SAN FRANCISCO (GenomeWeb) – Genomic testing of a couple can help identify the cause of rare genetic diseases that are lethal prenatally or shortly after birth, according to researchers from the University of Exeter Medical School and the Royal Devon & Exeter Hospital.
The Exeter clinical lab offers parental exome sequencing for couples who have previously had a pregnancy in which the fetus was affected with a lethal disorder that was suspected to be genetic but where not enough fetal material was available for testing. In a study published this month in Prenatal Diagnosis, the researchers described their first 50 cases, showing that parental sequencing found a diagnosis for 52 percent.
Sian Ellard, professor of genomic medicine and senior author of the study, said that finding a diagnosis is important because it helps couples make reproductive choices, including giving them the option to choose preimplantation genetic diagnosis or an early prenatal test for future pregnancies. The exome sequencing test costs £1,595 ($2,142) out of pocket.
Sequencing couples' exomes to diagnose lethal fetal disorders retrospectively is a new use of the technology that adds to the growing array of NGS-based tests in the reproductive health field. It differs from both NIPT and invasive prenatal testing in that it analyzes DNA from the parents, not the fetus. In addition, it identifies variants that wouldn't be picked up by carrier screening tests, even the recently available expanded ones — because these prenatal lethal disorders are so rare, the genes are sometimes unknown, so they are not included in carrier screening tests.
Ellard said that the team began looking into the possibility of using sequencing to uncover the cause of some cases of fetal demise or newborn death after a clinician had discussed a case in which a couple had gone through two pregnancies in which problems weren't uncovered until a 20-week ultrasound scan. Standard genetic testing had not delivered a diagnosis in either pregnancy. Such cases leave parents in heart-wrenching situations — knowing that even if the fetus survives to full term, it is unlikely to live outside of the womb. The dilemma of this particular couple was whether or not to try and have another child. Because they already had two affected pregnancies, Ellard said, the disorder was likely autosomal recessive, meaning that their recurrence risk would be 25 percent. And since the disorder was still unknown, there would be no way to know if the baby would be affected until ultrasound scanning midway through pregnancy.
In general, Ellard said, it is difficult to diagnose lethal fetal genetic disorders since many different genes can be involved and accurate phenotyping of a fetus mid-gestation is very difficult. That makes single-gene and even gene panel testing not very useful.
In an initial proof of principle study published in 2015, the researches evaluated parental samples from three couples, each with multiple affected pregnancies. After demonstrating that they were able to find a molecular diagnosis for the couples, they began offering the test as a service to couples who have had at least one affected pregnancy.
Over the last three years, Ellard said that the researchers have evaluated 50 cases, identifying causative mutations in just over half. She expects that as more clinicians are aware of the service, test orders will increase. In addition, she said, the team has also now implemented trio exome sequencing to diagnose complex pediatric disorders, and trio sequencing along with the use of GeneMatcher, an online tool that allows researchers to share information about genes of interest and clinical features of affected patients, which has enabled them to identify six novel disease genes.
In the 50 cases described in the Prenatal Diagnosis study, Ellard said, clinicians first identified a problem with the fetus at the 20-week ultrasound in the majority of cases, but there were some cases where the fetus appeared to be healthy but died soon after birth.
The process of diagnosis is very similar to other clinical exome sequencing pipelines, except that the team does not have the exome of the proband. The key step is the filtering process to narrow down the list of potential variants. Variants are removed from consideration that do not pass a series of filters, including those that are not annotated with a gene name, those in which one of the parents is homozygous, those that have population allele frequencies too high to be associated with a rare, lethal disorder, and more.
This filtering process also minimizes the chances of uncovering an incidental finding, since only genes where both partners are heterozygous for rare variants are looked at. However, Ellard said that in a few families, the team has found that the parents are carriers for a second recessive disorder. "That information is shared with family in order to offer future prenatal testing for both conditions," she said.
After narrowing down the list, the candidate variants in known disease-causing genes are reviewed and ultimately, potential disease-causing variants are confirmed by PCR and Sanger sequencing or droplet digital PCR. For the 50 couples tested in the study, there was not enough fetal DNA to sequence its entire exome, but there was enough fetal DNA to confirm the specific variant.
In the study, pathogenic variants were found in 24 disease genes in the 26 cases that were diagnosed. One family had an X-linked disorder, while the other cases were autosomal recessive. Copy number variants were identified in two families, and four couples had newly identified disease-causing variants.
For couples that did not receive a diagnosis, Ellard said, the variant could be in a noncoding region or in a region that was not well covered, or the disease gene may not yet be known. "There are still a number of genetic disorders for which the causative gene has not been identified," she said, "but over the next few years, we expect that more disease genes will be identified." She added that the sequence data for these cases will be stored and clinicians can order a re-analysis.
The average turnaround time for the test is four to eight weeks, with the fastest turnaround at eight days. "We're trying to reduce the reporting times to get couples answers as quickly as possible," Ellard said. The goal is to reduce the turnaround time to one to two weeks, which Ellard said the team will accomplish with a combination of investing in new library prep technology and training additional genetic technologists and clinical scientists. Reducing turnaround time could help provide options for couples who have had a previously affected pregnancy and are pregnant again.
Although Ellard said that her lab does not track patients once they are tested, she has heard from the referring clinicians that many couples that get a diagnosis choose to do IVF and preimplantation genetic diagnosis. A diagnosis could also allow for prenatal genetic testing via an amniocentesis or chorionic villus sampling, and potentially even bespoke noninvasive prenatal testing of cell-free DNA, Ellard said.
The latter is not done in her lab, but she said that two other laboratories in the UK — the Great Ormond Street Hospital lab and the West Midlands Regional lab — are developing noninvasive prenatal tests to diagnose single-gene disorders under a National Health Service project to develop noninvasive prenatal diagnosis tests for single-gene disorders.