention, and suggest that a person’s ability to recall emotional memories and their susceptibility to PTSD are linked, and are at least partially determined by which PKRCA alleles they inherit.

The exact mechanism by which PKRCA variants affect emotional memory is not yet known, but it is likely to be a result of differing levels of activity of the resulting enzyme. This suggests the possibility that future PTSD therapies could be tailored to an individual’s specific PKRCA allele combination and directed at manipulating the activity level of the enzyme. As the study’s lead author has pointed out, it is likely that several other genes will also influence susceptibility to PTSD, and future large-scale genome studies may elucidate some of these.


Research article   |   By Simon Leese   |   Published 11 May 2012

A study published in Nature appears to confirm the role of exposure to ultraviolet light as a cause of melanoma, as well as implicating a new region of gene mutations as a factor.

Melanoma is not the most common form of skin cancer, but is the most dangerous because of its tendency to metastasise (spread throughout the body) leading to a high level of mortality in advanced stages.

The genomes of 25 patients’ melanoma tumours were sequenced and compared to the genomes of their non-cancerous cells. A wide variety of different mutations were observed across the tumours, but their rate of occurrence rose in line with the amount of chronic sun exposure each patient had received. The patient with the highest level of sun exposure had a mutation rate more than ten times that of the lowest.

The genome comparisons also revealed that one particular gene known as PREX2 was mutated in 11 of the 25 tumours, and that in 9 of the remaining cases mutations had occurred very near to the gene. PREX2 produces a protein that inhibits another protein called PTEN that plays a role in preventing tumour development. The nature and effect of mutations in PREX2 were unusual in that they occurred over a widespread area rather than clustering in a few discrete regions and in that they all appeared to lead to an increase in the amount of protein produced, rather than affecting its level of activity.

It is not clear exactly how PREX2 functions, or whether the discovery of its contribution to melanoma will lead directly to new treatments. It is likely though that these findings will lead to a greater understanding of the complex process of melanoma tumour formation, and ultimately point towards more pathways that could be therapeutically targeted.


New reviews and commentaries

New reviews and commentaries, 1 May 2012

Reviews & commentaries : by Dr Philippa Brice

Testing times

Nat. Genet. 2012: 44(473):473.

 

Advancing the post-genomic era agenda: contributions from public health.

McGrath BB. Public Health Genomics. 2012;15(3-4):125-31. 

 

The impact of genomics on public health practice: the case for change.

Zimmern RL, Khoury MJ. Public Health Genomics. 2012;15(3-4):118-24.

 

The public health genomics translation gap: what we don't have and why it matters.

Williams MS. Public Health Genomics. 2012;15(3-4):132-8.

 

Harnessing genomics and genome biology to understand malaria biology.

Volkman SK et al. Nat Rev Genet. 2012 Apr 12;13(5):315-28. 

 

Histone methylation: a dynamic mark in health, disease and inheritance.

Greer EL, Shi Y. Nat Rev Genet. 2012 Apr 3;13(5):343-57. 

 

MicroRNA profiling: approaches and considerations.

Pritchard CCet al. Nat Rev Genet. 2012 Apr 18;13(5):358-69. 

 

Retinoblastoma.

Dimaras Het al.Lancet. 2012 Apr 14;379(9824):1436-46.

 

Promising new era dawns for cystic fibrosis treatment.

Corbyn Z.Lancet. 2012 Apr 21;379(9825):1475-6.

 

Reprogramming the genetic code.

Chin JW.Science. 2012 Apr 27;336(6080):428-9. 

 

Integrating genomes.

Zerbino DRet al.Science. 2012 Apr 13;336(6078):179-82.

 

Controversial research: Good science bad science.

Brumfiel G. Nature. 2012 Apr 25;484(7395):432-4.


Scientific evidence alone is not sufficient basis for health policy.

Humphreys K, Piot P. BMJ. 2012 Feb 27;344:e1316. 

 

In cancer drug resistance, germline matters too.

Cheng EH, Sawyers CL. Nat Med. 2012 Apr 5;18(4):494-6.

 

Children of the 90s: Coming of age.

Pearson H. Nature. 2012 Apr 11;484(7393):155-8.

 

China's stem-cell rules go unheeded.

Cyranoski D. Nature. 2012 Apr 11;484(7393):149-50. 

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