Fighting Blindness
The British Retinitis Pigmentosa Society
GENETIC TESTING FOR RP
Extracts from a Discussion Paper Prepared for the Board of
Trustees by
Stephen Jones
Development Manager
October 2009
Genetic Testing for RP
CONTENTS
Background
This Discussion Paper
Why Have Genetic Testing for RP?
Do RP Patients Want Genetic Testing?
Do Clinicians Want Genetic Testing for their RP Patients?
Is Genetic Testing Available?
What is the Official Position?
What are the Potential Solutions?
What Should RP Fighting Blindness Do?
Research
Advocacy Campaign
Other Considerations and Related Issues
Types of Tests and Associated Ethical Issues
Different Methods of Testing and their Costs
Commercial Testing and Private Payment
Annex 1 Sir Alan Rudge’s Letter to Prof Farndon of the UK Genetic Testing
Network
Annex 2 Prof Black’s Project in Manchester
Annex 3 The Process for Adoption and Approval of Genetic Tests and the
Organisations Involved
Annex 4 Genetic Tests and Service Levels (UKGTN Website)
Annex 5 References and Links
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Genetic Testing for RP
Background
The subject of genetic testing has been a discussion point within RP Fighting
Blindness for some time. The largest research grant ever awarded by the charity
was to Prof Graeme Black in Manchester (refer to Annex 2) to develop genetic
testing services for RP. This grant started in 2005 and is on-going.
Considerable interest in genetic testing has been raised within the membership
of the charity. Some members have been tested through NHS channels while
others have been refused. All this has taken place within the context of a rapidly
changing scientific base, an emerging policy environment and widely different
experiences for patients in different parts of the country.
This complicated picture has led to questions being raised as to whether the lay
membership of RP Fighting Blindness, led by the trustees, should be taking a
more proactive role in trying to promote the interests of RP patients in relation to
genetic testing. If so, should this be done through some form of advocacy
campaign and if so, to whom should this be directed?
The subject was discussed at a Board of Trustees meeting on28th January 2009
at which it was decided that Sir Alan Rudge would write a letter, based on a draft
prepared by Prof Tony Moore, to Prof Farndon of the UK Genetic Testing
Network. This letter, reproduced in Annex 1, was sent on 24th March 2009 and
led to a subsequent telephone conversation between Prof Farndon and Sir Alan.
Prof Farndon made various points, including a request that we should send case
studies of RP patients who had experienced problems in obtaining testing. Two
short case studies were subsequently sent.
This Discussion Paper
At Sir Alan’s request, Stephen Jones was asked to carry out some background
research and prepare a discussion paper. A few meetings have taken place with
certain key individuals, including Prof Tony Moore and a number of other
contacts.
In an effort to limit the number of pages in the main part of this report, much of
the background material has been presented in annexes.
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Genetic Testing for RP
Why Have Genetic Testing for RP?
Some of the reasons for testing are outlined below:
1. A genetic test can lead to a better diagnosis of an RP patient’s condition
and a better prognosis of the way the disease may develop in the future.
In some cases, knowing the actual genetic mutation may help
ophthalmologists in the clinic to make clinical judgements and to
recommend genetic counselling where appropriate. Also, by knowing the
exact gene in question, clinicians may be able to save time and money by
not testing patients for syndromic symptoms that might otherwise have
been important to check for.
2. RP patients and their partners/spouses may be better placed to make
important life decisions, particularly relating to having children
(reproductive choice, in the jargon). For example, parents with one child
with suspected Leber congenital amaurosis (LCA) may greatly value a
genetic test and counselling when considering whether or not to have
more children. Similarly, a woman who knows she is at risk of carrying Xlinked RP, which could be passed on to her sons, may greatly value a
genetic test and counselling.
3. Genetic testing allows family members to be tested if they wish. For
example, in the case of families with dominant RP, young adults may wish
to be tested at the time of making career choices.
4. As more and more clinical trials are planned for gene therapy and some
other possible treatments for RP, it is essential that researchers can
identify RP patients with the particular gene mutation in question so that
candidates for the trials can be selected.
5. As RP genetic tests are developed further, it will become possible to
engage in various forms of testing which are not yet commonplace,
including pre-natal testing and pre-implantation selection of embryos.
Clearly, such practices raise enormous ethical issues.
6. Well into the future, it is expected we will enter a period with increased use
of pharmacogenetics – individually tailored treatment according to genetic
background.
Do RP Patients Want Genetic Testing?
Anecdotal evidence appears to indicate that there is widespread interest among
RP patients wishing to be tested. An approach to collecting more rigorous data
about the motivations of RP patients is currently underway by Dr Martin
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Genetic Testing for RP
McKibbin, an ophthalmologist working in Leeds. Preliminary findings of his work
suggest that there is a high demand for testing among RP patients.
A suggestion about improving the quality of the data about RP patients and their
preferences in regard to genetic testing is made later in this report. In the
meantime, and in the absence of better data, we will have to proceed on the
basis of evidence gained from meetings, the helpline and individual contacts,
which indicate dissatisfaction, at least in some parts of the country, that genetic
testing is not available.
A request in the e-newsletter of 18th April 2009 for members to come forward with
their genetic testing experiences, elicited only six responses, one of which was
from the USA. Only two of the responses described problems with obtaining
tests and these were used as the case studies that were sent to Prof Farndon.
Do Clinicians Want Genetic Testing for their RP Patients?
For the reasons set out in the section “Why Have Genetic Tests for RP”, it
appears that specialist ophthalmologists with a high workload in RP want their
patients to be tested in most cases although some are more accepting than
others of arguments about testing only being justified if clinical utility can be
proven. If treatments existed for RP, it would be easier to prove clinical utility but
the absence of treatments means that the tests must be justified on other
grounds.
Other things being equal, and setting aside funding issues for the moment, it
appears that most ophthalmologists would like to have access to genetic testing
for their RP patients. The experiences of some ophthalmologists with regard to
the availability of tests are presented in the next section.
Is Genetic Testing Available?
Prof Graeme Black is concerned that some people within RP Fighting Blindness
have been promoting the idea that every RP patient should have a genetic test.
In the first pace, he points out that many genes causing certain types of RP have
not yet been discovered. Secondly, tests have not yet been developed for some
types of RP. For example, his team in Manchester are still in the relatively early
stages of developing tests for some types of recessive RP. Thirdly, he is not
convinced that all RP patients will necessarily benefit from having such a test,
particularly where there is little evidence of clinical utility.
From the contacts made with clinicians working in eye clinics, it appears that their
experiences on behalf of their RP patients vary greatly. The Manchester area is
well served for testing and some clinicians in other areas report few problems in
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Genetic Testing for RP
obtaining approval for testing for their RP patients, including Prof Moore of
Moorfields and Prof Wright of Edinburgh. Dr Susie Downes of the John Radcliffe
Hospital in Oxford reports that she likes to test all her RP patients where an
appropriate test exists. She submits requests through her hospital genetics
department and has never been refused.
However, other clinicians experience considerable difficulties, including Prof
Lotery of Southampton. He reports extreme difficulty in getting approval for
testing for his RP patients. He would like to get most of his patients tested but
the majority of applications are rejected and he does not even bother submitting
applications for some RP patients because he knows the outcome in advance.
Dr Martin McKibbin of St James University Hospital, Leeds, reports considerable
frustration at what he perceives to be the unequal treatment in his area. He
makes applications to the Yorkshire Regional Genetics Service and finds that RP
is treated as unimportant in comparison to many other genetic conditions. He
finds that one of the best chances for being accepted is pre-pregnancy testing
when couples are making decisions on whether or not to try to become pregnant.
What is the Official Position?
As described in Annex 3, a highly convoluted process, involving a plethora of
organisations, is in place, firstly, to test and approve new genetic tests for use
within the NHS and, secondly, to manage the approval process at the level of the
individual patient.
Once a laboratory, such as Manchester, has developed a new genetic test it
must seek approval for use within the NHS through official channels starting with
the UK Genetic Testing Network (UKGTN). Once a test has received technical
approval and been through the GenCAG process, clinicians in eye clinics can
then request genetic tests for particular patients. However, ophthalmologists
must channel these requests through genetic clinics which fulfil a “gate-keeping”
function. Local NHS bodies must then decide if an application for a test is to be
allowed on the basis of clinical utility and cost.
The interested reader who wishes to delve much more deeply into these issues
is referred to Prof Tony Moore’s report “Genetic Ophthalmology in Focus”
published in April 2008. The full reference and link are given in Annex 5. This
report makes recommendations in relation to specialist genetic ophthalmology
services.
The even more interested reader who wishes to place these issues in the context
of genetic testing for all conditions is referred to the House of Lords report on
Genomic Medicine (a full reference and link is given in Annex 5).
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Genetic Testing for RP
The official reason given for refusing permission for genetic tests for RP is
usually to do with clinical utility. If treatments existed for RP then it would be
easier for clinicians to demonstrate clinical utility but in the absence of treatments
a case must be made along other lines to do with diagnosis, prognosis and family
decision-making. The fact that an RP patient wants a test is not sufficient. The
strength of the argument for clinical utility depends to some extent on the type of
RP in question, but it appears that NHS Commissioners in different parts of the
country make very different decisions for similar cases. If clinical utility is not
proven then the official position is that the genetic test is needed primarily for
research reasons and should be paid for from research funds, such as the
research budget of RP Fighting Blindness, rather than from NHS funds. A whole
chapter of Prof Moore’s report is devoted to the subject of clinical utility.
It is also important to note that testing patients in preparation for future clinical
trials does not form part of the clinical utility debate. Therefore, this argument in
favour of carrying out tests needs to be made vocally and separately from
arguments concerned with clinical utility.
Tony Moore emphasises that funding is the main reason for genetic tests being
rejected for patients. Official explanations of refusals may be couched in terms
of clinical utility not being proven but the underlying reason is lack of funding.
There is some confusion about exactly which bodies are the key decision-makers
for funding decisions in particular cases. As already noted, requests from
ophthalmologists are passed through their local genetics service, acting as the
“gate-keepers”, with onwards involvement of Primary Care Trusts (PCTs) and
Specialised Commissioning Groups (refer to Annex 3).
What are the Potential Solutions?
It may be stating the obvious, but if funding is the key issue, then a substantial
reduction in the cost of tests would ease the situation. The costs of tests carried
out in Manchester are given on their website and the links are given in Annex 2.
As more tests are carried out and as new technologies are introduced, the costs
should reduce, but it is difficult to know what the timescale will be for these
developments to happen.
One project to watch with interest in the future is the development of tests using
high throughput gene sequencing at the John Radcliffe Hospital in Oxford. This
is being led by Dr Susie Downes and her colleague, Dr Andrea Nemeth, a clinical
geneticist. Using very expensive Roche 454 Life Sciences equipment they will
develop new tests for submission to UKGTN and may subsequently be in a
position to offer testing for RP patients through the NHS. It is intended to work in
collaboration with Manchester. Significant developments are expected in the
next few months. Such testing does offer the prospect of cheaper tests but it is
too early to be certain that this will be the case.
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Genetic Testing for RP
In the meantime efforts must be made to work within the existing system. It is
clear that problems are being experienced in particular parts of the country.
The role for RP Fighting Blindness is discussed below.
What Should RP Fighting Blindness Do?
On the basis of discussions with various key players, the consensus appears to
be that RP Fighting Blindness should proceed down two complementary paths:
1. Research
Continue supporting research efforts to develop genetic testing for RP.
This need not be exclusively in the form of support for Prof Black and his
team in Manchester but they are likely to be the main recipients. The
existing project and Prof Black’s work are described in Annex 2 where it is
also noted that he has recently secured £0.5 million of funds from Fight for
Sight for RP genetic testing. A further application to RP Fighting
Blindness has also been flagged up.
In simple terms, the more research that is undertaken, the more gene
dossiers will be submitted to UKGTN (ref Annex 3) and the more RP tests
will be listed in the Directory for future access by clinicians.
2. Advocacy Campaign
Any advocacy campaign must have very clear objectives. It is
conceivable that one objective could be to campaign at a national level for
more money to be devoted to RP testing by engaging in a lobbying
campaign in Westminster. However, a full scale lobbying campaign would
almost certainly require specialist help and would be very expensive,
probably well beyond the means of RP Fighting Blindness.
An alternative objective would be to focus on the specific problem
areas relating to RP testing and have an advocacy campaign designed to
address those problems. The targets for such a campaign include:
UK Genetic Testing Network – Sir Alan Rudge has already written to
UKGTN (Annex1) and had a telephone conversation with the director. As
well as being the body that approves tests, UKGTN also has a remit to
provide equal access to testing in all parts of the country and that is
patently not happening at the present time. Further pressure could be
exerted on UKGTN, backed up by support from ophthalmologists who are
experiencing problems in obtaining approval for tests for their RP patients
Genetics Commissioning Advisory Group (GenCAG) – as pointed out
in Annex 3, GenCAG is the next step in the chain after UKGTN and might
also be a suitable target for the same sort of campaign as described
above.
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Genetic Testing for RP
NHS Commissioners – the decision on whether or not to approve
applications for genetic tests for particular RP patients is taken by local
commissioners after referral from clinical geneticists. The actual bodies
responsible vary and may change over time according to the success of
efforts to reform the system. Where individual Primary Care Trusts
(PCTs) are the bodies responsible there is little opportunity for RP Fighting
Blindness to try to influence their decisions because there are simply too
many of them. But where Specialised Commissioning Groups (SCGs)
are responsible there would be a real opportunity for RP Fighting
Blindness to approach and try to influence them. There are only 10 such
bodies and the ones with the worst record in approving RP tests could be
identified and then approached by the charity. The Genetic Interest Group
(GIG) has offered advice in implementing such a scheme.
Such efforts could be supplemented by a limited lobbying campaign at
Westminster. RP patients refused testing could approach their MPs who
would ask questions to Ministers in the usual way. A question in the
House planted by RP Fighting Blindness is also a possibility. Again. GIG
would offer advice.
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Genetic Testing for RP
Other Considerations and Related Issues
Types of Tests and Associated Ethical Issues
Up to this point genetic testing has been mentioned in a general sense but there
are, in fact, many types of tests. A categorisation of tests and service levels,
extracted from the UKGTN website, is presented in Annex 4 to illustrate the
range and complexity of the tests.
Included in the list are prenatal diagnosis and pre-implantation testing. Such
tests are seldom carried out at the moment for RP patients but may be more
prevalent in the future. All genetic tests involve ethical issues but these tests, in
particular, raise very serious moral questions. Some parents, for example, may
seek to use IVF techniques to select an embryo without RP. In rare cases
involving prenatal tests, the situation may arise where parents want to abort a
foetus which tests positive for RP.
It is beyond the remit of this paper to engage in these debates but it is important
to flag up these issues because they will undoubtedly become more significant in
the future. There is also the question of whether people who have had tests
must report the results to prospective employers or to insurance companies. The
current position relating to the insurance industry is that a moratorium has been
placed on this issue until 2014 although there is evidence that insurance
companies are already taking such information into account when quoting
premiums.
Different Methods of Testing and Their Costs
Again, it is beyond the remit of this layman’s paper to discuss the different testing
methods except to note that there are different methods and the costs for tests
vary greatly. The BRPS funded project in Manchester is based on molecular
testing and the costs are given on the website (link given in Annex 2).
Other methods of testing include the use of microarrays (gene chips), for
example, available from Asper in Estonia (www.asperophthalmics.com). The
uses and limitations of this service are pointed out on page 72 of Genetic
Ophthalmology in Focus.
Another method, high throughput gene sequencing, has already been
mentioned in the context of the project at the John Radcliffe in Oxford and some
people think this will be the testing method of the future. Prof Black’s new
project, funded by Fight for Sight, includes a component on high throughput gene
sequencing. This holds the prospect that costs per test could be reduced. If this
could be achieved, it would go a long way to resolving the problems experienced
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Genetic Testing for RP
by RP patients whose tests have not been approved for funding reasons. There
would still be a need for funding but at a lower and more affordable level.
Looking further into the future, some scientists predict that nanopore technology
will be used for genetic testing.
Commercial Testing and Private Payment
A number of commercial companies are now offering genetic tests for a wide
range of genetic conditions. A number of companies, including deCODEme and
23andMe, have received a great deal of publicity. A particular criticism of such
direct-to-consumer tests is that an individual receives results, which may be very
difficult to interpret and should be accompanied by advice from a clinician and
genetic counsellor which are seldom part of the package.
In recent times, some members of RP Fighting Blindness have received
approaches by email offering testing for RP. The company in question is based
in Belgium. The email quotes the cost of a test for recessive and sporadic RP at
Euro 2800. Prof Moore has provided advice on this subject which is available to
be passed on to members. We may find that many more offers of this type are
made in the future.
The Human Genetics Commission is currently carrying out a consultation on
direct-to-consumer marketing of genetic tests. The reference is given in Annex
5.
Another aspect of private payment, flagged up by some RP Fighting Blindness
members, is that they have offered to pay the costs of a genetic test while
wishing to remain an NHS patient. This appears to be a grey area, with
uncertainty about whether it might be allowed in certain circumstances. The
prevailing view appears to be that it is not allowed.
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Annex 1 Sir Alan Rudge’s Letter to Prof Farndon of the UK Genetic Testing
Network
24 March 2009
Professor Peter Farndon
UKGTN
Clinical Genetics Unit
Birmingham Women’s Foundation NHS Trust
Metchley Park Road
Edgbaston
Birmingham
B15 2TG
Re Molecular Genetic testing for patients with inherited retinal disease and
their families
Molecular genetic testing for some forms of retinitis pigmentosa and other
inherited retinal diseases is available as an NHS service provided by the
Regional Genetics Service in Manchester. It makes sense for molecular genetic
testing for eye disease to be concentrated in a single specialist laboratory and
the genetic laboratory in Manchester provides an excellent service. At present
there are a limited number of tests available and BRPS has provided seed
funding to the Manchester laboratory to develop further tests for retinal disease
that could be made available as an NHS service. It is evident from the feedback
that we have from our members and from discussions with ophthalmologists
around the UK that there is a strong demand for molecular genetic testing. This
is likely to increase as more clinical trials of novel therapies get underway; many
of these trials will require knowledge of the specific mutation causing the retinal
disease.
It is also clear that many patients are unable to access the genetic testing that is
available because of lack of funding and other factors such as poor
communication between ophthalmologists, geneticists and general practitioners.
Many specialist ophthalmologists are unable to arrange testing as clinical
geneticists act as ‘gate keepers’ managing limited budgets and may not see
ophthalmology as a priority area. There is a striking degree of geographical
disparity in access to specialised genetic ophthalmology services and molecular
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Genetic Testing for RP
genetic testing. The major determinant of whether a patient can access
molecular genetic testing is where they live. This is clearly not acceptable.
Our organisation contributed to the GTN commissioned report “Genetic
ophthalmology in focus: a needs assessment and review of specialist services for
genetic eye disorders”
(www.phgfoundation.org/pages/work2.htm#ophthalmology) and the major
concern highlighted by patient groups that took part in the discussions that
informed the report was inequitable access to genetic testing. This issue is now
the major cause of concern for our members. It is raised repeatedly at our local
and national meetings. Perhaps you would be kind enough to let me have your
comments or observations on these concerns and how they might be addressed
in the future and how such services might be improved.
c.c.
Mr Alistair Kent, Director, Genetic Interest Group
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Annex 2 Prof Black’s Project in Manchester
In April 2004, Prof Graeme Black of the University of Manchester submitted an
application to BRPS for a five year project at a cost of £385,000 under the title,
“RP – widening access to genetic testing services”. Manchester is home to one
of only two National Genetics Reference Laboratories (the other being in
Salisbury).
The lay summary included the following “this project aims to develop cost
effective strategies for genetic testing and to demonstrate the clinical utility of
testing to Health Service Commissioners with a view to integrating a defined test
for RP into the NHS and making it accessible to the UK population”
The project was approved and started in January 2005. Emphasis at first was on
testing for X-linked RP, then dominant forms, with the intention of including
recessive forms in the later stages of the project.
Prof Black’s 4th Year report was considered and approved by the trustees at their
meeting of 29th April 2009. The full report was circulated to trustees in advance
of the meeting. The report included a geographic breakdown (table and map) of
the reports of X-linked and dominant RP issued by the Regional Molecular
Genetics Service in the period 2005-8.
Information about the Manchester genetics service is available at:
http://www.mangen.co.uk/
Examples of the RP tests and their prices are available at:
ADRP http://www.mangen.co.uk/media/10538/cat10_552008225933.pdf
X-linked RP http://www.mangen.co.uk/media/10811/cat10_552008234157.pdf
Prof Black has indicated that he will be seeking further funding from RP Fighting
Blindness. It is also known that the Manchester team are to receive £0.5 million
from Fight for Sight for a project connected with genetic testing for RP. Official
details about this project have not yet been released but it is understood that
about half the money will be used for developing new tests including use of high
throughput gene sequencing and the other half will be devoted to developing
data about patient views and perceptions about testing. As Prof Black points out
this will improve the data relating to those who are tested but does not take
account of those patients whose testing has been refused by NHS
Commissioners.
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Annex 3 The Process for Adoption and Approval of Genetic Tests and the
Organisations Involved
UK Genetic Testing Network (UKGTN)
http://www.ukgtn.nhs.uk/gtn/Home
“The UK Genetic Testing Network advises the NHS on genetic testing across the
whole of the UK. It aims to ensure the provision of high quality equitable genetic
testing services. The network is a collaborative group of genetic testing
laboratories, clinicians and commissioners of NHS genetic services and involves
patient support groups.”
“A core function of the UKGTN is the clinical and scientific evaluation of proposed
new molecular genetic tests for adoption as mainstream NHS services. Gene
Dossiers are submitted by member laboratories to the UKGTN for initial
evaluation against agreed criteria. The UKGTN recommends to NHS
commissioners those tests that meet the criteria. However as NHS
Commissioning remains within local arrangements it is recognised by the
UKGTN that inclusion in the Directory does not guarantee NHS funding”
The tests adopted for RP can be found at
http://www.ukgtn.nhs.uk/gtn/Search/Search+by+Disease+or+Gene and typing in
retinitis pigmentosa.
UKGTN is a sub-group of GenCAG.
Genetics Commissioning Advisory Group (GenCAG)
http://www.dh.gov.uk/en/Publichealth/Scientificdevelopmentgeneticsandbioethics
/Genetics/Geneticsgeneralinformation/DH_4117687
“The Genetics Commissioning Advisory Group was set up to take a strategic
national overview of genetics in healthcare delivery. It aims to provide advice to
commissioners of genetics services to enable them to provide appropriate
services for NHS patients and their families.
Members are drawn from relevant professional bodies and groups and Royal
Colleges, an umbrella patient support group (the Genetic Interest Group - GIG)
and from the specialised commissioning groups which commission these
services in the NHS”
GenCAG looks at the UKGTN recommendations from the commissioners’
perspective in terms of criteria such as value for money. GenCAG effectively
signs off the UKGTN recommendation and passes to commissioners.
Genetic testing is defined by the NHS as a Specialised Service. In England
Specialised Services are commissioned by Specialised Commissioning Groups
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Genetic Testing for RP
(SCGs). There are separate arrangements in Scotland, Wales and Northern
Ireland.
Specialised Commissioning Groups (SCGs)
SCGs commission services on behalf of their Primary Care Trusts (PCTs).
There are 10 SCGs in England and their boundaries are the same as for the
Strategic Health Authorities (SHAs). Each SCG covers a population of between
2.5 and 7 million.
The SCGs report to the National Specialised Services Commissioning Group
(NSCG) which has a remit to coordinate specialised services commissioning for
England.
There is yet another body known as the National Commissioning Group (NCG)
which is responsible for commissioning services for extremely rare conditions
where the total number of patients is usually less than 400.
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Genetic Testing for RP
Annex 4 Genetic Tests and Service Levels (UKGTN Website)
Service level fields and definitions
Sequencing of entire coding region
Determination of the nature and order of the nucleotide bases of the gene being tested.
This analysis includes the exon and intron-boundaries.
Sequencing DNA identifies most nucleotide bases that vary from the normal (wild-type)
sequence.
Types of sequence alterations that may be detected
Pathogenic sequence (disease-causing mutation) reported in the literature
Sequence alteration predicted to be pathogenic but not reported in the literature
Sequence alteration of unpredictable clinical significance (missense)
Sequence alteration predicted to be benign but not reported in the literature
Benign sequence (polymorphism) reported in the literature
Possibilities if a sequence alteration is not detected
Patient does not have a mutation in the tested gene (e.g., a sequence alteration
exists in another gene at another locus
Patient has a sequence alteration that cannot be detected by sequence analysis
(e.g., a large deletion)
Patient has a sequence alteration in a region of the gene (e.g., an intron or
regulatory region) or in another gene/exon not covered by the laboratory's test
Adapted from the ACMG Recommendations for Standards for Interpretation of Sequence Variations (2000).
Sequencing of select exons
Determination of the nature and order of the nucleotide bases of specific exons of a gene.
Specific exons of a gene are sequenced when these have been identified as the regions of
the gene most likely to contain pathogenic mutations. This analysis will include the DNA
sequencing of the exon and intron-boundaries of each of the selected exons
Types of sequence alterations that may be detected
Pathogenic sequence (disease-causing mutation) reported in the literature
Sequence alteration predicted to be pathogenic but not reported in the literature
Unknown sequence alteration of unpredictable clinical significance
Sequence alteration predicted to be benign but not reported in the literature
Benign sequence (polymorphism) reported in the literature
Possibilities if a sequence alteration is not detected
Patient does not have a mutation in the tested exons (e.g., a sequence alteration
exists in another exon or in a gene at another locus)
Patient has a sequence alteration that cannot be detected by sequence analysis
(e.g., a large deletion)
Patient has a sequence alteration in a region of the gene (e.g., an intron or
regulatory region) not covered by the laboratory's test
Adapted from the ACMG Recommendations for Standards for Interpretation of Sequence Variations (2000).
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Mutation Scanning
The screening of DNA by one of a variety of methods to identify variant gene region(s).
Regions identified as variant with respect to the normal (wild type sequence) are further
analysed to identify the specific sequence alteration.
Methods commonly in use for mutation scanning by UKGTN laboratories are CSGE;
DGGE; SSCP; DHPLC.
Some Clinical Implications:
Mutation scanning is used when mutations are distributed throughout a gene, when
most families have different mutations (private mutation) and when sequence analysis
would be excessively time-consuming due to the size of a given gene.
Mutation scanning may include the entire gene or only select regions.
Targeted mutation analysis
Testing for the presence of common mutations found in most or a high proportion of
individuals with a specified disease
Examples are:
i) Glu6Val for sickle cell anaemia
ii) the trinucleotide repeat expansion associated with Fragile X
iii) deletions associated with Duchenne muscular dystrophy (dosage)
iv) a set of mutations (e.g., a panel of mutations for cystic fibrosis), as opposed to
complete gene sequencing or mutation scanning.
Confirmation of known mutations
Testing of at-risk family members for their family-specific (private) mutation where the
mutation
has been identified as part of a diagnostic service. This includes predictive tests but not
confirmation of mutations identified in a research laboratory
Gene Tracking
Testing DNA sequence polymorphisms (normal variants) that are near or within a
gene of interest to track within a family the inheritance of a disease-causing (pathogenic)
mutation in a given gene
The three steps of gene tracking (linkage analysis) are:
i) Establish haplotypes for each individual: Multiple DNA markers lying on either side
of (flanking) or within (intragenic) a gene region of interest are tested to determine
the set of markers (haplotypes) of each family member.
ii) Establish phase by comparing haplotypes between family members: By comparing
the haplotypes of family members whose genetic status is known (e.g., affected,
unaffected), the haplotype associated with the disease-causing allele can be identified.
iii) Determine genetic status: Once the disease-associated haplotype is established, it is
possible to determine the genetic status of at-risk family members.
Some Clinical Implications
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Genetic Testing for RP
This method is often used when direct DNA analysis is not possible because the gene of
interest is unknown or a mutation within that gene cannot be detected in a specific family.
Prenatal diagnosis (synonym: prenatal testing)
Testing performed during pregnancy to determine if a fetus is affected with a particular
disorder.
Chorionic villus sampling (CVS), amniocentesis, periumbilical blood sampling (PUBS),
are examples of procedures used to obtain a sample for testing
Preimplantation diagnosis: (synonym: preimplantation testing, PGD)
A procedure whereby analysis for a genetic mutation is carried out on a single cell
removed from early embryos conceived by in vitro fertilisation.
Other
Analysis of patient samples not identified in the previous service levels. These could
include for example,
i) clinical confirmation of mutations identified in a research lab
ii) analysis of a patient sample using testing procedures or new technology not described
in
the available service level fields
Comprehensive analysis
Analysis of a patient sample using all or a subset of the service levels described above.
Example
i) gene tracking to identify which one of a group of genes to test
followed by
ii) targeted mutation analysis for the common mutations in the identified gene
followed by
iii) mutation scanning of the gene for those negative in (ii).
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Genetic Testing for RP
Annex 5 References and Links
Title: Genetic Ophthalmology in Focus
A Needs Assessment and Review of Specialist Services for Genetic Eye
Disorders
Report for the UK Genetic Testing Network
Tony Moore and Hilary Burton
April 2008
Published by the PHG Foundation
The full report (97 pages) and a summary (4 pages) can be downloaded at
http://www.phgfoundation.org/pages/work2.htm
Title: A Common Framework of Principles for Direct-to-Consumer Genetic
Testing Services
Principles and Consultation Questions
Human Genetics Commission
The full 27 page report can be downloaded at
http://www.hgc.gov.uk/Client/Content.asp?ContentId=816
Title: Genomic Medicine
House of Lords
Science and Technology Committee
July 2009
www.publications.parliament.uk/pa/ld/ldsctech.htm
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