Italian Team Validates Preimplantation Screening Method Behind Illumina's Upcoming Commercial Test | Clinical Sequencing News | Clinical Genomics | GenomeWeb
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Thursday, March 27, 2014
Italian Team Validates Preimplantation Screening Method
Behind Illumina's Upcoming Commercial Test
In this issue of Clinical
March 26, 2014
Sequencing News
By Molika Ashford
Type size:
Researchers from Italy's Genoma Molecular Genetics
Laboratory in Rome have published a validation of an Illumina
sequencing method for preimplantation genetic diagnosis and
screening that they said reflects closely the methodology
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behind the VeriSeq commercial PGS test Illumina plans to
launch later this year.
The study, published online this month in the journal Fertility and Sterility,
retrospectively compared the sequencing approach to established aneuploidy results
from previous array-CGH testing of 68 embryos, as well as results in single cells from
cultured amniotic fluids or products of conception.
Italian Team Validates
Preimplantation Screening Method
Behind Illumina's Upcoming
Commercial Test
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Cancer Dx Labs Explore NGS Gene Fusion
Assays from Enzymatics, Fusion Genomics
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According to the authors, the sequencing method, which involved paired-end
sequencing on the Illumina HISeq2000 of amplification products created using
BlueGnome technology, showed 100 percent sensitivity and specificity in identifying
aneuploid embryos, a promising indication of its clinical validity and potential utility
compared to current methods.
Francesco Fiorentino, the study's first author told Clinical Sequencing News in an email
that his group decided to work with Illumina to validate the method because it believed
sequencing-based PGS could reduce costs and enhance precision compared to
current methods, which rely on various types of microarrays.
"We wanted to use Illumina's sequencing technology because of its reliability, wider
experience in the NGS field compared to other technologies, [and] also because
[these] NGS instruments were already available in [our] lab," Fiorentino wrote.
According to Fiorentino, "from [a] technical point of view," the protocol used in his
team's study is "very similar" to the protocol behind the commercial sequencing PGS
test, VeriSeq, that Illumina has said it plans to launch during the second quarter of this
year.
Based on the results of the lab's completed validation work so far, Fiorentino said
Genoma will "certainly adopt" VeriSeq after its launch.
"We are very keen to introduce this technology on [a] clinical basis," he wrote, adding
that the lab would consider other NGS approaches to PGS "only after being thoroughly
validated and after having demonstrated similar performances and characteristics."
Tristan Orpin, senior vice president of Illumina’s reproductive and genetic health
business told CSN in an email that Genoma has been a customer "for a number of
years and was selected to take part in the beta validation and early access of the PGS
solution using NGS [while] a number of other groups around the world are also
validating this application on Illumina sequencing platforms.”
Apart from the Genoma lab's efforts using Illumina sequencing, other groups are also
exploring alternate sequencing strategies for NGS-based preimplantation screening.
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Reproductive Medicine Associates of New Jersey announced earlier this year that it is
currently enrolling patients in a clinical validation trial of a targeted NGS strategy using
the Ion Torrent PGM and a set of sequence-specific primers for preimplantation
genetic testing to aid in the selection of embryos for transfer as part of in vitro
fertilization.
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Dagan Wells from the University of Oxford's Nuffield department of obstetrics and
Xiaoliang Sunney Xie from Harvard University have also reported on single-cell
sequencing techniques to improve IVF success rates.
BGI has also been testing a method, published in PLoS One, for detecting copy
number variants from single-cell, low-pass, whole-genome sequencing on couples
undergoing IVF, and China's Berry Genomics offers a single-cell sequencing test for
preimplantation genetic diagnosis called Chrosure.
According to Fiorentino, though interest is growing, no group has yet published an
extensive validation of NGS-based PGS.
"We are hopeful that publication of our work in a full, peer-reviewed format will allow
others to assess and reproduce our data and begin to assess the use of NGS for
preimplantation genetic screening and perhaps other forms of preimplantation genetic
testing methodologies," he wrote.
According to Fiorentino and Illumina, the Genoma group's published study represents
the first section of a three-phase strategy to validate the use of the Illumina method for
comprehensive aneuploidy screening as a preclinical step "toward its routine use in the
diagnosis of chromosomal aneuploidy on embryos."
These first validation results showed that the approach was 100 percent consistent in
its aneuploid embryo calls with array-CGH results using Illumina’s 24sure array, a
current widely-used test originally developed by BlueGnome, which Illumina acquired
in 2012.
A recent survey found
that oncologists have
varying degrees of
"genomic confidence,"
which affects their
use of certain genetic
tests. How do you
think physicians'
genetic knowledge
can be bolstered?
Medical schools should
emphasize genetics and
genomics.
Continuing medical
education in genetics and
genomics should be
encouraged.
Guidelines for the use
of such tests should be
developed.
Diagnostic companies
should explain the benefits
of their tests.
All of the above
The second phase of the three-part validation strategy has focused on clinical
application of the NGS protocol in a prospective trial involving analysis of human
embryos at blastocyst stage of development.
None of the above
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Beyond this, the team is also studying pregnancy rates following transfer of screened
embryos to establish that the NGS method does as well or better than current array
methods in terms of its ultimate outcome in allowing successful births.
"The only effective way to demonstrate its clinical usefulness is to perform a well
designed and well executed [randomized controlled trial], showing actual
improvements in clinical outcomes. The results of the above study will be critical when
considering the use of this new technology in a clinical setting and will help to outline
the potential for routine clinical use of NGS-based preimplantation embryo
assessment," Fiorentino wrote.
Fiorentino told CSN in a later interview that the team's followup prospective study is
already complete and the group is submitting it now for publication.
"The results overlapped well with the validation that has just been published," he said.
"We compared [NGS again] to array CGH results using the BlueGnome 24sure array
and we achieved a very high rate of pregnancy."
Moving forward, Fiorentino said Genoma is also working on a study using mixes of
euploid and aneuploid cells to assess the accuracy and resolution limit of the Illumina
method for detecting chromosomal mosaicism.
"Now that trophectoderm biopsy is becoming the preferred stage for PGS, mosaicism
may represent an issue in the analysis and interpretation of the results after
[chromosomal screening]. Although its significance for implantation and the
developmental potential of embryos is still unclear, it is reasonable to assume that this
phenomenon is likely to influence IVF success rates," he wrote.
Illumina declined to comment further on when it expects to launch VeriSeq this year.
Molika Ashford is a GenomeWeb contributing editor and covers
personalized medicine and molecular diagnostics. E-mail Molika
Ashford.
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