Chromosomal Rearrangements Uncovered With Next-Generation Sequencing

Ricki Lewis, PhD

November 12, 2012

SAN FRANCISCO — Next-generation sequencing of prenatal genomes adds long-awaited precision to the determination of an association between de novo chromosomal rearrangements and known syndromes.

Researchers presented an intriguing case here at the American Society of Human Genetics 62nd Annual Meeting.

When a prenatal karyotype reveals a balanced translocation or an inversion, the next step is to determine whether a parent has the same rearrangement. If not, a clinician must rely on empirical data to determine the probability of the anomaly being associated with a syndrome.

"Up to this point, to give advice to a couple who are surprised to find that their fetus has a rearrangement that's not inherited, we relied on population cytogenetics that said there was about a 6.1% risk of an untoward outcome for a translocation and a 9.4% risk for an inversion," Cynthia Morton, PhD, clinical cytogeneticist from Brigham and Women's Hospital in Boston, Massachusetts, told Medscape Medical News.

During a 4-month period at the beginning of 2012, the researchers found 3 fetuses with de novo rearrangements. The rearrangements create chimeric DNA sequences that do not match whole-genome reference sequences — like mixing up the order of words in a sentence.

The researchers sequenced the complete genomes of all 3 fetuses, using cells cultured from the samples used to construct the karyotypes. They focused on translocations (where a sequence from one chromosome type is moved next to a sequence from another) and inversions (where a sequence is flipped, creating novel juxtapositions at the breakpoints). Sanger sequencing confirmed the next-generation sequencing results.

Two of the fetuses had rearranged sequences that have not been associated with a phenotype — the distressing so-called "variants of uncertain significance." Dr. Morton explained that "we aren't yet equipped to interpret everything because the human genome sequence is still being annotated."

CHARGE Syndrome Revealed

In the third case, the researchers discovered that the translocation disrupted the gene that causes CHARGE syndrome (coloboma, heart disease, atresia choanae, retarded growth and retarded development, and/or central nervous system anomalies, genital hypoplasia, and ear anomalies and/or deafness).

Zehra Ordulu, MD, a fellow in Dr. Morton's lab, presented the case to conference delegates. "At 19 weeks, fetal imaging revealed a severe heart defect. Starting at 27 weeks, additional abnormalities appeared, including polyhydramnios and a protruding upper lip."

When 2 L of amniotic fluid were removed at 33 weeks, the cytogenetics lab obtained fetal cells and constructed a karyotype, which revealed a balanced translocation between chromosomes 6 and 8. By the time the parents were karyotyped and it became clear that the fetal translocation was de novo, the baby had already been born.

CHARGE syndrome was diagnosed on clinical examination. The extra amniotic fluid had obscured the facial anomalies on ultrasound. Genetic testing revealed a causative mutation in the CHD7 gene. The baby had a severe clinical course, with intubation required during the birth; he was removed from the ventilator on day 10.

Next-generation cytogenetics done early in the pregnancy would have revealed the full nature of the syndrome. "We could have counseled the parents that the heart defect might not be the only defect, which might have changed their decision not to terminate. Or, if the parents had elected to continue, the medical team could have prepared for management beyond an isolated heart defect," Dr. Ordulu told Medscape Medical News.

With the escalating pace and declining cost of genome sequencing, routine next-generation cytogenetics is not far off. "We can do this in a clinical diagnostic setting," Dr. Morton said. "I'm looking forward to providing more reassuring information to couples that will allow them to continue pregnancies rather than placing them in a position of deciding whether to continue," she added.

The authors have disclosed no relevant financial relationships.

American Society of Human Genetics (ASHG) 62nd Annual Meeting: Abstract 70. Presented November 7, 2012.

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