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At ESHG, Researchers Present New Noninvasive Prenatal Tests, Disease Recurrence Risk Study

GOTHENBURG, Sweden (GenomeWeb) – Noninvasive prenatal genetic tests for detecting fetal disorders and preconception tests to assess disease recurrence risk continue to advance. At the European Society of Human Genetics Conference here in Gothenburg yesterday, researchers presented two new noninvasive prenatal testing methods and a new way to determine recurrence risk for diseases caused by a de novo mutation.

Julia van Campen of the Genetics Laboratories at the Guy’s and St. Thomas’ NHS Foundation Trust in London reported on work to develop a noninvasive prenatal test for sickle cell disease, an autosomal recessive disorder that affects about 300,000 newborns each year and is frequently diagnosed by invasive prenatal testing. Assessing this disorder noninvasively in the fetus is tricky because this usually requires samples from both the father and the mother, which are often not available.

For their test, the team, which also involved researchers from Viapath Genetics Laboratories and Nonacus, used an approach that is based on relative mutation dosage and does not require a paternal sample. Using unique molecular identifiers, they performed targeted sequencing of cell-free DNA from maternal plasma and quantified the number of reads they obtained from mutant and wildtype alleles. During the bioinformatic analysis, they focused on DNA fragments shorter than 155 base pairs, which are enriched for fetal DNA.

Overall, they tested 24 samples from pregnant sickle cell disease carriers at a median gestational age of 16 weeks, sequencing them at 831X mean depth. For 21 of them, the result was concordant with the actual genotype of the fetus, while three samples were inconclusive, two of them because of low fetal fraction.

Future work will include the development of a size selection step for the cfDNA fragments, van Campen said, adding that other fetal autosomal recessive disorders could potentially be detected in a similar way.

In the meantime, researchers at BGI in China have developed a test that can detect three conditions at once: fetal chromosomal aneuploidies, fetal monogenic disorders, and maternal carrier status. The new method, called Targeted And Genome-wide simultaneous sequencing (TAGs-seq) and presented by BGI researcher Yicong Wang, relies on a combination of shallow genome-wide sequencing and targeted PCR-based sequencing at almost 3,000X depth.

For a validation study, the researchers performed TAGs-seq on 517 maternal plasma samples with known fetal outcomes from invasive testing, using the BGISEQ-500 instrument. They correctly called all 23 cases of trisomies, as well as nine cases of fetal de novo mutations that resulted in disorders such as beta thalassemia and achondroplasia, and 27 cases where the mother was a Mendelian disease carrier. A larger sample size will be needed for further clinical validation of the test, Wang said.

Finally, a study presented by Ummi Abdullah from the University of Oxford focused on the prediction of recurrence risk in families with a child born with a de novo mutation. Eighty percent of those are paternal in origin, mostly due to mutations that occur during spermatogenesis. While such mutations are usually one-off events that do not happen again, they do recur in about 1 percent to 2 percent of pregnancies because they resulted from gonadal mosaicism in one of the parents. In fact, for some families, the recurrence risk can be as high as 50 percent.

To identify families at high risk of recurrence of a de novo mutation, the researchers conducted the Precision Genetic Counseling and Reproduction, or PREGCARE, study, for which they have so far recruited 25 of a planned total of 100 families. For each family trio, they analyzed a small target of up to 150 base pairs around the de novo mutation in up to 14 tissue samples, including semen samples from the father, by ultra-deep Illumina sequencing. In addition, they performed haplotype phasing with long Oxford Nanopore reads to determine the parental origin of the mutation.

For most of the first 17 families analyzed so far, they were unable to detect the mutation in one of the parental samples. In two cases, they found that the mutation resulted from maternal mosaicism, while in others, it was traced back to the father.

Abdullah said that the results would allow her team to reassure about three-quarters of families that their disease recurrence risk is negligible, letting them focus on the remaining quarter of families with strategies to reduce their risk of future affected pregnancies, for example through preimplantation genetic testing.