New technologies pave way for fetal personalized medicine

Fetal genomic sequencing holds promise but heightens ethical concerns

Recent papers detailing whole genome sequencing (WGS) of fetuses using cell-free fetal DNA in mothers' blood underscore how new technologies are moving prenatal genetic testing beyond helping parents make informed decisions about pregnancies or plan for children's futures to determining future in utero treatments. Research teams from Stanford University and the University of Washington (UW) detail their WGS findings in Nature and Science Translational Medicine, respectively.

Current clinical technologies like chromosomal microarray, technologies using cell-free fetal DNA to detect aneuploidy, and promising reports on use of RNA in maternal blood, the placenta, and cord blood have identified many genes involved in placental and fetal development that could lead to individualized prenatal treatments, writes prenatal geneticist Diana Bianchi, MD [Bianchi, 2012].

“We are really at a time of paradigm shifting in prenatal diagnosis. We have had a well-established clinical algorithm, but that's about to change,” Dr. Bianchi tells “The AJMG Sequence.” She is Professor of Pediatrics, Obstetrics, and Gynecology at Tufts University in Boston, Massachusetts, past president of the International Society of Prenatal Diagnosis, and Editor-in-Chief of Prenatal Diagnosis.

As molecular technologies advance and costs decrease, genetic disease diagnosis in the first trimester of pregnancy could become common before prenatal treatments arrive in the clinic. But use of these technologies for traditional informational purposes is still expensive and fraught with ethical issues similar to those that arise from the use of WGS in infants and children. Those ethical concerns become more stark in prenatal testing because abnormal results may lead some parents to terminate pregnancies.

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New fetal genetic testing technologies are increasing the amount of information patents have—but there are many ethical questions about what to do with the data.

Fetal Genome Sequencing

The Stanford researchers, led by Stephen Quake, MD, built fetal genomes in two pregnancies without using fathers' samples, a feat that could have implications for situations involving disputed paternity or when a father can't or won't supply his genetic material [Fan et al., 2012].

The researchers deduced from fetal WGS that a mother with DiGeorge syndrome passed the disease-associated deletion to her fetus, providing an example of clinical utility, says first author Christina Fan, PhD, a Senior Scientist at the biotech startup ImmuMetrix and a former Stanford graduate student.

The Stanford team used haplotyping, which examines groups of alleles inherited together and involves comparing the relative levels of alleles from the mother and fetus. They then sequenced maternal plasma DNA from the fetus, Dr. Fan explains. To determine paternally inherited chromosomes, researchers detected alleles different from the mother's, combined with additional computational techniques and additional targeted sequencing. “We might have detected de novo mutations, but given that we don't have the father's genomic DNA as reference, we cannot differentiate de novo mutations from something that is inherited from the father,” Dr. Fan says.

The UW researchers, who also used haplotyping as well as DNA from the father's saliva, identified 39 of the baby's 44 new mutations, albeit with a huge number of false positives [Kitzman et al., 2012]. The team is working to diminish false positives, says first author Jacob Kitzman, a UW Genome Sciences PhD candidate. The researchers are more deeply sequencing DNA in maternal plasma by making many more readings. “The more you see the de novo mutation, the more you gain confidence that it's real,” he explains.

Dr. Bianchi's paper discusses various molecular tests that are either increasingly used or have the potential for use in prenatal diagnostics. Cell-free fetal DNA in maternal plasma, aside from its use in WGS, is also used in rhesus D genotyping, and in identifying aneuploidy, submicroscopic chromosome abnormalities, and single-gene disorders. Chromosome microarray analysis of fetal DNA obtained from amniocentesis or chorionic villus sampling can also determine single gene diseases, find submicroscopic fetal abnormalities, and detect copy-number variations in the genome, the paper notes.

Experimental methods that analyze cell-free RNA in amniotic fluid, maternal and core blood, and the placenta may improve knowledge of how fetal diseases progress, thus aiding the development of new biomarkers and therapeutic targets, Dr. Bianchi writes.

Ethical Problems

“This is a dynamic and exciting time, but an unsettling one for those on the front lines providing care,” says Dr. Bianchi. That's because new technologies used in prenatal care raise several ethical issues, which mostly mirror those in testing of infants and children. For example, microarray studies and WGS can yield copy-number variations of unknown clinical meaning or variants that cause varying phenotypes, resulting in unfounded parental anxiety. Also important are questions about proper informed consent and whether to reveal information about variants that can lead to adult-onset diseases.

In the prenatal setting, however, the stakes are higher because, without the benefit of providers' having seen infants and phenotypes as pediatric geneticists do, parents may consider terminating the pregnancy based on abnormal test results, says Dr. Bianchi.

In the case of Down syndrome, increasingly popular cell-free fetal DNA tests may, in the future, enable quicker decisions about termination because they would eliminate “several opportunities for reflection” that come with the current multistep screening process, she adds.

A recent statement from the International Society for Prenatal Diagnosis (ISPD) warns that these tests are not fully diagnostic, so their results need confirmation with an invasive method. ISPD calls for evidence of tests' efficacy in low-risk, twin, and in vitro fertilization pregnancies and their cost-effective, timely, and equitable use [Benn et al., 2012].

Questions about equity apply to all the new genomic technologies, says Jeffrey Botkin, MD, MPH, Professor of Pediatrics at University of Utah in Salt Lake City and a member of the US Department of Health and Human Services Secretary's Advisory Committee on Inherited Diseases in Newborns and Children. “If these technologies are beneficial, are we OK with making them available only if you have the money?” Dr. Botkin asks. “Are we pouring too many resources into this technology when they could go to other, proven ways to improve health outcomes, such as nutrition?”

In some states, it's difficult to get Medicaid coverage for prenatal genetic testing, notes Ellen Wright Clayton, MD, JD, Director of Vanderbilt University's Center for Biomedical Ethics and Society. “And even if a woman can get testing, termination isn't covered,” she points out, also noting that improving health outcomes depends on much more than WGS.

Informed consent “is an enormous problem” with fetal WGS and other new technologies, says Dr. Botkin, noting that parents often do not understand the purpose of less advanced prenatal tests. Additionally, some technologies can yield information about the father without his consent, he and Dr. Clayton both note.

Despite these concerns, use of WGS and other molecular technologies in fetal medicine will increase, Drs. Bianchi, Botkin, and Clayton agree. “We need to buckle down and invest in translational research on using genomic information in a safe and effective manner,” says Dr. Botkin.

“Medical geneticists should “take the lead in thinking about how women should be counseled before [advanced] tests,” Dr. Clayton adds.