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In the news
The Human Fertilisation and Embryology Authority (HFEA) has announced a significant increase in the payments that can be made to donors of egg and sperm cells.
From 2012, compensation payments will rise to £750 per cycle for egg donors and £35 per clinic visit for sperm donors; egg donation is an invasive procedure and involves significantly higher risks to the donor than sperm donation. These figures include expenses.
The decision follows a public consultation on the issue by the HFEA earlier this year (see previous news) and the primary purpose of these higher payments is to encourage more donors to contribute eggs and sperm for fertility treatments. The figures are much lower than donors can receive in countries such as the US; HFEA Chair Lisa Jardine commented that they had: “set a level of compensation which will not deter those interested in donation but will retain donors already in the system, without attracting those who are merely financially motivated”.
The HFEA is to review guidance on other forms of financial incentives such as egg-sharing schemes to ensure that clinics understand exactly what benefits can be offered.
Comment: A report from the Nuffield Council on Bioethics earlier this month recommended offering higher payments for donors who agreed to provide eggs for scientific research, as there is a preference for donation for fertility treatments (see previous news).
A task force set up to consider the future of genetics and genomics in relation to nursing and midwifery has released a report of its findings, which were presented to the Nursing and Midwifery Professional Advisory Board.
The group reviewed a number of areas including key drivers, scope of the science, patient expectations, education and ethical consideration amongst others. It found that the field is moving rapidly with implications across all of health care not just specialist genetic services. The report states that nurses and midwives are best places to optimise the benefits of genomic medicine for patients and urges prompt action in order to ensure that they have the appropriate competencies. In light of these findings twelve recommendations were made in the areas of policy, education, research and professional development.
The PHG Foundation has recognised the opportunities offered by genomic medicine for improved care and management across all health care sectors (see press release). The recommendations presented in the above report are an important contribution to future clinical practice.
The Archon Prize for Genomics has been revised to focus on sequencing the genomes of one hundred centenarians, it has been announced.
The $10 million prize, announced in 2006 (see previous news), will go to the team of researchers whose DNA sequencing technique will allow them to quickly and accurately decode 100 human genomes. Teams are to receive the 100 genomes at the start of January 2013 – the selection of centenarians is reportedly already underway – and judging will take place a month later, based on speed, accuracy and cost of sequencing. Error rates must be less than one per million base pairs and the cost must be below $1000 per genome.
The prize was originally aimed at sequencing the genomes from a selection of 100 celebrities, donors and members of the public, within ten days, with a view to driving breakthroughs in human genome sequencing and medical applications. Under new sponsors Medco Health Solutions, the new focus is on the genomics of health, with the data from the proposed group of 100 people of at least 105 years old to form a new public database for research into wellness.
Comment: The $1000 genome has been a goal since the early days of the Human Genome Project; now, at last, it may be within reach – even if the ten day limit originally planned by the Archon Foundation has proved a little too stringent.
- What is epigenetics?
- Obesity (UK Department of Health)
- Climb National Information Centre for Metabolic Diseases
Changes in genes identified in middle-aged men may be the result of a childhood lived in poverty, according to new research.
Analysing the DNA of 40 men, aged 45 at time of sample collection and raised in households belonging to the top and bottom 20 per cent of the socioeconomic scale, scientists have uncovered patterns in gene activation that seem to relate to the wealth or poverty in which the men were raised.
Of the 20,000 sites of the genome they examined, researchers found differences in activation patterns at 1252 sites associated with socioeconomically poor households, compared to 545 sites associated with a wealthy upbringing. Differences between these two groups were found at almost a third of sites. This suggests that something in a background of poverty may cause a lasting response in which a gene is switched either on or off. These responses, while possibly useful in terms of survival at the time, may be linked to heart disease, diabetes, cancer and other complex diseases in later life.
Epigenetic changes – the process by which genes are activated or silenced - have already been linked to psychotic diseases such as schizophrenia.
The researchers are now turning their attention to identifying when these changes occur in a new study of participants in the Avon Longitudinal Study of Parents and Children for whom blood samples are available from birth to around the age of 20.
The PHG Foundation’s latest report sets out a strategy for the UK National Health Services to make the most of new and emerging opportunities for better care thanks to whole genome sequencing (WGS) technologies.
Next steps in the sequence: the implications of whole genome sequencing for health in the UK is the first comprehensive overview of the impending medical impact of human genome sequencing. It reviews the relevant technologies, identifies the areas of medicine where genomics is having the most immediate impact – notably in diagnosis and management of inherited forms of disease and cancer - outlines the barriers to prompt and effective implementation within the NHS and makes recommendations for action to tackle these issues.
Key strategic challenges identified include the need for new biomedical informatics expertise, clinical databases and improved understanding of genomic data interpretation within the NHS.
The report also notes that these transformative technologies do not raise any fundamentally new ethical issues, but recommends that for the time being only targeted forms of genome analysis that minimise unexpected (incidental) findings are used, and that patients should be told only about medically important information.
James Peach, Director of Stratified Medicine at Cancer Research UK commented: “We’re only scratching the surface of what WGS technology can do for us…but there are problems about using it in the NHS, and the biggest problem is that we don’t know what to do with it”.
Sir John Bell, Regius Professor of Medicine at the University of Oxford and chair of HGSG, said that WGS technologies would have “a very substantial impact on human disease”, adding that the new report “takes you to the heart of all the issues”.
Dr Ron Zimmern, Chairman of the PHG Foundation, which celebrates its fifteenth anniversary next year, said that the big challenge for public health was no longer how to understand genomics from a public health perspective, but rather “how to practice public health in the genomics context”, noting that the recommendations of the new report showed that genomics was now “the responsibility not so much of individual clinicians, but of the health system as a whole”.
Summary and full versions of the report are available from the PHG Foundation website.
Company Sequenom has launched the first commercial non-invasive prenatal test for trisomy 21 (Down’s Syndrome) in the US.
The MaterniT21 test will be available in 20 regions of the country, although access will be available only via doctors and not direct-to-consumers. The test is expected to cost around $1900, a similar cost to that of invasive testing, though women may be able to receive it via their health insurance.
The clinical validation study behind the new text has been simultaneously published in the journal Genetics in Medicine (see previous news), demonstrating a detection rate of 98.6% in women with high-risk pregnancies of 10-22 weeks’ gestation. At this stage, the non-invasive approach is unlikely to replace the ‘gold standard’ of invasive testing and karyotyping, doctors hope that it will reduce the number of high-risk women who undergo invasive testing unnecessarily.
Invasive testing has an associated risk of miscarriage, and currently results in the deaths of significant numbers of healthy fetuses, since the accuracy of Down’s Syndrome screening tests (to identify high-risk pregnancies) is not perfect. However, karyotyping does have the added benefit of diagnosing additional chromosomal abnormalities that may be present. The ideal product would be a highly accurate, non-invasive test for a range of serious chromosomal defects, but whilst this scenario may eventually be fulfilled, the science is not there yet.
Comment: The publication and product launch mean that Sequenom is currently the market leader in non-invasive testing despite a delay of more than two years beyond their original planned launch date. This followed retraction of previously published study data, apparently due to inaccurate reporting of results. However, rival offerings may be close behind; companies including Verinata Health and Gene Security Network are said to be planning to launch similar products next year.
- Obesity (UK Department of Health)
- Climb National Information Centre for Metabolic Diseases
- World Health Organization
Health workers armed with global positioning systems (GPS) have been helping map the spread of typhoid in Kathmandu, Nepal, described in a 2008 report as ‘the typhoid capital of the world’.
Typhoid is a major public health problem, and taking effective action to curb outbreaks requires careful tracking of cases and how they spread. Tracking outbreaks in Kathmandu has been particularly challenging, as Nepal does not use street names, making it difficult to pinpoint disease clusters.
Researchers used recent advances in DNA sequencing analysis to examine changes in the typhoid genotype, which mutates as it spreads. Plotting the location of outbreaks and mutations on Google Earth showed that disease clusters appear unrelated to population density, and spread was not by direct human to human transmission.
Instead, scientists have identified communal water spouts as the main conduit for contamination. People living at lower water elevation (i.e. downstream) are also at a much higher than average risk of catching the disease.
Dr Jimmy Whitworth, Head of International Activities at the Wellcome Trust, which funded the research, said: "This study, which combines accurate mapping with the latest in genotyping technology, further reinforces the importance of improving the quality of water supplies and infrastructure for sanitation if we are to seriously tackle diseases such as typhoid".
The European Court of Justice has ruled that stem cells derived from human embryos are not patentable.
The decision upholds an earlier ruling to the same effect (see previous news) on the basis that patenting any cells or cell lines derived from the destruction of human embryos would be ethically unacceptable.
However, the court did clarify that the use of human embryos for ‘therapeutic or diagnostic purposes which are applied to the human embryo and are useful to it’ were patentable, but use for scientific research was not.
As expected, European stem cell researchers have reacted angrily to this blow, saying that it will damage research into potential stem cell treatments of serious diseases and effectively drive research overseas.
Professor Oliver Brustle, of Bonn University, over whose patent the case originally arose, said: "With this unfortunate decision, the fruits of years of translational research by European scientists will be wiped away and left to the non-European countries. European researchers may conduct basic research, which is then implemented elsewhere in medical procedures, which will eventually be reimported to Europe. How do I explain this to my students?".
Comment: This case highlights the growing dilemma posed by different national and regional regulations (and ethical concerns) in a global scientific market. As there are strong arguments on either side in cases such as this, the problem is perpetuated, since countries must seek to uphold their own laws and ethical values – but at the same time seek to benefit from medical research to yield beneficial and profitable new treatments.
Following on from a new stem cell paper for which the researchers obtained large numbers of human oocytes (egg cells) by paying donors (see previous news), the Nuffield Council on Bioethics has said that women donors should be paid in the UK too.
In fact the US payments are limited to financial compensation for expenses, and practice varies across the country, but sums can amount to several thousand dollars (see previous news). The Nuffield Council report suggests a level of hundreds rather than thousands of pounds, but say that women ‘who donate eggs for research, like healthy volunteers in clinical trials, undergo medical procedures that involve discomfort, inconvenience and potential risks to their health, in order to contribute to the common good of research’ and deserve compensation.
They also note that donating eggs for research may be less compelling as an altruistic gesture than donating them to infertile women attempting to become pregnant, since the benefits are less immediate. Women donating eggs can also receive discounted fertility treatments of their own, which amounts to thousands of pounds of value.
The report therefore proposes a pilot scheme to try out their proposals, with suitable safeguards to protect donors and associated research on the long-term effects of egg donation.
Comment: The ethics of egg donation are certainly very complex – there is a need to be fair to women who chose to donate for different reasons, and stem cell researchers are keen to see improved supplies of egg cells. However, if women genuinely feel happier about donating eggs to directly help others have children than for research, financial incentives may have little effect – except for those in financial need, in which case there is a danger of compulsion.
- The ethics of stem cells
- International Society for Stem Cell Research
- Stem cells - information from Learn.Genetics
Researchers have created partially patient-specific human embryonic stem (HES) cells by cloning.
Growing human embryos from adult patients is a key goal for many who are trying to develop stem cell therapeutics, as stem cell lines derived from such embryos would be a perfect match for the adults and could be used to treat various diseases. It was reported to have been achieved by South Korean scientist Hwang Woo-Suk, but this work was later discredited (see previous news).
In the latest publication, researchers successfully produced early human embryos by fusing adult skin cell nuclei with donor egg cells. They found that leaving the donor egg cell genetic material in place allowed the resulting cloned embryo to develop to the blastocyst stage – much further than when the donor genetic material was removed, as in previous techniques, and enough to give rise to stem cell lines.
Although the resulting embryos contained too many chromosomes (three sets instead of two) and would not be usable as a source of cells for therapy, the scientists say that, ‘with a reliable source of human oocytes’ it should prove possible to generate stem cells with the correct levels of genetic material.
Comment: Whilst technically interesting, this work raises significant ethical concerns, since the large number of human egg cells (oocytes) it used were procured by paying women donors. Ethical guidelines typically oppose any form of financial inducement for egg donation, which carries health risks for women, and concerns over ethical probity in obtaining human eggs were the first problem to beset the South Korean laboratory (see previous news). However, the scientists said that since women in the US could receive $8000 for egg donation for reproductive purposes, offering the same fee was essential to secure the eggs they wanted.
DNA extracted from the teeth of medieval corpses has helped reveal the genetic code of the germ responsible for the Black Death.
The bacterium, Yersinia pestis, rampaged through Europe in the mid-1300s killing about 50 million people and, scientists say, is the “grandmother’ of all current plague.The research team found few genetic differences between the ancient and modern version of the germ, which now kills around 2,000 people globally each year. The findings give important clues as to the spread of pandemics, suggesting these are caused by a ‘perfect storm’ of circumstances such as the environment and general health of the population, rather than a deadly ‘superbug’ alone. "For so many years, people focused on the pathogen," said Hendrik Poinar, a lead researcher from the study "it’s one thing to talk about the pathogen, but it's another thing to talk about the disease." The process of rebuilding the genetic code was described as ‘not easy’. The teeth were cracked open to reveal biological material including the pathogen’s DNA, which was extracted through a process of purification and enrichment. The researchers believe the techniques they have developed in this work can be used to study the genomes of other ancient diseases. The study was published in Nature
In pioneering work published today, researchers have combined gene therapy with stem cell therapy to correct a genetic liver defect.
Writing in Nature, the research team reports work to combat the genetic disorder alpha-1 antitrypsin deficiency (A1ATD), which is caused by a mutation in the A1AT gene and leads to liver cirrhosis. The condition is relatively common, affecting around 1 person in 2000 in Europe, and in severe cases, the only treatment is a liver transplant.
The researchers took skin cells from A1ATD patients and turned them into induced pluripotent stem (iPS) cells. They then used a zinc-finger nuclease molecule (see previous news) to cut out the mutated part of the A1AT gene and replaced it with a normal sequence. Finally, the iPS cells with the genetic correction were induced to form cells closely resembling normal liver cells, and transplanted into mice. Within a fortnight, some of these new cells has become incorporated into the livers of the mice, appeared to function as normal liver cells, and were producing normal human A1AT proteins.
Comment: Although this research has gone only halfway to actual gene therapy in humans – since they have yet to move to clinical trials showing a therapeutic effect in people – it is a very exciting combination of leading scientific techniques that could ultimately create a treatment breakthrough for A1ATD patients.
The ethics of returning results from research studies was a topic at the 4th annual meeting on Personal genomes at Cold Spring Harbour. An increasing number of individuals are having their DNA sequenced for research projects which may identify genetic variants that have a medical significance for the individual and/or other family members. In most cases researcher are not obliged to report such information to participants; in the US federal law prohibits reporting back of these results unless they are verified in a certified lab. This creates an ethical dilemma for many researchers and is becoming an issue for physicians as well where sequencing is used to inform diagnosis and treatment and the boundaries between research and clinical application become blurred. Although differing views were aired, it is generally felt that this is an important issue to deal with in light of the increasing use of sequencing in both research studies and the clinic (see previous news).
This issue is also discussed in the PHG Foundation’s new report Next Steps in the Sequence which will be launched in London on 24th October.
- Climb National Information Centre for Metabolic Diseases
- Wellcome Trust Sanger Institute
- The Biomarkers Consortium
People are definitely curious about their personal genomic information, according to a survey by Nature magazine.
The survey, which generated 1,588 responses, examined attitudes towards genome sequencing. While only 18.2% of respondents had had their genome sequenced or analysed, 66% of those who hadn’t would take the opportunity should it arise. Curiosity was quoted by both groups as the main single influencing factor. Cost, for these two groups, was the main bar.While half of tests uncovered health risks and almost half uncovered other previously unknown, but non-health related information, 95.5% of those tested reported no negative outcomes from having their genome sequenced or analysed. The most common type of analysis was a genome scan (57.8%), with only 9.0% of those undertaking a test having had their full genome sequenced. However, whole genome sequencing would be the test of choice - 83.6% would opt for this given the opportunity. Scientists dominated the survey sample, although the fields of public health and medicine were also represented. For those who would not have their genome sequenced or analysed, worries about what might be found, concerns about privacy and doubts about the overall usefulness of the information were the strongest deterrents.
A news piece in Nature outlines some of the recent developments in clinical use of whole genome sequencing. Past examples are cited ranging from the identification of mutations causing Miller Syndrome and a secondary genetic disorder in one family (see previous news) to the selection of an appropriate therapy for a woman with leukaemia (see previous news).
Recent research has also produced new synthetic human genome reference sequences, and its use in analysis of genomes from a family with inherited thrombophilia. The new forms of reference sequence were adjusted to represent typical healthy genomes from three different ethnic groups, the better to identify disease-associated variants from a common genetic background. In this instance, researchers were able to identify multiple variants associated with increased risk of blood clotting disorders in an affected father and his daughter, as well as to predict appropriate types and doses of drug treatments.
The scientists and clinicians interviewed in Nature seem sure that widespread clinical adoption is inevitable as the speed of sequencing continues to increase and the costs fall. However, there are concerns about what this will mean in practice, with issues such as incidental (unexpected) findings, a lack of genomic expertise within health systems, and the difficulties of interpreting the clinical implications of highly complex genomic data.
The first definitive analysis of the impact of whole genome sequencing on a health system, the PHG Foundation’s significant new report Next Steps in the Sequence will be launched in London on 24th October. Focusing on the UK National Health Service (NHS), this report considers both recent and likely future technical developments in genome sequencing, which applications will be used first in clinical practice, and the logistical, educational, ethical and economic issues that will arise.
A single gene could be the link to reversing type 2 diabetes, scientists believe.
Researchers at the Garvan Institute in Australia say the gene, known as ID1, appears to be the master switch for other genes involved in insulin production. In mice, the equivalent gene (Id1), normally dormant, is switched on in response to a high-fat diet. In its active mode, it disrupts beta cells that reside in the pancreas and, when fully functioning, express genes that help them secrete insulin. Pancreatic tissue from human diabetes patients contains high levels of the Id1 protein. Dr Ross Laybutt, a member of the research team, said: “Not only does the presence of Id1 appear to initiate all the other gene expression changes that take place in dysfunctional beta cells, its absence completely protects the beta cell”. Id1 is already known to promote growth of cancer cells, and a chemical compound to keep the gene in its switched-off mode is being used safely in cancer patients. The team at the Garvan will test the compound on diabetic mice to see if it can delay the onset of diabetes or improve insulin secretion.
This research is in the early stages, but this gene could prove to be a valuable drug target in the hunt for effective new treatments for diabetes, which along with overweight and obesity is a rapidly expanding public health problem in developed countries.
- Academy of Medical Sciences
- European Science Foundation
- UNESCO Ethics of Science and Technology Programme
Excessive EU bureaucracy is hampering research into new treatments and doing nothing to enhance the safety of patients, say medical research organisations.
The group of 16 organisations - including the European Organisation for Research and Treatment of Cancer and the UK Medical Research Council – have asked the EU to review Clinical Trials Directive 2001/20/EC. The directive aims to standardise the conduct of clinical trials that investigate the safety or effectiveness of a medicinal product in humans. However, the group says the ‘one size fits all’ approach– where trials on well-understood drugs are regulated in the same way as trials of completely new drugs - pushes up the time and costs of conducting clinical trials. Figures from Cancer Research UK’s Drug Development Office comparing 2003 and 2007 (when the directive had taken effect) showed a 65% increase in the time it took researchers to get approval for studies and a 75% increase in administrative costs. They also argue that varying interpretations of the directive limit multinational trials. The group recommends a proportionate approach to the assessment and regulatory requirements of clinical trials that takes into account previous experience with the agent being tested and the patient population.
The group recommends a proportionate approach to the assessment and regulatory requirements of clinical trials that takes into account previous experience with the agent being tested and the patient population. These proposals seem to strike a reasonable balance between maintaining the safety of trial participants and providing a supportive environment for testing new interventions.
- Born Healthy
- US National Newborn Screening and Genetics Resource Center (NNSGRC)
- UK Newborn Screening Programme Centre
The Secretary’s Advisory Committee on Heritable Disorders in Newborns and Children (SACHDNC) has recommended the inclusion of Critical Congenital Heart Disease (CCHD) as one of the conditions that should be included in all newborn screening programmes in the US.
Congenital forms of heart disease accounts for around 3% of infant deaths in the US. Most babies born with CCHD are identified prenatally or soon after birth due to observed heart anomalies or symptoms, but some cases are not picked up until later. Many of the conditions that collectively make up CCHD can be treated.
The US Health and Human Services (HHS) Secretary Kathleen Sebelius has now decided to adopt the SACHDNC recommendation and include a pulse oximetry test for CCHD in newborn screening programmes, along with existing blood spot analysis and hearing tests. This approach was endorsed by the American Academy of Pediatrics (AAP) earlier this year.
Comment: Even countries with well-developed health systems such as the US and UK may be able to improve detection and care for congenital disorders, also known as birth defects, by building on new evidence as it becomes available. The Born Healthy campaign established by the PHG Foundation aims to make prevention, diagnosis and care for birth defects a priority around the world, and provides a new tool to help plan appropriate services in low and middle income countries.
The international Structural Genomics Consortium (SGC) has announced confirmation of a total of more than £31 million in new funding.
Founded in 2004 and based in Oxford, UK and Toronto, Canada, the SGC is a non-profit public-private research partnership that drives the discovery of new medicines via scientific research, most notably solving the structures of proteins of biomedical importance (human and pathogen) to facilitate drug development. Open-access publishing of research makes new findings freely available to the whole scientific community.
Companies Eli Lilly Canada and Pfizer join previous consortium funders (the Canadian Institutes for Health Research, GlaxoSmithKline, the Novartis Research Foundation, the Ontario Ministry of Research and Innovation, and the Wellcome Trust) in a joint commitment of £31 million funds and resources worth a further £6 million over the next four years. This will fund research including a new programme on proteins involved in epigenetic mechanisms of disease.
Comment: The SGC has made a substantial contribution to biomedical knowledge already, releasing the structures of over 1200 proteins. This new phase of the project will be of broad interest for both basic and applied biomedical research and development efforts.
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The International Mouse Phenotyping Consortium (IMPC), consisting of 15 international members has begun the first phase of a ten year project aimed at better understanding the function of every gene in a mouse. This phase of the project aims to create 5000 different knock-out mice and study their phenotypic characteristics and gather clinical information. Each of the consortium members will use standardised techniques to study these mice and deposit their findings in a single database which will be available to other members of the scientific community. The clinical investigations on the mice have been designed so that they can also provide information relevant to human diseases such as heart disease and diabetes.
Mice and humans share many genes and mouse models are often used to gain a better understanding of human diseases. This large scale project will create a valuable resource for disease researchers as well as pharmaceutical companies. It can be used for a number of purposes including determining functions of genes, creating better mouse models of disease and for identifying and validating drug targets.
The German Ethics Council has issued recommendations on the use of animals containing human material (ACHM).
The report on this issue reportedly takes an in-depth and philosophical view of what counts as human and which genetic alterations involving animal material constitute a violation of human dignity, in comparison with the recent report from the UK Academy of Medical Sciences on the same issue (see previous news), which was more concerned with public acceptability.
The panel behind the recommendations came to broadly similar conclusions as the UK group, distinguishing between standard research applications such as the use of transgenic mice containing human genes, which is considered acceptable, unethical practices requiring complete prohibition, and intermediate scenarios requiring regulatory oversight.
However, the German recommendations include a complete ban on fertilisation involving human eggs or sperm in an animal, which the UK group cited as an example of something that would have to be considered by the regulator. The German council also recommended prohibition of any introduction of animal material to the human germline or implantation of an animal embryo in a human.
No consensus was reached on the creation of human-animal chimeric embryos produced by insertion of a human cell nucleus into an animal egg cell with the nucleus removed, a technique that is permitted in the UK subject to regulatory approval and licensing (see previous news). Just over half the council were in favour of allowing this approach, despite German law forbidding research that harms human embryos.
Comment: Whilst Germany is typically very conservative in ethical terms, these new recommendations appear relatively liberal. One council member reportedly commented that the report ‘strikes a fair balance between public accountability and burdening scientists with too many bureaucratic hurdles’.
Research articles
- A Guide to Your Genome
- The ENCODE Project: ENCyclopedia Of DNA Elements
- Wellcome Trust Human Genome website
| Study: | A high-resolution map of human evolutionary constraint using 29 mammals |
| By: | et al. (64 authors total) |
| In: | Nature |
| Link: | http://dx.doi.org/doi:10.1038/nature10530 |
Compare DNA sequences from different mammals in order to identify DNA regions that have a regulatory role and how they function.
The genomes of 29 different mammals were sequenced and compared to identify sequences that had not changed overtime in the different species. The function of these sequences was determined through looking at their overlap with known genes, specific patterns of conservation and comparisons with experimental data sets.
Over 3.5 million constrained elements were identified – these encompass approximately 4% of the human genome. Function was assigned to around 60% of these elements, this ranged from previously undetected exons to new RNA structures. The function of the remaining 40% is unknown.
Such studies allow identification of elements which are evolutionarily conserved across species as well as those that have changed. This together with information from studies on disease genetics and biochemistry can provide a better understanding of human biology. In addition knowledge of these elements can be used to prioritize disease-associated variants.
The majority of the human genome consists of non-coding regions that are thought to play an important regulatory role however, until now the function of many of these regions was unknown. This study improves our understanding of the human genome and provides an important resource for many researchers including those interested in human diseases, by allowing them to elucidate how mutations in these regions are involved in health and disease.
- Professor Dennis Lo
- Cell-free fetal nucleic acids for non-invasive prenatal diagnosis
- Down's Syndrome Association (UK)
| Study: | DNA sequencing of maternal plasma to detect Down syndrome: An international clinical validation study |
| By: | et al. (12 authors total) |
| In: | Genetics in Medicine |
| Link: | http://dx.doi.org/10.1097/GIM.0b013e3182368a0e |
To clinically validate prenatal screening for Down’s syndrome using measurement of circulating cell-free DNA in maternal plasma, to improve existing diagnostic procedures.
A study was designed with a group of almost 5,000 pregnancies with high risk for Down’s syndrome based on maternal age, family history, positive serum analysis and/or sonographic screening.Maternal blood samples were drawn and sent to two independent, CLIA-certified laboratories for testing using the massively parallel shotgun sequencing method (MPSS). The results were compared to fetal karyotyping.
Once compared to fetal karyotyping the Down syndrome detection rate was 98.6% and the false-positive rate was 0.20%. Testing failed only in 0.8% of pregnancies. The cases were distributed evenly between the first and second trimester of pregnancy.
In high-risk pregnancies, nearly all cases of Down syndrome can be detected from cell-free, maternal plasma DNA with a very low false-positive rate. This study provides evidence of clinical validity of this test and potential to substantially reduce the need for invasive diagnostic procedures and related pregnancy losses.
This study follows and enhances previous attempts to validate the use of non-invasive prenatal testing for Down’s syndrome (see previous news). This is particularly relevant in the current context of sequencing costs falling at a high pace. With this validation study we move even closer to the potential use of this powerful technique in a clinical setting, which could also reduce the amount of necessary invasive diagnostic procedures carrying a non-negligible risk of miscarriage.
| Study: | Genome-wide association study identifies three new melanoma susceptibility loci. |
| By: | et al. (76 authors total) |
| In: | Nature Genetics |
| Link: | http://dx.doi.org/10.1038/ng.959 |
The researchers from the melanoma genetics consortium undertook a genome-wide association study. The discovery phase involved nearly 3,000 melanoma patients of European and Israeli descent and over 7,500 controls of European descent. Single nucleotide polymorphisms (SNPs) showing evidence of association were further tested in a replication phase of 1,500 melanoma patients and 2,000 controls of European descent with data from both phases combined in a meta-analysis.
In addition to confirming several previously identified loci, the discovery phase highlighted seven further loci showing association. SNPs within these seven regions were genotyped in the replication phase with the combined analysis showing strong evidence of association for three loci located on chromosomes 2, 11, and 21 with a potential fourth locus also on chromosome 11.
The study reports three new loci associated with melanoma bringing the total known loci to 11. Half of these loci are thought to act through the skin pigmentation phenotype and a further three through nevus phenotype, suggesting that “at least two of the newly identified loci appear to influence risk through a new mechanism, opening up potential directions for melanoma research”.
This study not only confirmed several known loci but also identified three new associations that show no real link to well-known melanoma risk factors such as skin pigmentation and nevus count. Two of the three associations near the CASP8 and ATM genes have been previously linked to other cancers but the third locus on chromosome 21 near the MX2 gene has not. The study authors note that with larger study numbers it may be possible to identify additional novel loci further suggesting that alternative unknown mechanisms may play a role in disease aetiology, with further research required.
| Study: | Transcriptional modulator H2A histone family, member Y (H2AFY) marks Huntington disease activity in man and mouse |
| By: | et al. (12 authors total) |
| In: | Proceedings of the National Academy of Sciences |
| Link: | http://dx.doi.org/ 10.1073/pnas.1104409108 |
To identify biomarkers for Huntington’s disease (HD) for use in monitoring disease activity and the evaluation of new medications.
Transcriptome data from blood samples from 8 HD patients and 111 controls (including 83 with different neurodegenerative diseases) were analysed.
The chromatin regulator H2AFY was overexpressed in the blood and brains of HD patients compared with controls, a result that was replicated in independent studies of 96 people (including 36 HD patients and 9 HD mutation carriers without disease), and a 2-3 year study of a further 25 HD patients and 21 controls.
If confirmed in further studies, H2AFY may ‘become a biomarker of disease activity and therapeutic response’ that can aid drug trials in identifying promising new treatments for HD. The protein may even play a role in the disruption of chromatin structure in HD, along with the mutant huntingtin protein.
Huntington's disease (HD) is a severe neurodegenerative genetic disease with unusually high penetrance – that is, virtually everyone who inherits a mutation in the huntingtin gene will eventually develop the disease in later life. An effective treatment is urgently needed, so if this latest discovery is replicated and can help efforts to develop one, it is a very important step forward for families affected by this devastating condition.
| Study: | Large-Scale Gene-Centric Analysis Identifies Novel Variants for Coronary Artery Disease |
| By: | et al. (104 authors total) |
| In: | PLoS Genetics |
| Link: | http://dx.doi.org/10.1371/journal.pgen.1002260 |
To undertake genetic analysis for both common and low frequency genetic variants associated with Coronary Artery Disease (CAD).
The team genotyped 11,202 European and 4394 South Asian participants from 12 current coronary artery disease and myocardial infarct studies. They analysed 2100 candidate genes, looking for novel and previously known genetic associations with CAD.
Results refuted previous genetic association study results whilst identifying five novel genetic variants. These were found downstream of the LIPA gene – implicated in the breakdown of cholesterol and triglycerides; the ABCG5 gene – associated with biliary removal of sterols; and the IL-5 gene – an inflammatory protein that may protect against atherosclerosis.
Discovery of novel genetic associations may bring to light important cellular pathways contributing to coronary heart disease. This analysis of known variants refutes some of the ambiguous results seen in previous genome wide association studies.
This study was impressive, taking a large sample from an ethnically diverse population. The results have shown new variants, which will require further study in order to fully confirm their role in heart disease. The genes implicated in CAD by these variants all encode proteins associated with cholesterol and triglyceride regulation, which appears to be a promising discovery. Most notably, the IL-5 gene has been implicated in atheroprotection and the LIPA gene, encodes an enzyme that breaks down cholesterol (cholesterol esterase). However, the LIPA genetic variant, which up regulates the enzyme, showed no altered lipid activity in participants carrying the variant. Thus, the pathways and mechanisms of action for all these genes will have to be deciphered before any drugs are to be produced to counter the effects of their altered functioning.
| Study: | Genomewide association between GLCCI1 and response to glucocorticoid therapy in asthma. |
| By: | et al. (24 authors total) |
| In: | The New England Journal of Medicine |
| Link: | http://dx.doi.org/10.1056/NEJMoa0911353 |
The researchers used a family-based screening design within a randomized controlled trial involving 118 trios (child and both parents) randomly assigned to inhaled budesonide to assess response over time. Data on over 500,000 single nucleotide polymorphisms (SNPs) were available, with replication of initial findings conducted in patients from a further three trials. Additional replication was also conducted along with functional work.
Thirteen SNPs were identified for replication of which twelve were successfully genotyped in the replication populations. One SNP, rs37972, was found to be associated with changes to FEV1 in three of the four populations tested. Whilst conducting functional work on this SNP, an additional SNP (rs37973) in complete linkage disequilibrium was also identified and that both these SNPs lie in the promoter region of the GLCCI1 gene. The rs37973 SNP was also shown to be associated with a significant decrease in FEV1, consistent with rs37972.
The study authors conclude from their work that “it is fully plausible that rs37973 causes decremental response to inhaled glucocorticoids in patients with asthma through changes in GLCC1 expression” and that patients “who were homozygous for the mutant allele were about two and a half times as likely to have a poor response to inhaled glucocorticoids as were those who were homozygous for the wild-type allele”.
With around a third of asthma patients failing to benefit from inhaled glucocorticoid therapy, a means of identifying that third before prescribing medication would no doubt be advantageous. This study takes us a step closer to this possibility although by no means is it the complete answer. As the study authors themselves note, their study has several limitations including size and lack of data in non-white ethnic groups. The rs37973 variant only accounted for less than 7% of the variability observed within their study suggesting that additional functional variants may also be present within the GLCCI1 gene and that further detailed studies should be conducted in addition to further testing of this SNP as a potential screening tool for inhaled glucocorticoid therapy for asthma patients.
New reviews and commentaries
Genomics, health care, and society.
Hudson KL. N Engl J Med. 2011 Sep 15;365(11):1033-41
Is it time to commence newborn screening for congenital adrenal hyperplasia in Australia?
Wu JY et al. Med J Aust. 2011 Sep 5;195(5):260-262.
Genomics education for health care professionals in the 21st century.
Feero WG, Green ED. JAMA. 2011 Sep 7;306(9):989-90.
Understanding the contribution of synonymous mutations to human disease.
Sauna ZE, Kimchi-Sarfaty C. Nat Rev Genet. 2011 Aug 31;12(10):683-91.
Assessing and managing risk when sharing aggregate genetic variant data.
Craig DW et al. Nat Rev Genet. 2011 Sep 16;12(10):730-6.
Evolving research and stakeholder perspectives on pharmacogenomics.
Beitelshees AL, Veenstra DL. JAMA. 2011 306(11):1252-3.
Health technologies and innovation in the global health arena.
Sinha SR, Barry M. N Engl J Med. 2011 Sep 1;365(9):779-82.
Cancer: Let sleeping DNA lie.
Venkitaraman AR. Nature. 2011 Sep 7;477(7363):169-70.
Demystifying DNA demethylation.
Nabel CS, Kohli RM. Science. 2011 Sep 2;333(6047):1229-30
A grand challenge in biology.
Alberts B. Science. 2011 Sep 2;333(6047):1200.
Where is public health leadership in England?
Horton R. 2011 378(9796): 1060
Disease priorities.
Nature. 2011 Sep 14;477(7364):250.
Mendelian disorders of membrane trafficking.
De Matteis MA, Luini A. N Engl J Med. 2011 Sep 8;365(10):927-38.
Health inequalities and cystic fibrosis.
Taylor-Robinson D, Schechter MS. BMJ. 2011 Aug 23;343:d4818.
Rare and common LRRK2 exonic variants in Parkinson's disease.
Tan EK. Lancet Neurol. 2011 Aug 30. [Epub ahead of print]
Aboriginal genome shows two-wave settlement of Asia.
Gibbons A. Science. 2011 Sep 23;333(6050):1689-91.
A DNA Tower of Babel
