80% of rare diseases are genetic. That's why whole genome sequencing can help with diagnoses

Caption

Jansen Jones plays with Legos in her family home in Buckhead.

Credit: Family photo

Jansen Jones wasn’t using her hands or legs.

She lacked muscle tone and was too weak to bear weight using her extremities.

The baby could lift and move her head, but she didn’t seem as strong as a 5-month-old should be, her mother believed.

"She is my third child," Suzanne Jones said, which means she's witnessed developmental milestones twice previously.

Doctors at Children’s Healthcare of Atlanta diagnosed Jansen with a nonspecific, global developmental delay.

“We were just told, ‘She's behind. No big deal. Do some physical therapy,’” Jones said.

But a lot of babies seem really strong, and it was clear to Jones that Jansen was not. She would curl up in a sort of ball, and sat looking sweet and happy, but did not engage with her environment.

A neurologist said a muscle biopsy might explain the deficiency, but there are false positives with muscle biopsies.

"That is invasive and leaves a scar and scared us," Jones said. "You know, you're basically cutting on her arm or leg."

When Jansen didn't babble as expected, they started speech therapy. Then, they added occupational therapy.

"We just did hours and hours of therapies nonstop for years," Jones said.

A neuro-psychological exam led doctors to say Jansen was intellectually disabled.

This happened about the same time as rare, fleeting seizures caused Jansen to space out for a second or two.

An electroencephalogram (EEG) test confirmed abnormal electrical activity in her brain. 

"Well, they just said she has epilepsy," Jones said.

But Jones said the family continually witnessed symptoms that suggested that Jansen was struggling in different ways.

The idea of genetic testing came up by the time Jansen was 3 years old.

"In my opinion, if it's genetics, that's the underlying cause of everything and so that should show us what is going on," Jones said.

Jones’ doctors described the 46 chromosomes in the body as chapters in a book. Whole exome sequencing was like scanning the book to see whether any chapters were missing or duplicated.

For example, the characteristic features and developmental problems of a person with Down Syndrome is caused by an extra chromosome 21.

Think of that as Chapter 21.

But after having Jansen's whole exome sequenced, they still had no solid answers.

"And so we got results back when she was 3 and it did not show us what was going on," Jones said.

All the Joneses could do was treat Jansen's symptoms, which included behavior problems.

Despite managing Jansen through applied behavior therapy and medication, Jansen acted out — and she couldn't control it. Nightmares made her want to sleep in bed with her parents.

"It's not clear to me why the whole exome sequencing didn't catch it," Jones said. But it's not an infallible test.

An exome is a collection of 180,000 exons responsible for protein coding, but the human exome only comprises about 1% of the human genome.

Now, whole genome sequencing is available.

"And that is what ended up catching it," Jones said.

Jansen was diagnosed just before her 11th birthday with a disorder caused by a single gene mutation: SYNGAP1.

"This mutation was discovered only a year before Jansen was born."

Jansen's frustration stemmed from an inability to reason and communicate.

She turned 13 in October 2023.

"It's not easy," Jones said. "They have a SYNGAP snap. Sometimes their brain just [goes] haywire. And you can't you can't reason with somebody who can't reason. So behaviors can be really difficult."

"Compared to other single-gene mutations that cause epilepsy, SYNGAP1 children have a lot of problems with behavior," Jones said. "And luckily with that being a spectrum, my child has those issues, but it's not constant; it's not as prevalent."

If you have a rare disease, there is an 80% chance that it’s genetic. That doesn’t mean the cause has been identified — yet.

Karen Grinzaid with Emory University School of Medicine said she believes everyone planning a family should conduct genetic testing.

"The reason is there are genetic diseases that can happen that haven't shown up in your family yet," she said.

We all carry a number of recessive genes, but we don't know what those genes are unless either we have an affected child, or we do genetic testing.

But a whole genome test like Jansen’s might make would-be parents more nervous than is necessary.

"When you do broader testing like that, it may turn up problems where it's not clear what the implications are," Grinzaid said. "So, I just can't overemphasize the importance of genetic counseling to help people through this journey."

Suzanne Jones said even though her daughter’s diagnosis hasn’t changed her daughter’s developmental issues, the genomic sequencing was worth it.

"It's an answer," she said. "We can finally say we understand what all these different symptoms are caused by."

And that, Jones said, makes it a lot less scary to be a parent.