(The following is a summary from James O'Brien, IPWSO Board member, from Australia, who attended the recent IPWSO Conference in Toronto)
A Novel FMR1/SNRPN methlation test for Fragile
X Syndrome and chromosome 15 imprinting disorder screening of symptomatic
children and newborns.
By David Godler, Cyto-Molecular Diagnostics
Research Laboratory, Victorian Clinical Genetics Services, Murdoch Children’s
Research Institute, Melbourne, Australia.
David Godler
spoke about his research into newborn bloodspot screening over the past 18 months,
primarily into Fragile X diagnostic. Recent funding from the Foundation for
Prader-Willi Research, USA, has enabled David to expand his work with fragile X
to include the Chromosome 15 imprinting disorders: Prader-Willi Syndrome (PWS),
Angelman Syndrome and 15Q Duplication Syndrome.
The
presentation was about David’s two new methods of testing blood collected in a
tube and blood spots from adults, children and newborns. A newborn blood spot
is the tiny spot of dried blood on blotting paper that is already taken through
a heel pin prick for almost all newborns within the first few days of life in many
countries. The tests currently performed on this material identify 30 or so
conditions including phenylketonuria, hypothyroidism and cystic fibrosis, but
not PWS.
Initially
David and his team developed a new Methylated Specific Quantitate Melt Analysis
(MS-QMA) test for Fragile X. To enable him to test 100,000 newborn bloodspots
he also developed technologies to automate the process and to confirm positive
findings. He is now able to test 100 samples in 90 minutes rather than the old
2 to 3 day turnaround for each test. At the same time his team developed new
software to monitor both the results and accuracy of the test, and this method
had been published for Fragile X. Accuracy of this test appears to be nearing
100%.
The beauty
of his new test is that it can be performed on blood spot material left over
from other routine testing. This means that the babies suspected of PWS would
not be required to undergo collection of another blood sample required for more
traditional diagnostic methods. It would also mean that the PWS babies that may
not be tested for PWS and initially missed because they may be premature or may
not have typical PWS, would be picked up by this new test. This would be
because newborn blood spot testing reaches virtually all babies born
irrespective of symptoms, but current PWS testing is only performed on babies
that show symptoms that are recognized by doctors to be associated with PWS.
David’s
first step in PWS test development was to analyse blood DNA samples from
patients that had PWS symptoms, with only 9 patients confirmed to have PWS by
standard DNa testing. From the first 30 symptomatic referral samples tested, his
MS-QMA test confirmed 100% agreement for samples positive by standard testing.
In addition to these 3 previously undiagnosed cases of PWS were
identified. In order to prove that his new test was not simply showing false
positives, David needed to develop an even more accurate second line
confirmation test.
His second
test he has called CINQ Droplet Digital PCR, which looks at individual
methylated and unmethylated chromosomes suspended in miniature droplets. Exact
details of how this new test works (or what the letters even stand for) are not
yet published, however, its accuracy appears to be much higher again than
standard testing, able to detect abnormal methylation down to an unprecedented less
than 0.1% in the PWS deletion group. Furthermore, the new test has
confirmed positive MS-QMA results missed by standard testing, and is showing
that a number of previously diagnosed Uni Paternal Disomy (UPD) individuals may
actually be Triasomi 15. The unexpressed male 15 chromosome appears to be
hiding in the background rather than showing up on previous more traditional
tests.
Furthermore,
a new group of Mosaic PWS is likely to emerge. David is doing some further work
on this subset. (With mosacizm PWS may not be present in every cell in the
body. Depending on which cells in the body have the PWS variations may result
in changes in how the characteristics of the Syndrome present, especially in
UPD).
So, what does this mean for children with PWS?
- · David and his team have come up with two new and seemingly very accurate methods of testing for PWS using blood spots and other sample types.
- · The tests appear to be picking up previously unconfirmed cases of PWS.
- · A new subset of T15 within the UPD group seems likely.
- · A new phenotype of Mosacizm is possible.
- · Bloodspots can be taken at newborn or at any age, resulting in a less invasive, more accessible and sensitive method of obtaining a PWS DNA test than is currently available.
Where to from here?
In 2015
David and his team have been awarded a large NHMRC grant to test 100,000
newborns for fragile X (the world’s largest fragile X prevalence study), and is
hoping to use the remaining materials and expensive infrastructure initially
developed for Fragile X, for PWS testing. Funding is currently an issue for
this larger project, and David is now applying to multiple granting bodies to
make this possible. In a less expensive project, over the next 3 years David
and his team has started recruiting and assessing PWS patients to perform
analysis of how the low level mosaicism identified by his two new tests related
to variation in severity of PWS, especially in UPD. Concurrently, PWSA
Australia has commissioned a Health Economics Report to analyse the financial
benefit of early diagnosis. If the test is proven accurate, David and PWSA
Australia will approach State or National Newborn Bloodspot Screening Programs with
his two tests and our Health Economics Report to apply for the inclusion of PWS
in their testing programs for all babies born in Australia.
If
admission to the NBS programs is successful:
· We should start to see a diagnosis
within a few days of birth avoiding unnecessary multiple tests and prolonged
family stress when waiting for a diagnosis.
· Doctors, specialists and scientists
will be able to develop a more detailed understanding of the various phenotypes
of PWS, possibly enabling better targeted clinical interventions.
· Testing of all babies will give a
definitive answer regarding the prevalence of PWS live births in Australia.
David cited
individual colleges that are assisting in the research from Cyto-Molecular
Diagnostic Research Group, Victorian Clinical Genetics Services, Royal
Children’s Hospital, Victorian and New South Wales Newborn and Metabolic
Screening laboratories, Genetics and Learning Disabilities Services (Newcastle
and The Children’s Hospital (Westmead, Sydney).
David also
acknowledged assistance from a number of organisations including VCGS, Royal
Children’s Hospital Foundation, The Marion and EH Flick Trust, Australian
Government, Thrasher Research Fund, and Foundation for Prader Willi Research
Note: This
report is James O’Brien’s understanding of David Golder’s presentation and may
contain inaccuracies in its interpretation. 4 August 2016