Ambry Genetics Makes Advances in RNA Genetic Testing
The majority, if not all, clinical genetic testing is performed on DNA. In human cells, DNA and RNA play different roles, although they have similar but different molecular structures. For example, RNA is single-stranded, and DNA is double-stranded.
Their primary roles are related. DNA replicates and stores genetic information. As such, it is a blueprint for all the genetic information held inside an organism, whether a plant or a human being, with few exceptions (some viruses, for example). RNA converts the genetic information of the DNA into a format that can be used to build proteins, then moves that format to ribosomes where the proteins are actually manufactured.
“Our study goal was to determine if supplemental RNA testing could help overcome a limitation of DNA testing, that being the high number of genetic variants that are reported as ‘uncertain’ because they cannot be clearly interpreted,” stated Rachid Karam, Director of Ambry’s Translational Genetics Lab. “Our results tell us that it can.”
But what does that mean?
At one level, it means that the RNA testing, performed in tandem with current DNA tests, can provide significantly more nuance and accuracy, particularly when it comes to currently ambiguous test results. By classifying what are known as variants of uncertain significance (VUS), the tests should provide more accurate results. And potentially, in some areas where these markers—such as cancer testing—play a crucial role in deciding which drugs to use when, it will have a greater impact on patient care.
As the company’s poster, “RNA Genetic Testing in Hereditary Cancer Improves Variant Classification and Patient Management,” states, “The interpretation of germline variants remains a challenge to medical providers. Variants predicted to impact splicing are frequently classified as uncertain (VUS) and likely pathogenic (VLP). This is due to the fact that, despite computational predictions indicating these variants may lead to a null effect, confirmation of the impact requires RNA analysis.”
Brigette Tippin Davis, Ambry’s Senior Vice President of Research and Development, told GenomeWeb that they had been performing RNA genetic testing on a research basis for more than two years and “have seen success in improving our variant classification. We have completed the clinical validation. We look forward to making this available to healthcare providers and their patients this year.”
Researchers with Ambry collaborated with scientists from the Dana Farber Cancer Institute, Cedars-Sinai Medical Center and others to evaluate the “feasibility and impact” of variant reclassification with RNA genetic testing data.
The first part of Ambry’s analysis looked at 64 likely splice site variants, which had previously been identified with DNA testing. The variants were in 13 genes linked to hereditary breast and ovarian cancer (HBOC), Lynch syndrome, or hereditary diffuse gastric cancer (HDGC).
When just using DNA testing, 90% of the splice variant in HBOC genes were VUS, about 75% of the HDGC gene variants were VUS and all of the variants in Lynch syndrome genes were VUS. But, when Ambry’s team included RNA genetic testing data, only 10% of HBOC gene variants were VUS, and 50% to 40% were classified as likely pathogenic.
They reported similar improvements for the variants in HDGC and mismatch repair genes in Lynch syndrome when RNA testing was added to DNA testing.
The researchers then took the next step and evaluated healthcare records to determine if medical management would have changed with this additional information. One difference right away was that if a VUS was reclassified to likely pathogenic, they were typically directed to cascade testing, which is a systematic way of identifying people at risk for a hereditary condition, and often includes biological and/or at-risk relatives.
The team analyzed 307,812 people who had previously had genetic testing on 18 hereditary cancer genes. Of the tens of thousands of variants identified, more than 2,500 variants were predicted that would alter splicing, which would include both VUS and pathogenic variants. Essentially, Ambry estimates that about one in 50 patients receiving DNA tests for hereditary cancer diseases would benefit from RNA-based variant classification.
Although there are several different methods of RNA testing that could be used, the research presented at the ACMG meeting by Ambry was high-throughput, massively parallel, RNA sequencing called CloneSeq, which involves sequencing cloned transcripts created from RT-PCR products. Karam and others provided data on CloneSeq in a Frontiers in Oncology paper published in 2018, where they used the technique to evaluate germline BRCA1 and BRCA2 variants in hereditary breast and ovarian cancer (HBOC).
The bottom line is that Ambry showed there is value in adding at least some level of RNA testing into some DNA genetic tests to provider clearer, more accurate genetics tests, particularly in areas where there is a known level of ambiguity and variability.