Embryo Genetic Testing Like Illumina And BlueGnome's Version Doubles Rate Of 'Singleton' Babies From In Vitro Fertilization

| About: Illumina, Inc. (ILMN)

Millions of infertile women will soon get the biggest baby boost in a generation from preimplantation genetic diagnosis (PGD), which identifies their healthiest embryos at in vitro fertilization (IVF) clinics.
The blastocyst, when the embryo has reached 50-150 cells, is a very favorable stage for implantation and pregnancy. The inner cell mass contains the cells that will give rise to the actual cells of the fetus. The other cells that surround and protect the inner cell mass give rise to the fetal part of the placenta. Photo: Robert Shabanowitz, Gesinger Medical Cente
Completed studies and preliminary results from others show that PGD doubles the chances of a woman in her mid-30s to early-40s of delivering a single, healthy baby per IVF attempt to nearly 60 percent from the current U.S. average of about 31 percent.

Biotech opportunities

Biotech companies, including Affymetrix (NASDAQ:AFFX), BlueGnome Ltd, GE Healthcare (NYSE:GE), Illumina (NASDAQ:ILMN), Life Technologies (NASDAQ:LIFE), Perkin Elmer (NYSE:PKI), Qiagen, Inc. (NASDAQ:QGEN), Rubicon Genomics, Sigma-Aldrich Corp., (NASDAQ:SIAL) and others are racing to improve the technologies needed in commercialized PGD platforms. The result will be technology moving from the research lab to commercial availability of faster, more accurate genetic analyses of genomes of single cells biopsied from embryos.

To pick winners in this race, alliances and acquisitions matter. PGD requires two technologies: one to amplify 100,000 times the genome of a single or a few cells biopsied from an embryo's coat of placental cells; and the second is DNA microarrays with thousands of specific sequences that act to interrogate the embryonic cells for correct chromosome number. Both whole genome amplification and microarrays are required, and they must be compatible.

The only company with both is DNA sequencing and microarray giant Illumina (ILMN), which in September acquired Cambridge, U.K.-based BlueGnome Ltd., for an undisclosed amount. Illumina has a highly effective array technology and the privately held BlueGnome has developed a type of DNA-amplification that, when combined with Illumina's arrays, generates a PGD in 24 hours.

"It's always easier to have 'one-stop shopping' for IVF clinics," said William Quirk, an analyst with Piper Jaffray. "No doubt Illumina will optimize the protocols, further improving workflows, an important and frequently overlooked feature."

In an electronic push-pad audience survey taken Oct. 22 in an auditorium of about 200 IVF clinicians at the American Society for Reproductive Medicine annual meeting in San Diego, Calif., 85 percent of the audience said they offer PGD to their patients. Research presented at the meeting suggests that it may soon become the standard of care for women seeking IVF services.

Preimplantation genetic diagnosis (PGD)

Preimplantation genetic diagnosis is designed to identify embryos with too many or too few chromosomes, a condition called aneuploidy. The healthiest looking euploid, or normal embryo with two pairs of 22 chromosomes plus an XX or XY pair is transferred to a patient at an in vitro fertilization (IVF) clinic. Image: Eric Forman, Reproductive Medicine Associates of New JerseyStudies have shown that most instances of failed pregnancies are due to the transfer of embryos with too many or too few chromosomes. However, transferring a single embryo with the correct number of 46 chromosomes not only increases the rate of ongoing pregnancies and viable births per IVF attempt, but also nearly eliminates multiple births, which can be dangerous to mother and children and are expensive.

The results of 384 IVF clinics in 2001 and 443 clinics in 2010 compiled in the Assisted Reproductive Technology Report by the U.S. Centers for Disease Control and Prevention (CDC) said, respectively, 21 percent and 31 percent of women less than 35 years old delivered a "singleton" baby per IVF cycle. For women aged 41-42, only 8.5 percent and 12.4 percent delivered a singleton baby per IVF cycle, respectively, in 2001 and 2010, according to the CDC report.

A new study of 170 women presented at the American Society for Reproductive Medicine's annual meeting reported that adding PGD to the evaluation and selection of the healthiest embryo increases the rate of singleton births to close to 60 percent per IVF cycle in women over age 35 up to age 42.

The new PGD technology adds about $5,000 to the $12,400 average cost of an IVF cycle, according to fertility doctors. However, the greatly enhanced rate of single births per IVF cycle is expected to increase demand for those IVF services that offer PGD.

Picking healthiest embryo
Dr. Mandy Katz-Jaffe examines embryos microscopically at the Colorado Center for Reproductive Medicine in Lone Tree, Colo. Photo: Colorado Center for Reproductive Medicine
Women aged 35 produce an average of 12 or more embryos per hormone-enhanced IVF cycle, half of which have the correct number of 46 chromosomes. The number of embryos decline with age, and the percent of embryos with too few or too many chromosomes, a condition called aneuploidy, increase with maternal age.

PGD involves a biopsy of each embryo to determine its aneuploidy status: one or a few cells must be taken from the outer layer of each 5-day-old embryo produced. These cells, which are destined to become the placenta, can be removed with no ill effects.

The DNA from a single cell is multiplied about 100 million times and added to a DNA array screening to determine if the correct number of chromosomes is present in the cell. These tests can take as few as four hours to as long as three or four days.

All the currently available PGD technologies require whole genome amplification to generate enough DNA to work in the DNA array screening tests. However, each kind of whole genome amplification now used suffers from random, incomplete or preferential amplification artifacts, according to a review paper published in the March 27, 2012, issue of Frontiers in Genetics.

The review by Belgian genome-research experts said new whole-genome amplification techniques being developed by Sigma-Aldrich and BlueGnome "are an improvement over previous" methods. In addition, BlueGnome and Perkin Elmer have developed the accompanying DNA-array tests for the presence or absence of several thousand specific regions of all 24 human chromosomes. "Both commercial platforms have the potential to enable the detection of whole-chromosome aneuploidies in single cells in a 24-hour protocol as required in preimplantation genetic testing and provide custom software tools for copy number variation calling," said the authors of the paper in Frontiers in Genetics.

The clinical director of Reproductive Medicine Associates of New Jersey reported that his clinic's in-house PGD service is capable of generating PGD results in four hours, which means that when a woman's 5-day-old embryos are tested, the healthiest one can be implanted the next day. Testing that requires three to four days require that the embryos be frozen: the healthiest embryo can then be thawed with no ill effects for transfer when its PGD results are known.

Richard Scott, MD, a leading U.S. fertility expert and co-author of several studies to be presented at the American Society for Reproductive Medicine's annual meeting, said PGD results in an ongoing pregnancy rate of nearly 70 percent per IVF attempt for women between the ages of 35 and 42. He said that percentage is based on his group's in-house PGD testing in a randomized study involving 170 women at one IVF clinic with and without PGD testing.

Scott said IVF clinics in the U.S. and other countries that use such validated PGD and follow best practices for IVF clinics should be able to reproduce a 60-70 percent rate for singleton births per attempt to women in their 30s to early 40s.

Fixing multiple-birth problem

However, the current accepted practice among most U.S. IVF clinics is to transfer two or more embryos per attempt to patients. The result is multiple births in 34 percent of the time in women less than 35 years old with live births, according to the CDC's 2010 Assisted Reproductive Technology Report.

Scott, clinical and science director of Reproductive Medicine Associates of New Jersey, said that such a high, unwanted rate of multiple births can be cut to near zero by transferring a single healthy embryo to each patient per IVF cycle. (A single embryo occasionally splits into two after it is transferred to patients, resulting in identical twins at birth.)

In Scott's most recent study to be presented at the annual meeting in San Diego, 68 percent of women 35-42 years old who were given a single embryo with the correct number of chromosomes gave birth or have a single fetus in an ongoing pregnancy. There were no multiple births or pregnancies.

Singleton birth rate

"We think that just 'pregnancy rate' is not the best way to estimate the success of an IVF cycle: to have a single baby is really ideal," said Eric Forman, MD, senior fellow at Reproductive Medicine Associates of New Jersey and co-author of the study with Scott. "The mothers and newborns involved in multiple births from IVF have more medical and health problems than singleton births and the additional costs are about $1 billion a year."

In cases where a male and female embryo each has the right number of chromosomes, patients can be confronted with which to choose. "In clinical practice, gender preference occasionally comes up, but we try to recommend against it," Forman said. He said the embryo that looks healthiest under the microscope, regardless of gender, is recommended for transfer.

Scaling genetic diagnosis technology

Reproductive Medicine Associates of New Jersey has refined a PGD test based on an Affymetrix platform. "We have begun offering this randomized-trial validated preimplantation genetic diagnosis technology to our patients in New Jersey and also to a limited number of IVF clinics around the country," Scott said. "And we're scaling up."

PGD is exempt from regulation in the U.S. because it is a politically charged medical topic, which means that companies may offer PGD services that haven't been validated in randomized-patient trials.

Scott is expected to soon be competing with the likes of Illumina with its newly acquired BlueGnome unit.

However, Scott argued that randomized patient trials of PGD services, which his service has reported, may be required by insurance companies and the medical community to ensure validation of their clinical accuracy. "The accuracy of the BlueGnome technology is assessed in laboratory cell lines, but it's not been validated in randomized trials involving patients," said Scott. "I'm not saying their answers are wrong, but I can't say they're right."

When asked about BlueGnome's technology, Jennifer Viera, a spokeswoman for Illumina and BlueGnome, said, "We aren't able to comment on your questions at this time."

Chromosome number, quality

Simply ensuring that an embryo has 23 pairs of chromosomes is not a guarantee of a successful pregnancy and genetic health. Indeed, Scott points out that even in patients with a 70 percent success rate per IVF attempt, "What happened in the other 30 percent?"

The analysis of DNA in a single cell removed from an embryo may indicate that it has the correct number of 46 chromosomes; however, other untested cells in the same embryo may have a chromosome imbalance. If those embryos with so-called mosaicism are transferred to patients, a failed pregnancy could be the result, or baby born with a medical conditions requiring treatment.

To complicate matters, studies have found that 7 to 32 percent of embryos tested have segments of chromosomes that have rearranged in some way, which could adversely affect the rate of successful pregnancies or lead to health complications after birth.

Various PGD techniques are being developed by biotech companies and academic institutions and tested a small scale. In these experiments, whole-genome amplification combined with DNA microarrays are capable of identifying not only, chromosome aneuploidy, but also tell-tale changes in a single base pair in a gene, called single-nucleotide polymorphisms ((SNPs)). These SNPs are scattered at thousands of points across all human chromosomes. Knowing which ones are present in a given embryo's genome is extremely revealing about the health of a potential offspring.

SNP arrays being developed for PGD assess the presence of millions of unique sequences in the human genome, including many known to be associated with diseases. Such arrays will identify not only the potential offspring's sex and physical characteristics, but also any disease-causing mutations, predispositions to diseases, and mutations that cause late-in-life disorders such as Alzheimer's disease, certain forms of Parkinson's disease, and others.

More than 30 microarray companies, including leaders Affymetrix, Illumina, Agilent Technologies (NYSE:A) and Incyte (NASDAQ:INCY) and others are working on genome-amplification and array approaches capable of accurately diagnosing the presence of both aneuploidy as well as the presence of genetic defects that cause cystic fibrosis, Marfan syndrome, Lynch syndrome, polycystic kidney disease, breast and ovarian cancers, and many other inherited disorders.

In a view of what may soon be widely available, several scientific papers have described cases in which a woman's embryos were tested for disease-causing genes: healthy ones were selected for transfer, and the results were births of disease-free babies.

Better-off children

As PGD has become more widely used, many ethicists have taken a neutral position in it. Many argue that the technology is "morally permissible," but back away from focusing on the relative ethical merits of the duty to make a child better off versus making a better-off child.

Costs of medical care of potential children add another dimension to the debate. Who should pay for PGD? Janet Malek, a bioethics professor at East Carolina University, and Judith Daar, a law professor and associate dean at Whittier College Law School in California, say health insurance providers will be affected by how that question is framed.

"Ideally, recognition of a duty to use preimplantation genetic diagnosis would be accompanied by a mandate to provide coverage on the part of payers who would ultimately be responsible for supporting the health care of an affected offspring," Malek and Daar wrote in an article published in the March 27, 2012, issue of American Journal of Bioethics. "Shifting benefit outlays for significant post-birth health care to a far less costly preconception procedure strikes us as a worthy public policy trade-off."

As the speed, validation and sophistication of assisted reproductive technologies improve, current and future generations of PGD technologies should be embraced by all who care about making children better off, and making better-off children.

Disclosure: I have no positions in any stocks mentioned, and no plans to initiate any positions within the next 72 hours. I wrote this article myself, and it expresses my own opinions. I am not receiving compensation for it. I have no business relationship with any company whose stock is mentioned in this article.