Role of team

Rare disease patients present as medical mysteries.

Physicians listen to their stories, make clinical observations, and then often turn to genomic testing to find answers. The clinical reporting team serves as Sherlock Holmes: suggesting tests, deciphering results, and sometimes tapping into a vast database of unpublished data. “I would say that one of my significant roles as somebody who’s working on a clinical reporting team in a laboratory, is to understand if a clinician thinks that the patient has a certain disorder,” says Christin D. Collins, laboratory director at Revvity Omics. “I make sure that I am reviewing and reporting results for them that will answer their suspicions.”

The human genome is made up of approximately 3 billion nucleotides. “Of those 3 billion nucleotides, a single change – even just one nucleotide – can result in a clinically significant disorder,” Collins explains. It could be one change to a number of changes that Collins and her team are looking for that would ultimately solve the case for a patient.

“The population of China is about 1.4 billion people,” says Collins. “So, if you imagine interviewing everybody in China twice looking for that one person who could potentially be the culprit. That would be the scale that we’re talking about.”

Patients need these answers so that they can receive the appropriate treatment. Working alongside doctors, nurses, and genetic counselors, the clinical reporting team helps solve these medical mysteries for patients.

Burden of rare disease

Patients with rare diseases have much to gain from whole genome testing. Many times a condition may be so rare that physicians have neither diagnosed nor seen that particular condition. “On average from the time that a first symptom appears, an individual might see anywhere from 16 to 17 healthcare specialists before they get their diagnosis,” says Collins. “And that period of time on average is about seven to 10 years, which is a pretty significant amount of time that patients are searching for answers and trying to find out the cause of their medical issues.”

In the United States there are estimated to be 30 million individuals with one or more of the 7,000 documented rare disorders. “Rare disorders have a pretty significant healthcare burden,” explains Collins. Collins and her team spend a significant amount of time working with their healthcare partners to make sure that they understand not only which tests are available to them, but also which test would be the most appropriate if the physician is suspecting a particular disorder. In all cases, she explains, the focus is on what is good for the patient as well as which test is most likely to reduce healthcare burdens. The team helps physicians make the appropriate choices and educates physicians about the limitations of those choices.

Case 1

Collins gives as an example the unusual case of an 11-year-old boy with a history of toe walking, motor delay, and elevated creatine kinase. The physician suspected that the child had Becker muscular dystrophy, a more mild form of Duchenne muscular dystrophy, and so ordered sequencing of the DMD gene associated with Duchenne and Becker muscular dystrophy as well as a copy number variant analysis of the DMD gene. This approach tackled the mystery from two angles: sequence variants and copy number variants.

But both of those tests came back negative. This surprised the physician, because they did all the right testing and they couldn’t find the answer, so he was searching for what his next steps should be. The key to the next steps was understanding what the test limitations are. To better understand the case, Collins said, it’s helpful to understand that DNA is really made up of coding and non-coding regions. The coding regions make the proteins – essentially effector molecules of your body – that allow everything to happen. But the coding region is only 1 percent of all your DNA – and most standard assays are just looking at that 1 percent.

The non-coding regions don’t code for proteins, but they can still potentially impact the ability to create a normal protein. At the moment, it’s estimated that about 15 percent of disease-causing variants are found in these non-coding regions, Collins said.

“So we decided that it would be appropriate to do a test that could look at these non-coding regions,” said Collins, “and that was the whole genome test.”

The test revealed a variant of uncertain clinical significance or VUS. “This is the bane of all healthcare providers – getting a variant back and we can’t really tell you if we truly think this variant is pathogenic, or if we think this variant is benign, we just don’t know. The data is not there to help us determine that.” The clinical reporting team decided the next step was RNA sequencing, to see if perhaps the non-coding change could impact the type of transcript that’s produced, and result in abnormal protein. To do that, they used cutting edge-technology that is considered Research Use Only testing at Revvity Omics.

“We’re just now really exploring all of the things that RNA sequencing can offer for us,” said Collins. “We found that this change really did impact splicing, and it resulted in reduced expression and unstable dystrophin in the patient. It really had a functional impact. And this would be one of those 15% of non-coding changes that are found for this patient and was only detected because we were looking in those non-coding regions with our genome.”

Case 2

Collins explains that the solution unfolded in a different way for an 8-year-old boy presenting with delayed motor development, delayed language development, growth hormone deficiency, and muscular dystrophy. The physician first ran a microarray test to identify any genetic copy number variation. The results indicated that the patient had a deletion on chromosome 9q34.3 which was consistent with Kleefstra syndrome.

“This diagnosis, however, didn’t fully explain the patient’s clinical presentation, particularly the muscular dystrophy, and left the physician wondering, ‘What other testing might be appropriate for the patient?’” Collins explains. With guidance from the clinical reporting team, the physician then ordered a low-pass genome test to look for variations in the gene associated with Duchenne muscular dystrophy.

“In this case, the test revealed something quite remarkable and unexpected; this patient had two, separate genetic diseases that were both working together to create a blended phenotype,” Collins described. Not only was there a large deletion of chromosome 9q34.3 associated with Kleefstra syndrome, but there was also a small deletion in the DMD gene associated with Duchenne muscular dystrophy.

Case 3

As her last example, Collins describes the case of a 20-year-old male from South Asia who presented with muscle weakness and elevated creatine kinase. In this case, Revvity Omics’ laboratories in Asia supplied the additional evidence needed to identify the variant.

The clinician suspected that the patient had Nonaka myopathy or GNE myopathy; however, when he sequenced the genes associated with those inherited conditions, he only found a single pathogenic variant in the GNE gene associated with GNE myopathy. “For this particular disorder, you actually need two pathogenic variants to cause disease, one on each chromosome. So, in this case, the physician was really trying to figure out what this hidden variant was,” Collins explains.

Her team turned to whole genome sequencing to look at the non-coding region, which was not covered in the original assay, and found that the patient had a deletion in an intron in the GNE gene. The clinical reporting team was able to query its database of individuals from South Asia and determine that this variant in the intron had been documented in patients with a similar clinical presentation. Further examination reinforced that this variant in the intron constituted the second variant necessary for a diagnosis of GNE myopathy.

Conclusion

Collins relishes solving these mysteries. “Really working with this group of folks on the clinical reporting team is something that has been a true delight and makes me excited every single day to come into work and see what I can find,” says Collins. “Every case is different… And so that constant challenge, the investigations, and puzzle solving really makes it rewarding for me.”