NEW YORK (GenomeWeb) – Researchers at Oregon Health & Science University and elsewhere have tested the clinical utility of genome sequencing for preconception carrier screening, finding that it offers improved sensitivity over targeted testing but also generates significant numbers of variants of unknown significance.
"By using whole-genome sequencing, we're casting a very large net over a lot of different clinical conditions," Sue Richards, a geneticist at OHSU and the senior author of the study, said in a statement. "We're looking at hundreds of genes, not just a handful of genes or targeted panels, which means this method provides much more information."
Results from the analysis, which involved 221 participants, were published yesterday in the American Journal of Human Genetics. The project is part of the NextGen study under the National Human Genome Research Institute's Clinical Sequencing Exploratory Research (CSER) program, which is led by researchers at the Kaiser Foundation Research Institute.
For their project, preliminary results of which were presented at a conference three years ago, the researchers first sequenced the genomes of 131 women, all members of the Kaiser Permanente Northwest healthcare system. For those with a positive carrier result, the researchers invited their male partners to get tested, resulting in 71 additional genomes sequenced.
For carrier screening, they analyzed the data for variants in 728 genes related to inherited disease, including autosomal-recessive and X-linked conditions. They included lifespan-limiting, serious, mild, unpredictable, and adult-onset disorders. In addition, they looked for medically actionable variants — so-called secondary findings — in 148 genes, which included the American College of Medical Genetics and Genomics' 59-gene list.
Sequencing was conducted at Illumina's CLIA-certified Clinical Services Laboratory, and variants were called by researchers at the University of Washington. Scientists at OHSU interpreted the variants and confirmed pathogenic or likely pathogenic ones by orthologous methods, which were reported to clinicians and participants.
Results were reported in two phases: first the carrier results and later the medically actionable secondary findings. All participants received results for the lifespan-limiting conditions of the carrier screen, whereas the other results were optional.
Of note, 93 percent of participants opted to receive all categories of carrier results, and 99 percent asked for their medically actionable secondary findings.
Of the 202 participants, 78 percent received at least one positive carrier result, and the number of variants reported per person range from zero to five. Twelve of the 71 couples tested turned out to be carriers for the same condition, and three women were carriers for an X-linked condition.
Seven individuals, or 3.5 percent of participants, received secondary findings, and all but one of these would have been picked up by the ACMG-59 list.
The analysis also resulted in 808 variants of unknown significance, an average of four per person, which were not reported.
One challenge, the researchers wrote, was to interpret novel variants predicted to result in a loss of function, since they don't cause a phenotype in the carriers. For the same reason, it was difficult to classify novel variants in a gene associated with clinical heterogeneity, for example, a gene that can cause two different conditions depending on where it is mutated. "Thus, in our experience, the ability to accurately classify variants and predict outcomes is more challenging in a healthy population than in an affected individual and is less robust than in individuals presenting with an adverse phenotype," they wrote.
Overall, next-gen-sequencing-based carrier screening panels can detect a lot more rare and novel pathogenic variants than traditional mutation screening panels that are designed for specific ethnic groups, they said, and whole-genome sequencing can get around some of the biases and errors associated with targeted sequencing, and provide better structural variant detection.
However, they wrote, current NGS methods still don't pick up all types of important variants, for example those causing triplet repeat disorders like fragile X syndrome. "However, these challenges will be short-lived because the implementation of long-read DNA sequencing (third generation) technologies coupled with advances in bioinformatic pipelines for detecting short tandem repeats and copy number variation is imminent in the clinical laboratory," they wrote.
NGS, they concluded, "may soon replace other methodologies and become a unifying platform for performing most molecular genetic tests."