Gavin's Story: Whole Exome Sequencing Finds Mystery Mutation

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Monday, December 5, 2011

By Ricki Lewis

In a hotel ballroom on the campus of the University of Pennsylvania on a midsummer Saturday in 2010, an unusual roll call was under way at the Family Conference for the Foundation for Retinal Research.

Betsy Brint, co-head of organization, was calling out what sounded like code words – CEP290, GUCY20, LRAT. After each one, a few people would stand, excited, then form little groups. After all 18 abbreviations had been called, representing the genes known to cause Leber congenital amaurosis (LCA), a few sets of parents were left standing. Troy and Jennifer Stevens, of Chino, California, were among those whose children’s genes and mutations were still a mystery.

In October 2008, Jennifer had sensed instantly that something was wrong with her newborn. “They handed me a perfect-looking baby and I knew. It was an overwhelming feeling that I couldn’t dismiss.”

She was right. Gavin couldn’t see.

After a nearly-year-long medical odyssey -- from pediatrician to ophthalmologist to pediatric retinal specialist – the diagnosis of LCA loomed. Jennifer and Troy quickly learned that LCA came in several types, and Gavin would need genetic testing to find out which one he had. But a doctor at Children’s Hospital Los Angeles said not to bother, for there was no treatment – unaware that gene therapy for one type of the disease, LCA2, had already given vision to a few young adults and an 8-year-old.

Ignoring the doctor’s dire prediction, the Stevens’ sent Gavin’s blood to a genetic testing lab that specializes in eye diseases. It was December 2009, and Gavin was 14 months old and completely blind. Troy and Jennifer had met other LCA families on Yahoo and Facebook who’d used the lab, “and they got results in 2 months, some in 6. But every time I e-mailed the lab, they said ‘oh, we’re working on it,” Jennifer recalls.

Then at the family conference seven months later, Jennifer and Troy met with the director of the testing lab, who couldn’t believe they’d been waiting so long. “He called the lab as we sat there listening, and then he said, ‘The results are inconclusive. Gavin doesn’t have one of the genes.’ I don’t know how long they had that information but had not given it to us,” Jennifer says.

Part of the confusion was that at that time, the lab only tested for a few of the 16 genes then known to cause LCA, and only the most common mutations in them. This strategy minimizes costs while maximizing diagnoses, but generates false negatives and erroneous equating of “we didn’t find a mutation” to “there’s no mutation.” It is of little help, but potentially great expense, for patients with rare variants of rare diseases.

A few parents distressed by the partial test results had told Troy and Jennifer about John (Pei-wen) Chiang, PhD, who was then at the University of Denver and is now director of the Molecular Diagnostic Laboratory at the Casey Eye Institute in Portland, Oregon. And so at 11 PM on that Saturday night Jennifer, distraught, e-mailed Dr. Chiang. She was stunned at the speed of his reply.

“I called her back within a half hour, and promised to do my best to help. Then I read her blog and learned all about Gavin,” Dr. Chiang picks up the story.

“As soon as we flew home, we went to the hospital and got bloodwork done and sent it to Dr. Chiang,” Jennifer recalls. He tested Gavin’s blood for all known LCA genes – and not just the common parts of them – in two months. “He wouldn’t take no for an answer. If we’d went with what our first doctor said – it’s so far out from a treatment there’s no rush on bloodwork -- we’d still be sitting here with our hands tied behind our backs,” she adds.

Dr. Chiang describes his passion simply: “This is not a tube of DNA with a number, there is a human being behind it.” And when Gavin’s DNA didn’t match any of the known LCA genes, Dr. Chiang facilitated the next leap: whole exome sequencing. The exome is the part of the genome that tells the cell which proteins to make, which is what lies behind a trait or a disease. Looking at an exome is a little like downloading a book to a Kindle or Nook, compared to a chapter (sequencing a gene) or a few paragraphs (the common mutations in a gene). The answer is in there, but requires searching.

Dr. Chiang sent DNA from Gavin, Troy, Jennifer, and the grandparents to Ming Qi, PhD, at the Beijing Genomics Institute, where sequencing would be done fast. A few weeks later, a big excel file came back, which Dr. Chiang analyzed over the course of several weekends. He set three criteria for finding Gavin’s gene: “First, because it is a rare condition, variations must be novel. Secondly, because Gavin is very severely affected, he must have at least one nonsense mutation (in which the encoded protein is very short). The third criterion is that it is recessive,” meaning that Jennifer and Troy were carriers.

Gavin’s DNA revealed two different mutations in a gene, one that Jennifer got from her mom, the other that Troy inherited from his dad. Dr. Chiang has already found the mutation in other families, and is now trying to figure out how the gene blocks vision. The gene is known, but not until now associated with LCA. Dr. Chiang explains his strategy of helping families while contributing knowledge. “When we don’t find a mutation, we sequence every gene involved, and when we still don’t find a mutation, those samples become very valuable to find new disease genes. That’s the reason I took the whole exome approach for Gavin.” The finding may one day help Gavin, and others, because the first step towards gene therapy is to identify the genetic error. Researchers must learn what to replace.

The day is fast approaching when whole genome and exome sequencing become the norm, for researchers and then clinicians, replacing pricy panels of specific gene tests. “Next- generation” DNA sequencing and improved data analyses are already bringing the price down. At the summer 2010 meeting where Jennifer and Troy learned the first lab couldn’t identify their gene, the lab director estimated it would cost $50,000 to $100,000 to do exome sequencing on a family. Yet today, at least two companies, Knome and Complete

Genomics offer sequencing and interpretation of human exomes and/or genomes for about $5,000 each, to researchers. Sums up Jennifer, “I hope more parents get the phone call saying ‘we have identified your gene’. After being in limbo for years, it’s nice to finally have an answer.”

At the next Foundation for Retinal Research meeting, Jennifer, Troy, and Gavin will be able to stand when their gene is called. It’s a first step towards a cure.

Read more about Gavin and other kids with LCA in ”The Forever Fix: Gene Therapy and the Boy Who Saved It” from St. Martin’s Press in March 2012.

Please contact Ricki if you have a story to share about exome or genome sequencing for a

rare disease (rickilewis54@gmail.com)

Source: Checkorphan

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