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.

In the news

News story   |   Published 14 February 2007

The UK Stem Cell Bank and the US National Stem Cell Bank (NSCB) have announced they will work together on common goals such as promoting research, forming international standards and making distribution of their stem cell lines more efficient. (see news story). Glyn Stacey, director of the UK Stem Cell Bank stated, “Our main focuses are very similar: we want to promote the research and development of potential therapies in the future.” Together the banks hope to foster a rewarding partnership that will advance this form of research.

The UK Stem Cell Bank was created in 2004 (see news story). It is hosted by the UK National Institute for Biological Standards and Control and funded by the Medical Research Council and the Biotechnology and Biological Sciences Research Council. It houses human stem cells lines of all types and “…has been developed to supply well characterised cell lines under appropriate and accredited quality systems both for basic research and for the development of clinical applications.” Currently it has four stem cell lines available for distribution. Researchers must apply to the Bank’s Steering Committee for approval to access a stem cell line.

The NSCB opened in 2005; it is located at the WiCell Research Institute, a non-profit body that is a supporting organisation of the University of Wisconsin, Madison. NSCB was created to acquire, characterise and distribute 13 of the 21 human embryonic stem cell lines which are eligible for use in federal funded projects. President Bush’s stem cell policy states that that human embryonic stem cell lines created prior to 9 August 2001 could continue to be used in research projects funded by federal money, provided that the embryo involved was created for reproductive purposes, informed consent was given and there was no financial inducement to donate. After this date federal money can not be used to create new embryonic stem cell lines (see news story).


News story   |   Published 15 February 2007

US Congressman Xavier Becerra, a Democrat from California, has introduced a draft bill, the Genomic Research and Accessibility Act in the US House of Representatives to prohibit the patenting of human genetic material (see press release). It is cosponsored by Republican Congressman Dave Weldon from Florida. The bill text is short, calling for chapter 10 of the title 35 of the United States Code, which deals with the patentability of inventions, to be amended to add a section prohibiting patents on human genetic material. Specifically the bill text states, “Notwithstanding any other provision of law, no patent may be obtained for a nucleotide sequence, or its functions or correlations, or the naturally occurring products it specifies.” The bill also says that this amendment will not apply to patents already issued prior to the date the legislation is enacted into law.

The concern is the belief that gene patents are hindering scientific research. According to the press release, twenty percent of the human genome, which is made up of about 35,000 genes, is covered by patents granted by the US Patent and Trademark Office. “One-fifth of the blueprint that makes up you…me…my children…your children…all of us…is owned by someone else. And we have absolutely no say in what those entities do with our genes,” stated Congressman Becerra. He believes this legislation will “…fix a regulatory mistake…” and will not hamper innovation, but will encourage it. There are conflicting views on this issue. A recent study on the global impact of gene patenting, funded by the EU Sixth Framework Programme, indicated that it was probably too early to find evidence that patents were hindering research and access to healthcare (see news story).

The bill has been referred to the House of Representatives Committee on the Judiciary for further discussion. In order to become law the bill will have to be passed by both the House and the Senate and then signed by the President. There is no guarantee this legislation will gather favour with other members of Congress. Many other genetics-related bills, including ones on genetic discrimination (see news story), have never successfully made it through the legislative process.


News story   |   By Dr Philippa Brice   |   Published 13 February 2007

The latest contribution to the field of genetic profiling of human cancers is a new paper in the advanced online edition of Nature Genetics. There have been many papers concerned with the application of microarray analysis to identify patterns of gene expression associated with different molecular subtypes of cancer, and the development of prognostic indicators based on the expression of key sets of genes. The new work by a team of scientists based at the Dana-Farber Cancer Institute in the US takes a slightly different approach by setting out a form of genetic tumour screening for the presence of key mutations that could direct the development of novel, genetically targeted therapeutics.

Overall, there are hundreds of potential mutations in multiple oncogenes that may direct the formation and progression of cancers. However, the researchers theorized that by selecting genetic assays for the most common mutations in major oncogenes, it should be possible to identify a large proportion of oncogenic mutations with a limited number of assays. They therefore employed high-throughput genotyping processes to detect the presence of 238 previously characterized oncogenic mutations (in seventeen key oncogenes) in a total of 1000 human tumour samples [Thomas RK et al. (2007) Nat Genet. Feb 11; Epub ahead of print]. The oncogenes selected for analysis were all of high prevalence, or had established associations with clinical features or therapeutic responses.

Mutations were identified in around a third of the samples, and included novel mutations as well as sets of different mutations that tended to occur together. New insights into the genetic nature of different tumours may aid the development of new therapeutics targeted to these unique genetic features. The total cost of mutation profiling for each sample in the study was reported to be in the region of $50-$100 (approximately £25-£50). The research team proposes that the technique has clinical potential as a rapid, cost-effective and accurate means of correctly diagnosing cancer; in the future, by determining the genetic tumour profile, it may also be possible to select the most appropriate therapeutic. Lead author Dr Levi Garraway said: "It is a step toward the day when cancer patients will routinely have their tumors scanned for specific mutations, and treatment will be based on the cancer's particular genetic profile" (see press release).


News story   |   By PHG Foundation   |   Published 13 February 2007

A new report in the advance online version of Science reports reversal of Rett syndrome symptoms in mice by the reactivation of the MECP2 gene.

 Rett syndrome is a dominantly inherited autism spectrum disorder that mainly affects girls, caused by mutation of the MECP2 gene located on the X chromosome. The syndrome is associated with neurological problems, which result in progressive loss of mobility and cognitive development from early childhood; breathing irregularities are also common.


 Researchers created a mouse model of the disease by blocking expression of the MECP2 gene; affected mice developed Rett-like symptoms including impaired mobility and breathing difficulties. They report that reactivation of the MECP2 gene in affected mice caused rapid disappearance of most of the symptoms.This work does not herald an imminent therapy for Rett syndrome, as the technique could not be used in humans, but does suggest that the neurological symptoms are theoretically reversible. Previously, it was assumed that the expression of mutated Mecp2 protein during development caused permanent neurological damage. This could also have implications for other autism spectrum disorders.

 

Keywords : autismsyndromesGene Therapy

News story   |   By Dr Philippa Brice   |   Published 8 February 2007

The Food and Drug Administration (FDA) has approved the Agendia MammaPrint® test for marketing within the US (see press release). MammaPrint® is a microarray-based prognostic test that analyses expression of a set of seventy key genes in breast tumour cells to predict the risk of metastasis. Developed by Netherlands-based company Agendia, the test has been available since 2005, and guides therapy by indicating which lymph node-negative breast cancer patients are likely to require chemotherapy in addition to surgical intervention.

The test is the first In Vitro Diagnostic Multivariate Index Assay (IVDMIA) to receive market clearance from the FDA under new guidance developed for the regulation of complex molecular tests that assess the expression of multiple genes (see previous news story). Previously, tests developed and administered by single companies have been exempt from normal FDA regulation, but it was considered that tests based on more complex systems such as microarray analysis required scrutiny to ensure maximum safety and efficacy, and that tests can be clearly interpreted by clinicians.


News story   |   By Dr Philippa Brice   |   Published 8 February 2007

The UK Academy of Medical Sciences and Royal Academy of Engineering have published a new joint report: Systems Biology: a vision for engineering and medicine. Systems biology is a relatively new field that applies computer modelling techniques and systems engineering concepts to biological research, by combining and integrating information from multiple sources (for example, genomic, proteomic and metabolomic information). Such approaches are proving necessary to adequately consider the vast array of interacting networks that operate in the human body. The function of cells and organs in health and disease in terms of their interactions with other cells, organs and systems within the body is thought to hold the key to a wealth of valuable information in terms of understanding, predicting, preventing and treating different forms of disease. It is already being used in pharmaceutical drug discovery and development. Systems biology also has wider applications, such as in the development of biofuels.

The report hails systems biology as a groundbreaking new approach to scientific research in medicine and engineering” and calls for immediate efforts to ensure that the UK is at the forefront of international progress. Joint chair of the working group Sir Colin Dollery warned that: “Success could make the UK a leader in a key field; failure could have serious repercussions on scientific and economic progress with the UK losing its competitive edge over other countries such as the US and Japan" (see press release).Specifically, the report calls for an investment of £325 million over the next ten years, to establish between three and five new systems biology centers of excellence; in addition, the report also calls for reforms to higher education and traditional working practices to ensure that there are enough suitably qualified researchers. Joint chair of the working group Professor Richard Kitney commented: “The UK can become a leader in this field, but institutions must overcome the barriers posed by traditional research structures which slow down interdisciplinary work. It should be natural for a molecular biologist to work closely with engineers, mathematicians and computer imaging specialists” (see press release).

News story   |   By Dr Philippa Brice   |   Published 8 February 2007

The annual audit of activity in UK National Health Service genetics laboratories for the year 2005-6 has been completed by the Clinical Molecular Genetics Society (CMGS). A total of more than 78600 postnatal tests were carried out, excluding those for leukaemia and DNA storage (banking); this represents a significant rise from the previous annual total (63,500 for the 2004-5 audit; see previous news story). The most frequently performed tests were for cystic fibrosis (15%) and Fragile X syndrome (13.6%), although these were smaller proportions of the total tests than last year (21% and 19% of the total, respectively). As for 2004-5, the next most common test indications were familial cancer BRCA gene mutations (6.9%), hereditary haemochromatosis HFE gene mutations (6.6%), and the Factor V Leiden mutation (3.6%). In all, more than 340 different types of test were carried out.

Prenatal testing levels have also risen, with a total of 1511 reports recorded (excluding those for aneuploidy) compared with 1327 last year and 1260 the year before. The distribution of prenatal test indications has changed, with sickle-cell anaemia now representing the most common test (24% of the total; previously 21%) and the previous lead indication, cystic fibrosis, dropping from 32% to 22% of the total.


Predictive and confirmatory testing is also recorded in the audit; this data is used by the Genetics and Insurance Committee (GAIC) to report to the Association of British Insurers. The total number of such tests has almost doubled since the previous year, increasing from 2586 to 4778, for some 85 different disorders, although tests for familial forms of cancer represent more than half of the total number of tests performed. Familial breast cancer (BRCA1/2 mutations) was as previously the single most common predictive test (more than 1700 in total), followed by tests for the familial colorectal cancers HNPCC and FAP (around 600 and 400, respectively), now more frequent than those for Huntingdon’s Disease, which was previously the second most commonly performed predictive test.


News story   |   By Dr Philippa Brice   |   Published 8 February 2007

UK Health Minister Ivan Lewis has announced that all newborn babies in England will be offered screening for the metabolic disorder Medium Chain Acyl CoA Dehydrogenase Deficiency (MCADD) as part of standard newborn screening by March 2009  (see press release). MCADD is an autosomal recessive genetic disorder that affects a key metabolic enzyme, impairing the ability to maintain normal blood sugar levels during metabolic stress; the condition is associated with high death rates and severe neurological damage in affected children. It is rare, affecting between one in 10,000 and one in 20,000 births, but early detection and simple clinical management substantially reduces the risk of death and disability.


The UK National Screening Committee (NSC) has been running a pilot study for newborn MCADD screening, with over a million babies screened since 2004; their final report is due in 2008, but sufficient evidence of clinical and cost efficacy has already accumulated for the NSC to recommend the implementation of a national screening programme for the disorder. National Clinical Director for Children Sheila Shribman said: "Evidence shows that screening newborn babies for this condition will not only save lives but it can significantly improve their quality of life. Simple treatment through dietary management will substantially reduce the risk

of death and the risk of acute, serious illness" (see BBC news report).

 

The MCADD testing will form part of the standard Newborn Screening Programme in England, which tests ‘heel-prick’ bloodspot samples from babies for the genetic diseases phenylketonuria, congenital hypothyroidism, sickle cell disorders and cystic fibrosis.


News story   |   Published 7 February 2007

Researchers from the PATGEN Project (The Patenting of Human DNA: Global Trends in Commercial and Public Activity) have released their final report. The project, funded under the EU Sixth Framework Programme, aimed “…to provide a global and comprehensive quantitative and qualitative analysis of patents, filed and/or granted during the period 1980-2003, which claim human DNA sequences.” The authors note that there have been widespread concerns that DNA patents will have an inhibitory effect on research, innovation and access to healthcare. However, while it may be too soon for those effects to be seen, there is now the opportunity to create a dataset on which key analyses can be conducted. Information was collected on patents granted by the three leading patent offices, the US, European and Japanese patent offices. In addition, qualitative interviews were conducted with 30 patent owning organisations from both the private and public sector.

The authors found that of the approximately 6,000 patent ‘families’ examined (the patents and patent applications associated with a single patent application), 94% contained a US patent, while only 13% had a European and 9% had a Japanese patent. The authors believe this reflects several factors including the US’ larger market size and that it is less expensive to get a patent granted in the US. As well, there are more stringent examination processes in Europe and Japan and both patent offices are slower at processing applications than in the US. Patents were most likely granted for research tools, diagnostics and therapeutics, with research tools in the majority. Most patents are held by US-based assignees (organisations or people). Many assignees had yet to exploit their patents; the authors found that 30% of patents granted in the 1990s in the US had been abandoned by 2005, due to commercial or technical reasons.

Assignees highlighted some of the problems in the field of DNA patenting. Patent offices had difficulties examining complex cases as well as keeping up with the large volume of applications. There is also public opposition to some human DNA patents. They also believed that “…the bar to patentability had been raised across patent offices,” due to new guidelines published by the US Patent and Trademark Office on the utility requirement for patentability and the reluctance to accept patents claiming large numbers of DNA sequence. Also, claims awarded in DNA patents had been narrowed and, in future, those interviewed expected that greater biological data will be needed to obtain claims. Therefore, there was an expectation that patenting downstream inventions, such as drugs, will be more attractive than patenting DNA-related research tools.

The authors note that, “…with the number of patent applications in decline, more stringent examination procedures, and the likely restriction of the scope of granted patents by case law, suggest that the negative impact of DNA patenting may turn out to be more limited than some had feared.” However, further research is needed, for instance, into the disparity between the number of US and European patents and whether this is adversely affecting the potential competitiveness of some European companies.


News story   |   Published 4 February 2007

Virgin founder Sir Richard Branson has launched a new company, Virgin Health Bank, for families who wish to store their newborns’ umbilical cord blood (see news report). The stem cells found in cord blood are used to treat diseases such as leukaemia. Some parents seem cord blood banking as an ‘insurance policy’ as stem cell research may provide treatments and perhaps cures for many more diseases in the future. Using one’s own cells in treatments is preferable as finding donor tissue that is a close match is often difficult and tissue rejection is a possibility. Therefore private cord blood banking has grown over the recent years. Clients of Virgin Health Bank will pay approximately £1500 to bank their child’s cord blood for a period of 20 years. 

 

There are several other such companies in existence but Virgin Health Bank states they are different. The Bank will act as a dual public/private facility. The cord blood will be divided into two portions – one portion will be put aside for the private use of the family and the other will be put into a public stem cell bank where the donation will be available for use by the family or by those in need of a donor transplant.  Sir Richard has also stated that profits from the Bank will go to a charitable foundation to fund initiatives to foster the use of stem cells. Another need is to increase availability for underrepresented ethnic populations.

 

The Royal College of Obstetricians and Gynaecologists (RCOG) has responded to the launch of the Bank, reconfirming its belief that there is little evidence to support private cord blood banking. In its June 2006 opinion paper it notes that the likelihood of a child from a low-risk family needing the banked cells is very low and therefore should be carefully considered. There are other options. The NHS has a publicly-available cord blood bank, albeit with a limited storage capacity. It currently has approximately 7000 donations. In addition, families who are a high risk for certain diseases, such as Fanconi anaemia, already have access to cord blood storage. The RCOG is also concerned about the impact the collection process might have on the mother and child during the birth process, as the collection “…could jeopardise the mother’s or the baby’s health.” Those collecting the cord blood should have proper training and contamination issues must be considered.  However, it “applauded” the intention of Virgin Health Bank to increase the availability of cord blood through its public bank. The RCOG plans to examine routine private cord blood banking further and intends to publish a report later this year. The Royal College of Midwives also acknowledges that many maternity units do not have policies in place regarding the collection of cord blood.

Keywords : Human TissueStem Cells

Research articles

Research article   |   By Dr Philippa Brice   |   Published 14 February 2007

Some laboratories already use the presence of free fetal DNA present in the maternal bloodstream to determine fetal sex, and there is a great deal of interest in exploiting the existence of circulating fetal DNA for other forms of non-invasive prenatal genetic analysis. A recent paper in The Lancet reports a new technique of determining the chromosomal copy number of fetuses from maternal blood samples.

 

Single nucleotide polymorphisms (SNPs) – sites of common genetic variation between individuals – were used to distinguish fetal from maternal DNA in each sample. The researchers then calculated the ratio of the unique fetal signal based on these SNPs to the combined maternal and fetal signal, and found that three of the samples analysed showed a discrepancy between the fetal and maternal levels of SNPs located on chromosomes 13 and 21, suggestive of the presence of aneuploidy (abnormal chromosomal copy number) in the fetus. Subsequently, it was shown that the chromosomal number had been correctly determined in 58 of the 60 samples tested; one case of trisomy 21 was not detected, and trisomy 21 was indicated in one normal fetus. The authors propose that, with further refinement, this method could be a useful complement to current prenatal screening and diagnostic tests [Dhallan et al. (2007) Lancet 369(9560):474-81].

 

Comment: The utility of the technique described in this paper depends on the sensitivity and specificity, and to determine this, a trial of a much larger number of pregnancies would be required to calculate the true false negative and false positive rate. However, this and other reports together suggest that the prospects for non-invasive prenatal diagnosis of genetic abnormalities are good.


New reviews and commentaries

New Reviews and Commentaries, 13 February 2007

Reviews & commentaries : by Dr Philippa Brice

The most recent edition of the English language Italian Journal of Public Health [Ital J Public Health 3(3-4)] is a special feature edition on Public Health Genomics, including an editorial on Public health genomics in Europe, and theme papers on various aspects of genomics, medicine and public health.

Huntington's disease. Walker FO (2007) Lancet 369(9557): 218-28. Full review including genetics and epidemiology, genetic testing and experimental treatments (PubMed).

Sorting out breast-cancer gene signatures. Massague J (2007) N Engl J Med. 356(3):294-7. Commentary accompanying report of a novel prognostic gene expression signature for different types of cancer, considering general prospects for clinical applications (PubMed).

Molecular signatures of lung cancer - toward personalized therapy. Herbst RS and Lippman SM (2007) N Engl J Med. 356(1):76-8. Editorial on another report of prognostic gene signature, this time for a form of lung cancer, and predicting future developments combining genomic, proteomic and clinical parameters to direct drug design and personalized therapeutics (PubMed).

Wilson's disease. Ala A et al. (2007) Lancet 369(9559):397-408. Review of this progressive genetic disease, which is caused by defective copper metabolism (PubMed).

National collaborative study groups: structure, benefits gained and potential for rare genetic diseases. Moore TB and McCabe ER (2006) Genet Med. 8(12):793-6. Commentary looking at the history of paediatric cancer trial groups as a model for establishing a similar study group for rare forms of genetic disease (PubMed).

Creating partnerships and improving health care: the role of genetic advocacy groups. Cody JD (2006) Genet Med. 8(12):797-9. Commentary based on personal experience of establishing the Chromosome 18 Registry and Research Society and on the benefits of creating such partnerships between clinicians and patients for different genetic conditions (PubMed).

The impact of CYP allelic variation on antidepressant metabolism: a review. Black Iii JL, O'Kane DJ and Mrazek DA (2007) Expert Opin Drug Metab Toxicol 3(1):21-31. Review of the pharmacogenomics of antidepressant medication (PubMed).

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New reviews and commentaries, 6 February 2007

Reviews & commentaries : by Dr Philippa Brice

Genetics of ischaemic stroke. Dichgans M (2007) Lancet Neurol 6(2):149-61 Review (PubMed).

The genetics of the polycystic ovary syndrome. Urbanek M (2007) Nat Clin Pract Endocrinol Metab 3(2):103-11 Review (PubMed)

The evolution of gene regulation by transcription factors and microRNAs. Chen K and Rajewsky N (2007) Nat Rev Genet. 8(2):93-103. Review (PubMed).

Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Lanctôt C et al. (2007)Nat Rev Genet. 8(2): 104-115. Review on the role of genomic repositioning movements in the control of gene expression (PubMed).

The evolution of sex: empirical insights into the roles of epistasis and drift. de Visser JA and Elena SF (2007) Nat Rev Genet. 8(2): 139-149. Review on new modelsinvolving genetic factors for theevolution of sex as a reproductive strategy (PubMed).

Educating health-care professionals about genetics and genomics. Guttmacher AE, Porteous ME and McInerney JD (2007) Nat Rev Genet. 8(2): 151-157. ‘Science and society’ perspective article on the importance of genetic and genomic awareness among primary health-care providers and efforts to achieve it (PubMed).

Advocacy groups as research organizations: the PXE International example. Terry SF et al. (2007) Nat Rev Genet. 8(2): 157-164. ‘Science and society’ perspective article on the role of patient advocacy groups as coordinators of translational research in genetic diseases (PubMed).

Overview of the pharmacogenomics of cigarette smoking. Ho MK and Tyndale RF (2007) Pharmacogenomics J [Epub ahead of print]. Review on current knowledge of genetic factors involved in smoking behaviours and how genetic variations may affect therapeutic outcomes for smoking cessation drugs (PubMed).

Pharmacogenomics and nutrigenomics: synergies and differences.Ghosh D, Skinner MA and Laing WA (2007) Eur J Clin Nutr [Epub ahead of print]. Review on the potential for increasing alignment of pharmacogenomics and nutrigenomics in the years ahead (PubMed).

Multiple mutations responsible for frequent genetic diseases in isolated populations. Zlotogora J (2007) Eur J Hum Genet [Epub ahead of print]. Review looking at possible explanations for autosomal recessive diseases that occur at high frequencies in isolated populations (PubMed).

Cancer risks among BRCA1 and BRCA2 mutation carriers. Levy-Lahad E and Friedman E (2007) Br J Cancer 96(1):11-5 Minireview of individualised risk prediction including genetic factors for breast cancer (PubMed).

The ethical implications of stratifying by race in pharmacogenomics. Lee SS (2007) Clin Pharmacol Ther 81(1):122-5. Article on the necessity to determine an accurate categorization of individuals and populations in order to link genetic variants with drug responses appropriately for applications in personalized medicine (PubMed).

The PharmGKB: integration, aggregation, and annotation of pharmacogenomic data and knowledge. Hodge AE, Altman RB and Klein TE (2007) Clin Pharmacol Ther81(1):21-4. Article on the Pharmacogenetics and Pharmacogenomics Knowledge Base (PubMed).

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