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21 December 2005The genome refers to an organism’s complete genetic information, generally taken to mean the total DNA/RNA sequence. The term epigenome has been used to refer to the additional heritable biological factors other than DNA sequence that can influence gene expression. Epigenetic modifications such as methylation or acetylation of DNA can significantly affect gene activity and may be involved in inter-individual variation in both health and disease; faults in normal epigenetic mechanisms have been identified in different forms of cancer.
An international group of cancer scientists have recently published a proposal for a large-scale international Human Epigenome Project (HEP) to map these epigenetic DNA modifications, based on the findings of a workshop held earlier this year. The report, published in Cancer Research, outlines the aims of the HEP and the high-throughput technologies required to implement the plans.
The stated goal of the HEP is to “identify all the chemical changes and relationships…that provide function to the DNA code, which will allow a fuller understanding of normal development, aging, abnormal gene control in cancer and other diseases, as well as the role of the environment in human health” (see HUM-MOLGEN report). Since epigenetic profiles vary not only between individuals but also between different tissues and in health and disease within the same individual, the report recommends the use of several reference epigenomes for high-resolution analysis along with a much larger group of samples
The proposals include a call for close co-operation between different international groups, including the European Epigenome Project, based at the Wellcome Trust Sanger Institute in Cambridge, UK and similar ventures in Japan and the US.
The charity CancerBACUP has conducted a survey of BRCA1/2 genetic testing in 23 regional genetics centres, to detect mutations associated with substantially increased risk of breast and ovarian cancer (see BBC news item). They report that in two of the 19 centres that responded, women are waiting up to nine months for their first appointment, and that in five centres women were waiting between one and two years for their test results. The survey also looked at the sixteen different molecular genetics laboratories that performed the genetic testing on behalf of the regional genetics centres, of which 12 responded to the survey; of these only six were currently testing 100% of all the BRCA gene variations linked to breast cancer.
The 2004 National Institute for Clinical Excellence familial breast cancer guidance said that for women at a very high risk of familial breast cancer referred for genetic testing of the BRCA1, BRCA2 and TP53 genes, testing should aim for 100% sensitivity and include analysis of the complete BRCA genes. Testing of these relatively large genes for the presence of any of the hundreds of mutations previously associated with breast cancer susceptibility (as opposed to detection of a specific mutation already identified in an affected family member) is a laborious process that necessarily takes many months to complete. In addition, centres are still working to complete re-testing of samples previously analysed for the most common BRCA mutations, which must now be fully sequenced in order to detect as close as possible to 100% of possible mutations. Two laboratories reportedly said it would take two years to clear this backlog.
CancerBACUP's genetic information project manager Dr Andrea Pithers said it was: "…important that centres speed up the time it takes to give women their test results. Although many of the centres say they will meet the government targets on this by 2006 [that test results should be available within eight weeks], our survey shows that some have a long way to go to achieve it". Although it is clearly desirable to provide genetic test results as quickly as possible, it should be remembered that full sequence analysis of the BRCA genes is an unusually complex procedure, and not comparable with many of the more rapid forms of genetic testing. A Department of Health spokesperson commented: "We are working with commissioners and providers of genetic services to ensure that patients are being appropriately referred in line with the NICE guideline, that backlogs of tests are cleared and that test results are delivered more quickly in the future".
12 December 2005Human embryonic stem (hES) cells have the capability to differentiate into any number of useful cell-types. This property means that they have the potential to be used to replace tissues that have been damaged by diseases such as diabetes and cardiovascular conditions.
Recently, embryonic stem cell lines have been derived from patients with specific medical conditions, including diabetes and hypogammaglobulinemia. These lines were demonstrated to be immunologically compatible with the patient donor, indicating that any cells or tissue derived from them could be transplanted back into the original donor with a very low risk of rejection (see Hwang et al. 2005 Science 308: 1777 – 1783). However, the process of producing individually matched stem cell lines is costly, time-consuming and technically challenging.
The authors of a new report in The Lancet (Taylor et al. 2005 The Lancet 366: 2019-2025) propose instead that national banks of stem cell lines are established in order to provide a source of stem cells that could be used in the general population for therapeutic purposes. An individual’s immune identity is made up of their HLA type and blood group, and in order to prevent transplant or graft rejection these must be matched between a donor and recipient. The HLA system demonstrates a large amount of variation between individuals, for example at least 25 different alleles of HLA-A have been reported. In kidney transplantation three HLA loci are matched; HLA-A, HLA-B and HLA-DR. Individuals may be hetereozygous at any of these loci and therefore there may be up to six different alleles present. HLA compatibility is usually assessed by the number of HLA mismatches between the donor and recipient, with the clinically acceptable ranging from zero HLA-A, HLA-B and HLA-DR mismatch to zero HLA-DR mismatch only. Although a degree of HLA mismatch is acceptable, a compatible blood group is essential.
The authors, based at Cambridge University, have created a model of hES cell bank by using data from organ donors and kidney transplant waiting list candidates, to estimate the number of stem cell lines needed for sufficient HLA diversity to provide a match for a reasonable percentage of the population. The researchers used data from 1500 consecutive cadeveric organ donors to find blood group compatible HLA matches for the 6577 patients registered on the UK kidney transplant waiting list. They found that the first 150 donors provided a full HLA match for 18.5% of the recipients, and that 85% of the recipient population could have a HLA-DR match. The authors also found that increasing the number of donors examined did not result in a proportionate increase in recipient matches. The authors also found that by selecting donors from blood group O, and homozygous for 26 common HLA haplotypes, only ten donor cell lines could be used to find acceptable matches for 78% of recipients. Again, increasing the number of donors beyond ten did not result in a significant improvement to HLA matching. This study suggests that a functioning hES cell bank could be created with a very small number of cell lines.
However, this research is based on a number of assumptions, which are acknowledged by the authors, and may impact on the practical benefits of creating and using such a bank. The modelling of HLA types of hES cell embryo donors was performed on the basis that it would be similar to the cadaveric organ donor database. This may have resulted in the under-representation of some ethnic groups, and additionally operates on the basis that those likely to donate organs would also donate embryos for research or clinical purposes. The study also assumed that a single hES cell line of the appropriate HLA type would be sufficient to treat all potential recipients. This may not in fact prove to be the case, and if more than one cell line were required for the same HLA type this would increase the total number of lines required. The authors also assume that the kidney transplant waiting list is representative of the population that may benefit from stem cell therapies. As this includes those with an array of conditions ranging from neurodegenerative diseases and spinal injury to diabetes, the organ waiting list may not truly reflect the ethnic and HLA diversity of the stem cell therapy candidate population.
A vast range of scientific hurdles need to be overcome before specialist, functional cell types are routinely produced for therapeutic use. However, this study does provide vital evidence that a bank holding a relatively small number of hES cell lines could potentially provide cell types of benefit to large sections of the population, thus avoiding the financial and technical costs of producing personalised cells for individual patients.
The full research paper can be found at:
Banking on human embryonic stem cells: estimating the number of donor cell lines needed for HLA matching. CJ Taylor, EM Bolton, S Pocock, LD Sharples, RA Pedersen, JA Bradley. (2005) The Lancet 366: 2019-2025. (Subscription required).
8 December 2005An international team of researchers, led by a team at the Broad Institute of MIT and Harvard have published the complete sequence of the dog genome. Their article in Nature [Lindblad-Toh K et al (2005) Nature 438, 803-819] provides details of the over 2 billion nucleotides that make up the genome of a female boxer named Tasha, whose DNA was sequenced. In addition, approximately 2.5 single nucleotide polymorphisms were identified. In addition, approximately 2.5 single nucleotide polymorphisms were identified. The National Human Genome Research Institute (NHGRI) funded the research at a cost of $30 million. The boxer was chosen as a representative of the average purebred dog, according to a NHGRI press release, to provide a reference sequence of the dog genome.
The dog genome was chosen as a sequencing project because it will aid researchers in understanding and treating human diseases. Dogs suffer from many genetic disorders in common with humans, such as heart disease, cancer, blindness, cataracts, epilepsy, hip dysplasia and deafness. According to Dr Francis Collins, Director of the NHGRI, “When compared with the genomes of human and other important organisms, the dog genome provides a powerful tool for identifying genetic factors that contribute to human health and disease.” Comparing the dog genome to the human and other genomes, “…will help researchers to narrow their search for many more of the genetic contributors underlying cancer and other major diseases,” said Dr Elaine Ostander, chief of the NHGRI’s Cancer Genetics Branch. The dog genome data can be found at the NIH's National Center for Biotechnology Information Dog Genome Resources or at the European Molecular Biology Laboratory's Nucleotide Sequence Database.
5 December 2005The UK Stem Cell Initiative (UKSCI) led by Sir John Pattison has announced its findings following its review of stem cell research in the UK and its future potential.
The UKSCI was established by the Chancellor of the Exchequer in March of 2005, following the commitment in this year’s Budget speech to make the UK the “world’s leading location for research-based, science-based and knowledge-based industries”. The speech specifically highlighted stem cell research as a key area of strength in the UK, and the UKSCI was tasked with “developing a ten-year vision for UK stem cell research, which seeks to make the UK the most scientifically and commercially productive location for this activity over the coming decade”. This strategic plan was also intended to be fully costed in order to inform future Treasury spending reviews and identify options for better coordination of UK research and its commercial translation.
The UKSCI report has made a total of eleven recommendations, these include:
Other recommendations relate to the establishment of centres of excellence, the proportionate regulation of stem cell research, and further public dialogue on this subject.
The UKSCI have estimated that the total cost of implementing all their recommendations will be in the region of £41-£104million per annum depending on what strategy is adopted. In order for this level to investment to be achieved UKSCI propose that the Government increases funding for stem cell research by between £11-£74million per annum, in addition to what is already available from other public and private sector sources.
The Government has accepted all the recommendations of the report, and has allocated an additional £50million of funding for stem cell research. Although it is unclear how this will be distributed, this brings the level of total public sector funding available for stem cell research to up to £100million over 2006-08. Welcoming the report’s findings, the Chancellor, Gordon Brown, said, “Britain should be the world's number one centre for genetic and stem cell research building on our world leading regulatory regime in this area… we are taking forward a new public-private partnership to invest in pre-commercial aspects of stem cell research and to coordinate future research.”
The entire UKSCI report and its recommendations can be found at the Department of Health website.
14 December 2005Testing for the presence of Down’s Syndrome is one of the most well established antenatal screening programmes in developed countries such as the UK and US. However, the protocol of choice has changed over time as new technologies have widened the available options for invasive and non-invasive forms of testing. A recent paper in the New England Journal of Medicine weighs the relative merits of first and second trimester screening approaches (and combinations of the two) by reporting on the First- and Second-Trimester Evaluation of Risk (FASTER) prospective trial [Malone FD et al. (2005) N. Engl. J. Med. 353, 2001-2011]. This trial, combining data from 15 US centres between 1999-2001, looked at women with singleton pregnancies who entered the study at gestation between 10 weeks 3 days and 13 weeks 6 days. First trimester risk at enrolment was calculated using the results from nuchal translucency measurement and two serum markers, pregnancy-associated plasmaprotein-A (PAPP-A) and free ß-human chorionic gonadotrophin (ß-hCG), combined with maternal age. Second trimester risk was calculated following quadruple serum screening at 15-18 weeks gestation, again in combination with maternal age. The quadruple test measures levels of four serum markers: ß-hCG, alpha-fetoprotein (AFP), unconjugated oestriol (uE3) and inhibin-A.
Patients in the trial received two separate risk estimates, based on the first and second trimester screening results. A positive result for Down’s Syndrome was taken to be a calculated birth risk of 1 in 150 or higher for the first trimester screening, and a risk of 1 in 300 or higher for the second trimester result. All women with positive test results as defined by these criteria were offered genetic counselling and the option for amniocentesis and genetic diagnostic testing.
The trial evaluated the following approaches to Down’s Syndrome screening:
The true chromosomal status of all fetuses or babies from pregnancies with a positive screening result was ascertained via amniocentesis, neonatal cord blood or tissue sampling (for dead foetuses and babies). A total of 117 cases of Down’s Syndrome were identified, which the authors propose represents complete ascertainment, given that the predicted number of cases from the 33,546 women in the trial was 112.
The researchers compared the performance of different screening strategies in a number of ways, including looking at the relative false positive rates for a given detection rate and at the relative detection rates for a given false positive rate. They found significantly different performance scores for all the strategies, except for nuchal translucency and first trimester serum screening, which performed equally well. First trimester combined screening was shown to be superior to either of these single approaches. Detection rates for serum integrated screening were equivalent to those obtained for first trimester combined screening, but did not require nuchal translucency measurement and hence was arguably a superior technique, since NT measurement requires skilled ultrasonography. The best method overall was fully integrated screening (serum integrated screening combined with NT).
The authors conclude that combined first trimester screening for Down’s Syndrome is highly effective and superior to single approaches, but that combinations of screens from the first and second trimesters provide higher detection and lower false positive rates, and that of these fully integrated screening was the best strategy. They propose that serum integrated screening would be a useful alternative where staff trained to perform NT measurements are not available. Independent sequential screening was found to produce relatively low accuracy and was not recommended, whereas stepwise sequential screening performed almost as well as fully integrated screening (albeit with a higher false-positive rate), but the authors note that further research would be required to identify the best method of stepwise sequential screening.
Comment: This US study provides similar results to the earlier 2003 UK Heath Technology Assessment, First and second trimester antenatal screening for Down's syndrome: the results of the Serum, Urine and Ultrasound Screening Study (SURUSS), which found fully integrated screening to be the best strategy overall, but also recommended first trimester combined screening or, if NT measurement is not available, serum integrated screening. The FASTER trial looked at women enrolled during the first trimester, but the SURUSS report also considered women who did not present until the second trimester, recommending that quadruple screening was the best strategy for this group. The issue of relative costs is not considered in the FASTER report.
An editorial accompanying the latest study notes certain objections to fully integrated screening, notably the relatively high proportion of women who fail to return for the second trimester test and the effective removal of the option to terminate affected pregnancies in the first trimester [Simpson JL (2005) N. Engl. J. Med. 353, 2068-2070]. The author actually recommends the adoption of universal invasive procedures (amniocentesis or chorionic villus sampling) and diagnostic karyotyping on the grounds that “neither procedure seems to be as risky as once thought”, citing a 0.15 percent procedure-related loss from amniocentesis in the FASTER trial, although this is around ten-fold lower than most estimates. He also noted the emergence of non-invasive approaches such as the analysis of fetal cells or DNA from maternal blood; whilst these techniques are not yet suitable for clinical implementation, they may in future provide the most reliable approach to Down’s Syndrome screening.
14 December 2005Stem cell banking: the size of the task. St John JC and Alderson J (2005) Lancet 366, 1991-1992. Commentary accompanying article that estimates a therapeutic hESC bank in the UK could be populated using 150 hES cell lines, calling for a national policy to “populate and exploit the potential of the National Stem Cell Bank”.
Sharing the benefits of genetic research. Schroeder D et al. (2005) BMJ 331, 1351-1352. Editorial on the World Trade Organization conference in Hong Kong, querying whether it will act to protect benefit sharing of human genetics research.
Economic analyses of human genetics services: A systematic review. Carlson JJ et al. (2005) Genetics in Medicine 7, 519-523.
Marfan’s syndrome. Judge DP and Dietz HC (2005) Lancet 366, 1965-1976. Seminar article giving comprehensive overview of this genetic disorder, including clinical genetic testing.
Marfan’s syndrome: a daily struggle. Brindusa C (2005) Lancet 366, 1977. Personal account of living with this disorder by an affected woman, who did not discover that it was genetic in origin until after she became pregnant; her son has the condition too.
Politically correct human embryonic stem cells? Solter D (2005) New Engl. J. Med. 353, 2321-2324. Perspective piece commenting on recent reports of ‘ethically acceptable’ techniques for the production of hES cells that avoid the destruction of viable embryos; the author concludes that neither technique would satisfy ethical opposition to hES cell research and objects to “manioulating science for the sake of politics”.