Earlier treatment. Targeted therapies. An answer and an open door to the possibility of identifying other families who have gone through similar experiences: a molecular diagnosis can bring such positive changes, but for many patients, it remains elusive. 

As genetic counselors, we see countless patients journey through their diagnostic odysseys. And lately, it feels like our career itself has been a sort of odyssey. Sometimes disappointing, sometimes fulfilling, but always with a forward trajectory marked by ever-expanding abilities that allow us to increase diagnostic yield. Ultimately, this lets us do the most important part of our job: helping patients find answers. 

When I was a genetic counseling student and early in my career, we ordered testing on patients one gene at a time — and that was for the cases where clinical testing was even available. When results came back negative, we discussed the merits of ordering deletion/duplication analysis on the gene we had just sequenced, again, if available. The process — while potentially successful and life-changing — usually tended to be long, iterative and restrictive.

As next-generation sequencing came into clinical use, our options expanded to include panel testing, and later, whole exome sequencing. Researchers discovered new gene-disease relationships at a rapid rate. We had so many new tests to offer our patients — which was especially exciting for helping those patients we had seen for years who were still seeking their answer. This was an exhilarating time to be in the field of genetics. Things were moving fast.

I will never forget the first whole-exome sequencing (WES) case I was involved with. My patient was a toddler with a history of seizures and uninformative test results. But the WES results were positive. The family had their answer. It wasn’t a good outlook, but the family was thankful nonetheless: they had their “why.” They had information they could use for reproductive planning. And they had an answer fast. No more subjecting their child to test after test after test. They had gained information that so many families didn’t have, and it allowed them to prepare and to move forward. 

But even with the advent of WES, we didn’t have all the answers. Although we worked together with families and fought with their insurers for coverage, around 75% of our patients were denied the opportunity or the ability to end their diagnostic odysseys (Yang et al., 2014; Balci et al., 2017). 

We were still learning and making progress, as we always are in genetics. We standardized the way we interpret genetic variants, and that process has continued to improve along with our technologies. As whole-genome sequencing becomes more commonly used clinically, we can now analyze so much more DNA than ever before. And yet, this substantial increase in the amount of DNA analyzed has brought with it a new challenge: prioritizing and interpreting variants for clinical use among such a wide array of data.

Enter RNA sequencing. RNA sequencing can be used to help classify suspicious DNA variants that may impact splicing. But if we use it more broadly by analyzing the transcriptome alongside the DNA, it can also be used to evaluate for aberrant gene expression or mono-allelic gene expression. With RNA sequencing, we can uncover things like skewed X-inactivation or uniparental disomy that we could not identify by DNA testing alone. We can also see benefits in other unique scenarios, like detecting gene fusions, resolving pseudogene interference, or confirming suspected mosaic variants. RNA is an important (and perhaps underutilized) tool to help with our interpretation and prioritization of DNA variants. This can improve our diagnostic yield by approximately 17% (Griffith et al., 2010; Cummings et al., 2017; Gonorazky et al., 2019; Frésard et al., 2019; Lee et al., 2020).

Alongside these technology breakthroughs, bioinformatic analysis is also improving, allowing us to detect and interpret new things with NGS — copy number variants, structural changes, repeat expansions, intronic variants — that used to require other types of testing. 

So, by using WGS along with RNAseq, we continue to chip away at the number of tests we need to order for our patients to find answers, bringing our positive yield higher than ever before. A single test that sequences the nuclear genome and mitochondrial genome at the same time with CNV analysis and reports out “tricky” findings, like repeat expansions or regions with absence of heterozygosity, is now in front of us. And tests such as Fulgent’s FulGenome WGS can combine those abilities with RNA sequencing to analyze for aberrant or monoallelic expression or aberrant splicing, bringing the diagnostic yield still higher. 

I know I’m not alone when I say that I love being in a field that is constantly evolving to help our health care team members and, even more so, our patients. From the perspective of a genetic counselor from the past, having the ability to detect so many possible disease-causing variants with a single test with a short turnaround time would be astonishing and awe-inspiring. I can’t wait to witness our next leap forward in improving diagnostics.

References

Yang Y, et al. (2014). Molecular findings among patients referred for clinical whole-exome sequencing. JAMA, 312(18), 1870–1879. https://doi.org/10.1001/jama.2014.14601 

Balci TB, et al. (2017). Debunking Occam's razor: Diagnosing multiple genetic diseases in families by whole-exome sequencing. Clinical Genetics, 92(3), 281–289. https://doi.org/10.1111/cge.12987

Griffith M, et al. (2010). Alternative expression analysis by RNA sequencing. Nature Methods, 7(10), 843–847. https://doi.org/10.1038/nmeth.1503

Cummings BB, et al. (2017). Improving genetic diagnosis in Mendelian disease with transcriptome sequencing. Science Translational Medicine, 9(386), eaal5209. https://doi.org/10.1126/scitranslmed.aal5209

Gonorazky HD, et al. (2019). Expanding the boundaries of RNA sequencing as a diagnostic tool for rare Mendelian disease. American Journal of Human Genetics, 104(3), 466–483. https://doi.org/10.1016/j.ajhg.2019.01.012

Frésard L, et al. (2019). Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts. Nature Medicine, 25(6), 911–919. https://doi.org/10.1038/s41591-019-0457-8

Lee H, et al. (2020). Diagnostic utility of transcriptome sequencing for rare Mendelian diseases. Genetics in Medicine, 22(3), 490–499. https://doi.org/10.1038/s41436-019-0672-1

Jamie Zdrodowski, MS, CGC (he/him/his)

Zdrodowski is a board-certified genetic counselor with over 15 years of experience. He earned his Bachelor of Science degree in cognitive science and biopsychology from the University of Michigan and his Master of Science in genetic counseling from Northwestern University. He is currently employed as lead product manager at Fulgent Genetics. Prior to joining Fulgent, Zdrodowski worked as a clinical genetic counselor in general genetics clinics at academic medical centers in Chicago and Detroit, as well as in various roles in diagnostic laboratories.