Download Lipoprotein lipase deficiency

Proposal form for the evaluation of a genetic test for NHS Service
Gene Dossier
Submitting laboratory:
Aberdeen RGC
1. Disorder/condition – approved name and symbol as published on the OMIM database (alternative
names will be listed on the UKGTN website)
If this submission is for a panel test please complete appendix 1 listing all of the conditions included
using approved OMIM name, symbol and OMIM number.
HYPERLIPOPROTEINEMIA, TYPE I/V
2. OMIM number for disorder/condition
If a panel test – see 1. above
238600 (Type1); (207750 (Type1B) ; 144650 (Type V)
3a. Disorder/condition – please provide, in laymen’s terms, a brief (2-5 sentences) description of
how the disorder(s) affect individuals and prognosis.
Lipoprotein lipase deficiency is a disorder of triglyceride clearance.
Individuals with 2 copies of the altered gene present with childhood onset of chylomicronaemia – a build
up of fat in the blood, and symptoms include severe abdominal pain, loss of appetite, musculoskeletal
pain and a general failure to thrive As the disease progresses, symptoms include recurrent episodes of
pancreatitis, development of type 2 diabetes and enlargement of liver and spleen. Death often occurs
due to recurrent pancreatitis and associated complications.
3b. Disorder/condition – if required please expand on the description of the disorder provided in
answer to Q3a.
Individuals with one copy of the altered gene present with similar symptoms but in middle age (or
pregnancy). These patients average 1-2 bouts of pancreatitis per year and 70% get diabetes secondary
to the pancreatitis leading to an increase in hospital admissions. Again death may occur due to
pancreatitis, the associated pancreatic cancer risk, and other complications of diabetes, or
cardiovascular disease.
4. Disorder/condition – mode of inheritance
If this submission is for a panel test, please complete the mode of inheritance for each condition in the
table in appendix 1.
Autosomal recessive but carriers maybe symptomatic
5. Gene – approved name(s) and symbol as published on HGNC database (alternative names will be listed
on the UKGTN website)
If this submission is for a panel test please complete appendix 1 listing all of the genes included using
approved HGNC name, symbol, number and OMIM number.
Lipoprotein lipase (LPL)
Apolipoprotein C-II (ApoC2)
Apolipoprotein A-V (ApoA5)
Glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1 (GPI-HBP1)
Lipase maturation factor 1 (LMF1)
6a. OMIM number(s) for gene(s)
If a panel test – see 5. above
609708 (LPL); 608083 (APO C2); 611761 (LMF-1); 606368 (APO A5); 612757 (GPI-HBP1)
Approval Date: September 2014
Submitting Laboratory: Aberdeen RGC
Copyright UKGTN © 2014
6b. HGNC number(s) for gene(s)
If a panel test – see 5. above
6677 (LPL); 609 (APO C2); 14154 (LMF1); 17288 (APO A5); 24945 (GPI-HBP1)
7a. Gene – description(s)
If this submission is for a panel test, please provide total number of genes.
5 genes - Genes involved in the production of functional dimeric lipoprotein lipase (LPL); its secretion
from cells ( LMF-1); its regulation (apoA5), its plasma co-factor (apoC2) and cell receptor (GPI-HBP1)
7b. Number of amplicons to provide this test (molecular) or type of test (cytogenetic)
(n/a for panel tests)
32 amplicons + MLPA
7c. GenU band that this test is assigned to for index case testing.
Band F (15 GENUs)
8. Mutational spectrum for which you test including details of known common mutations
(n/a for panel tests)
If this application is for a panel test to be used for different clinical phenotypes and/or various sub panel
tests – please contact the team for advice before completing a Gene Dossier
Small point mutation/duplication/deletions events in the coding region and immediate flanking regions of
the above 5 named genes. Large scale duplication/deletion detection in the LPL gene. 90% of severe
triglyceride disorders are caused by mutations in LPL, 4% in apoC2 and the rest in the other genes
(ApoA5> GPIHBP1> LMF-1).
9a. Technical method(s) – please describe the test.
PCR and direct Sanger sequence analysis for the 5 genes using standard techniques. Sequence
analysis using Mutation Surveyor. Multiplex Ligation dependent Probe Amplification (MLPA) analysis of
the LPL gene to identify any larger scale duplication/deletions.
9b. For panel tests, please specify the strategy for dealing with gaps in coverage.
n/a
9c. Does the test include MLPA?
(For panel tests, please provide this information in appendix 1)
Yes - as indicated above – MLPA for LPL gene only
9d. If NGS is used, does the lab adhere to the Association of Clinical Genetic Science Best
Practice Guidelines for NGS?
n/a
10. Is the assay to be provided by the lab or is it to be outsourced to another provider?
If to be outsourced, please provide the name of the laboratory and a copy of their ISO certificate
or their CPA number.
Yes – provided in this laboratory
11. Validation process
Please explain how this test has been validated for use in your laboratory or submit your internal
validation documentation. If this submission is for a panel test, please provide a summary of evidence of:
i)
instrument and pipeline validation, and
ii)
panel verification for the test
Please submit as appendices to the Gene Dossier (these will be included in the published Gene Dossier
available on the website). Please note that the preferred threshold for validation and verification is 95%
sensitivity with 95% Confidence Intervals.
Approval Date: September 2014
Submitting Laboratory: Aberdeen RGC
Copyright UKGTN © 2014
Standard laboratory techniques of PCR, direct Sanger sequence and MLPA are used in this test. These
methods are well validated in the laboratory. Sequences amplified and sequenced for the above genes
were checked against the relevant reference sequences. In addition, two positive controls (LPL) were
used to confirm mutation detection in this gene. MLPA analysis was again performed according to
standard laboratory conditions – no positive controls were available.
12a. Are you providing this test already?
Yes
12b(i). If yes, how many reports have you produced?
Service only started – first two samples in progress
12b(ii). Number of reports mutation positive?
n/a
12b(iii). Number of reports mutation negative?
n/a
12b(iv). Please provide the time period in which these reports have been produced and whether in
a research or a full clinical diagnostic setting.
Samples in progress – full clinical diagnostic setting
13a. Is there specialised local clinical/research expertise for this disorder?
Yes
13b. If yes, please provide details
Network of UK specialist lipid clinics linked and co-ordinated through the specialist assay services (SAS)
for lipids and cardiovascular disease biomarkers laboratories.
14. Based on experience what will be the national (UK wide) activity, per annum, for:
Index cases = 350
Family members where mutation is known
Based on information later in the GD expect 125 to be negative and therefore 225 to be positive and 4
family members per positive test = 900 family members
15. If your laboratory does not have capacity to provide the full national need please suggest how
the national requirement may be met.
For example, are you aware of any other labs (UKGTN members or otherwise) offering this test to NHS patients on a local area
basis only? This question has been included in order to gauge if there could be any issues in equity of access for NHS patients.
If you are unable to answer this question please write “unknown”.
This test is not offered in the UK . Requesting laboratories use service provided by Amsterdam Medical
Centre; The Netherlands.
16. If using this form as an Additional Provider application, please explain why you wish to
provide this test as it is already available from another provider.
Approval Date: September 2014
Submitting Laboratory: Aberdeen RGC
Copyright UKGTN © 2014
EPIDEMIOLOGY
17a. Estimated prevalence of conditions in the general UK population
Prevalence is total number of persons with the condition(s) in a defined population at a specific time. Please identify the
information on which this is based.
For panel tests, please provide estimates for the conditions grouped by phenotypes being tested.
Homozygous LPL deficiency = 1 in 1,000,000
Severe heterozygote LPL deficiency 1 in 50,000
Based on clinical experience of lipid clinics in the UK and unpublished data from the Very Large
Database of Lipids (VLDL) study in the USA which has identified 50 cases of LPLD in 2,000,000
secondary care referred patient samples.
Gotoda T et al: Diagnosis and management of type I and type V hyperlipoproteinemia. J Atheroscler Thromb.
2012;19(1):1-12. Epub 2011 Dec 1.
Surendran RP, et al. Mutations in LPL, APOC2, APOA5, GPIHBP1 and LMF1 in patients with severe
hypertriglyceridaemia. J Intern Med. 2012 Aug;272(2):185-96. doi: 10.1111/j.1365-2796.2012.02516.x.
17b. Estimated annual incidence of conditions in the general UK population
Incidence is total number of new cases in a year in a defined population. Please identify the information on which this is based.
For panel tests, please provide for groups of conditions.
350 new cases
18. Estimated gene frequency (Carrier frequency or allele frequency)
Please identify the information on which this is based. n/a for panel tests.
0.1%
Genetic surveys of the prevalence of LPL inactivating mutations
Maruyama T et al. Mutations in Japanese subjects with primary hyperlipidemia--results from the Research Committee of the
Ministry of Health and Welfare of Japan since 1996--.J Atheroscler Thromb. 2004;11(3):131-45.
Nordestgaard BG, et al. Heterozygous lipoprotein lipase deficiency: frequency in the general population, effect on plasma lipid
levels, and risk of ischemic heart disease. Circulation. 1997 Sep 16;96(6):1737-44.
Johansen CT, Heeled RA Genetic bases of hypertriglyceridemic phenotypes. Curr Opin Lipidol. 2011 Aug;22(4):247-53. doi:
10.1097/MOL.0b013e3283471972.
19. Estimated penetrance of the condition. Please identify the information on which this is based
n/a for panel tests
Homozygotes: ~100%
Heterozygotes: 25%
Penetrance increased by obesity, smoking, diabetes and conditions/drugs causing insulin resistance.
20. Estimated prevalence of conditions in the population of people that will be tested.
n/a for panel tests.
Homozygotes: 1 in 1,000,000
Heterozygotes: 1 in 50,000
Based on clinical experience of lipid clinics in the UK and unpublished data from the Very Large
Database of Lipids (VLDL) study in the USA which has identified 50 cases of LPLD in 2,000,000
secondary care referred patient samples. Also various estimates are cited in the literature
eg approximately 3-7% heterozygotes in population - Benlian et al: N Engl J Med 1996;335:848-54.
INTENDED USE (Please use the questions in Annex A to inform your answers)
21. Please tick either yes or no for each clinical purpose listed.
Panel Tests: a panel test would not be used for pre symptomatic testing, carrier testing and pre natal testing as the familial
mutation would already be known in this case and the full panel would not be required.
Diagnosis
Yes
No
Treatment
Yes
No
Prognosis & management
Yes
No
(n/a for Panel Tests)
Yes
No
Carrier testing for family members (n/a for Panel Tests)
Yes
No
Prenatal testing
Yes
No
Presymptomatic testing
(n/a for Panel Tests)
Approval Date: September 2014
Submitting Laboratory: Aberdeen RGC
Copyright UKGTN © 2014
TEST CHARACTERISTICS
22. Analytical sensitivity and specificity
This should be based on your own laboratory data for the specific test being applied for or the analytical sensitivity and
specificity of the method/technique to be used in the case of a test yet to be set up.
Please note that the preferred threshold for validation and verification is 95% sensitivity with 95% Confidence Intervals.
Direct sequence analysis used – estimated sensitivity of >99% when bi-directional sequence used (with
Mutation Surveyor software). Analytical specificity >99%.
23. Clinical sensitivity and specificity of test in target population
The clinical sensitivity of a test is the probability of a positive test result when condition is known to be present; the clinical
specificity is the probability of a negative test result when disorder is known to be absent. The denominator in this case is the
number with the disorder (for sensitivity) or the number without condition (for specificity).
Please provide the best estimate. UKGTN will request actual data after two years service.
Clinical sensitivity for homozygotes 90%; heterozygotes 60%
(Not all presenting cases will have mutations identified – possibility of other responsible genes in
pathway yet to be identified)
Clinical specificity for homozygotes 100%; heterozygotes 90%
24. Clinical validity (positive and negative predictive value in the target population)
The clinical validity of a genetic test is a measure of how well the test predicts the presence or absence of the phenotype,
clinical condition or predisposition. It is measured by its positive predictive value (the probability of getting the condition given
a positive test) and negative predictive value (the probability of not getting the condition given a negative test).
Not currently requested for panel tests
Clinical validity for homozygotes 90%; heterozygotes 55%
Homozygotes usually present with pancreatitis, and thus the test almost always consistent.
Heterozygotes are often asymtomatic and hence value lower.
Based on clinic population as no real published data.
For homozygotes: 5 true ‘LPLD’ homozygotes; 2 clinical homozygotes (genetic heterozygotes)
compared to 130 patients with TG>20mmol/L (99% homozygous normal; 1 heterozygote for LPLD)
PPV=83%; NPV=98%
25. Testing pathway for tests where more than one gene is to be tested sequentially
Please include your testing strategy if more than one gene will be tested and data on the expected proportions of positive
results for each part of the process. Please illustrate this with a flow diagram. This will be added to the published Testing
Criteria.
n/a for panel tests
Simultaneous testing of the 5 genes
90% LPL, 4% apoC2 and the rest in the other genes (apoA5> GPIHBP1> LMF-1).
CLINICAL UTILITY
26. How will the test change the management of the patient and/or alter clinical outcome?
Please describe associated benefits for patients and family members. If there are any cost
savings AFTER the diagnosis, please detail them here.
Homozygotes
A novel gene therapy has been licensed in the EU for treatment of homozygous LPL gene deficiency
with chylomicronaemia (Alipogene tiparvovec; Glybera). Genetic diagnosis required prior to its
administration.
Wierzbicki AS, Viljoen A. Alipogene tiparvovec: gene therapy for lipoprotein lipase deficiency. Expert Opin Biol Ther. 2013
Jan;13(1):7-10. doi: 10.1517/14712598.2013.738663.
Heterozygotes
Confirm aetiology of hypertriglyceridaemia. Will determine likelihood of drug response to certain drugs
e.g. fibrates (LPL, apopC2 synthesis activators through PPAR-alpha) and possibly eligibility for more
novel specific treatments for orphan disorders e.g. lomitapide.
Approval Date: September 2014
Submitting Laboratory: Aberdeen RGC
Copyright UKGTN © 2014
Viljoen A, Wierzbicki AS. Diagnosis and treatment of severe hypertriglyceridemia. Expert Rev Cardiovasc Ther. 2012
Apr;10(4):505-14. doi: 10.1586/erc.12.21.
27. If this test was not available, what would be the consequences for patients and family
members?
EMEA/MHRA protocols for the prescription of Alipogene tiparvovec (Glybera) require proof of an
underlying homozygous LPL mutation for its prescription. Patients would not receive this therapy in the
absence of genetic testing. Similarly though it is not essential good clinical practice for the off-label
prescription of lomitapide (Juxtapid) in severe hypertriglyceidaemia with pancreatitis requires
demonstration of a defect in the LPL-related pathways.
28. Is there an alternative means of diagnosis or prediction that does not involve molecular
diagnosis? If so (and in particular if there is a biochemical test), please state the added advantage of
the molecular test.
Lipoprotein lipase activity can be measured using an invasive day-case admission procedure involving
infusion of a heparin followed by repeated sampling. The assay is very difficult to perform, insensitive
and poorly standardised. A LPL ELISA assay exists but many patients with LPL deficiency have normal
mass of enzyme though no activity.
29a. What unexpected findings could this test show? For example, lung cancer susceptibility
when testing for congenital cataract because ERCC6 gene (primarily associated with lung
cancer) is included in a panel test for congenital cataract.
None expected
29b. Please list any genes where the main phenotype associated with that gene is unrelated to
the phenotype being tested by the panel.
N/A
30. If testing highlights a condition that is very different from that being tested for, please
outline your strategy for dealing with this situation.
N/A
31. If a panel test, is this replacing an existing panel/multi gene test and/or other tests currently
carried out through UKGTN using Sanger sequencing? If so, please provide details below.
N/A
32. Please describe any specific ethical, legal or social issues with this particular test.
None
IS IT A REASONABLE COST TO THE PUBLIC?
33. In order to establish the potential costs/savings that could be realised in the diagnostic care
pathway, please list the tests/procedures that would be required in the index case to make a
diagnosis if this genetic test was not available.
Costs and type of imaging procedures
Costs and types of laboratory pathology tests
(other than molecular/cyto genetic test proposed in this Gene
Dossier)
Costs and types of physiological tests (e.g. ECG)
Cost and types of other investigations/procedures (e.g. biopsy)
Total cost of tests/procedures no longer required
(please write n/a if the genetic test does not replace any other
tests procedures in the diagnostic care pathway)
Type of test
N/A
LPL assays
Cost (£)
£200 each
N/A
N/A
Approval Date: September 2014
£200/patient
Submitting Laboratory: Aberdeen RGC
Copyright UKGTN © 2014
34. Based on the expected annual activity of index cases (Q14), please calculate the estimated
annual savings/investments based on information provided in Q33.
Number of index cases expected annually
Cost to provide tests for index cases if the
genetic test in this Gene Dossier was not
available (see Q32)
Total annual costs pre genetic test
Total annual costs to provide genetic test
Additional investment for 100% positive rate for
index cases
Percentage of index cases estimated to be
negative
Number of index cases estimated to be negative
Costs to provide additional tests for index cases
testing negative
Total costs for tests for index patient activity
350
£200/patient
Total costs for family members
4 X £140 (specific mutation test cost) X 225+ve
index cases = £126,000
If there is a genetic test already available and
some of the family testing is already being
provided, please advise the cost of the family
testing already available
Total costs for family members minus any family
member testing costs already provided
Additional costs for all activity expected in a year
N/A
350 patients X £200 = £70,000
350 patients x £525 = £183,750
£183,750 - £70,000 = £113,750
~36% (combined homozygote and heterozygote
– assuming 90% sens homoz and 60% hets)
125 (combined homoz and hets)
£200 x 125= £25,000
113,750 +25000 = £138,750
N/A
138,750 +126000 = £264,750 investment
As noted above (Q27), EMEA/MHRA protocols for the prescription of Alipogene tiparvovec (Glybera)
require proof of an underlying homozygous LPL mutation for its prescription. Patients would not receive
this therapy in the absence of genetic testing. Similarly though it is not essential good clinical practice
for the off-label prescription of lomitapide (Juxtapid) in severe hypertriglyceidaemia with pancreatitis
requires demonstration of a defect in the LPL-related pathways.
Further genetic testing would be an advantage for the patient in terms of diagnosis rather that
lipoprotein lipase activity measurement as noted in Q28. (LPL acitivity is measured using an invasive
day-case admission procedure involving infusion of a heparin followed by repeated sampling. The
assay is very difficult to perform, insensitive and poorly standardised. A LPL ELISA assay exists but
many patients with LPL deficiency have normal mass of enzyme though no activity).
35. REAL LIFE CASE STUDY
Please provide a case study that illustrates the benefits of this test
The presentation was of a 25 year old woman who had had episodes of severe abdominal pain since
the age of 11. One severe recent episode resulted in an admission with pancreatitis at which point it
was noted her blood sample was lipaemic though the laboratory could not determine the extent of the
triglyceride elevation. She was then referred to a specialist lipid clinic for further evaluation at which
point it was found that her triglycerides were 35mmol/L. She was commenced on a ultra-low fat diet
which she found difficult to comply with and then fenofibrate and omega-3 fatty acid therapy. These
reduced her triglycerides to 20mmol/L but she still continued to have episodes of abdominal pain. She
was then referred to a tertiary centre and her lipid-lowering therapy was maximised by the combination
of a fibrate, statins and omega-3 fatty acids but here triglycerides never reduced below 11mmol/L. Lipid
ultracentrifugation determined that she had about 60% chylomicrons and 20% very-low density
lipoprotein cholesterol/ triglycerides with a diagnosis consistent with type I rather than type V
hyperlipidaemia Genetic analysis (Amsterdam Medical Centre) confirmed she had a familial
Approval Date: September 2014
Submitting Laboratory: Aberdeen RGC
Copyright UKGTN © 2014
hyperchylomicronaemia syndrome with point mutations in both LPL alleles. She is now a candidate for
alipogene tiparvovec therapy now this is licensed in the UK.
TESTING CRITERIA
36. Please only complete this question if there is previously approved Testing Criteria.
Please contact the UKGTN office if you are unsure whether testing criteria is available.
36a. Do you agree with the previously approved Testing Criteria? Yes/No
36b. If you do not agree, please provide revised Testing Criteria on the Testing Criteria form and
explain below the reasons for the changes.
Approval Date: September 2014
Submitting Laboratory: Aberdeen RGC
Copyright UKGTN © 2014
UKGTN Testing Criteria
Test name:
Lipoprotein Lipase Deficiency
Approved name and symbol of disorder/condition(s):
Hyperlipoproteinemia, Type I/V
OMIM number(s):
238600
Approved name and symbol of gene(s):
lipoprotein lipase; LPL
apolipoprotein C-II; APOC2
lipase maturation factor 1; LMF-1
apolipoprotein A-V; APOA5
glycosylphosphatidylinositol anchored high density lipoprotein binding
protein 1; GPI-HBP1
OMIM number(s):
609708
608083
611761
606368
612757
Patient name:
Date of birth:
Patient postcode:
NHS number:
Name of referrer:
Title/Position:
Lab ID:
Referrals will only be accepted from one of the following:
Referrer
Tick if this refers to
you.
Consultant Metabolic Medicine/Chemical Pathology
Consultant Clinical Geneticist
Consultant Metabolic Paediatrician
Minimum criteria required for testing to be appropriate as stated in the Gene Dossier:
Criteria
Tick if this patient
meets criteria
Fasting triglycerides > 20 mmol/L
AND History of admission for pancreatitis
AND Exclusion of secondary causes of hypertriglyceridaemia
e.g. excess alcohol; uncontrolled diabetes
At risk family members where familial mutation is known.
Additional Information:
If the sample does not fulfil the clinical criteria or you are not one of the specified types of
referrer and you still feel that testing should be performed please contact the laboratory to
discuss testing of the sample.
Approval Date: September 2014
Submitting Laboratory: Aberdeen RGC
Copyright UKGTN © 2014