Heralding what they hope is a new era of personalized genomic medicine, experts in the US have identified the gene behind a patient’s inherited neurological disorder, in this case a form of Charcot-Marie-Tooth disease, by sequencing his complete genome.
Details of the quest are published online in the 10 March issue of the New England Journal of Medicine. Among the authors is the patient, Dr James Lupski, vice chair of molecular and human genetics at Baylor College of Medicine (BCM) in Houston, Texas, and Dr Richard Gibbs, director of the Human Genome Sequencing Center at BCM, where the sequencing was performed.
Charcot-Marie-Tooth (CMT) disease (which gets its name from the three people who first identified it in 1886: Jean-Martin Charcot and Pierre Marie in Paris, France, and Howard Henry Tooth in Cambridge, England) is a not uncommon inherited neurological disorder that affects the nerves in a person’s limbs, hands and feet (the peripheral nerves).
According to the National Institute of Neurological Disorders and Stroke, CMT, which is also known as hereditary motor and sensory neuropathy (HMSN) or peroneal muscular atrophy, affects around 1 in 2,500 in the US.
Lupski told the press that he has known for 40 years that he has a “genetically-recessive disease”.
He and his colleagues have been working on tracking down the genetic causes of CMT for decades. In 1991 they published results of a study where they identified the first duplication on a chromosome that gave rise to CMT. Since then 40 other genetic mutations and changes have been identified as leading to CMT, but none of these explained the form of CMT that affects Lupski and some of his siblings.
The quest came to an end earlier this year when the team at BCM’s Human Genome Sequencing Center sequenced his entire genome and concluded that in his case the culprit is a gene called SH3TC2. Lupski has inherited two mutant forms of the gene, one from each parent.
“I have the disease and I have two mutant genes,” said Lupski.
Neither of Lupski’s parents had the disease, but four of their children inherited both mutant copies of the gene and inherited the disease.
The BCM researchers are excited because this is the first time they have tried to identify a disease gene by sequencing a patient’s entire genome.
“It demonstrates that the technology is robust enough,” said Lupski, “We can start to use this technology to interpret the clinical information in the context of the sequence – of the hand of cards you have been dealt. Isn’t that the goal or dream of personalized genomic medicine?”
The researchers also discovered that a person who carries only one of the recessive mutations is susceptible to carpal tunnel syndrome, a painful progressive condition caused by compression of a key nerve in the wrist and that usually affects people who perform repetitive motions.
Lupski said it makes you wonder how often it occurs that carrying only one gene for a recessive disease leaves a person susceptible for complex traits.
“Will we be able to look at some alleles (gene copies) like this to see what you might be susceptible to?”
Lupski’s is not the first genome to be sequenced, but so far there have been less than 10 reported cases, most of them intellectual exercises. In fact in 2007, Gibbs was one of the scientists who presented 1953 Nobel Laureate James Watson, co-discoverer of the DNA double helix and developer of the Human Genome Project, his full genome in a ceremony at BCM.
Lupski said decoding a genome is not an easy task and “one is struck with awe at the inability to interpret a lot of what we see”.
“Currently, we only know the function of 5 percent to 10 percent of the approximately 25,000 genes in our genome that it takes to make a human being. I think at least what this paper tells us is that the data are robust enough that we can start to use it to interpret clinical information in the context of the genome sequence,” he added.
To find a specific disease-causing mutation of a gene, the scientist must not only understand its sequence, but also the different ways it can change (the nucleotide switches, deleted or duplicated genetic material). And added to this is another layer of complexity: mutations in different genes can result in similar diseases.
For the study, Gibbs and colleagues used a “whole genome shotgun” approach, where they took Lupski’s genome, broke it up into small fragments called “snips” (short for SNPs, single-nucleotide polymorphisms) and then cloned them. They then isolated and sequenced the clones and used a computer algorithm to reassemble the genome.
They identified all the function variants in genes that were likely to be linked to CMT.
In one allele (member of the gene pair) for SH3TC2, they found what they called a “nonsense” mutation that results in a premature stop to a protein-building instruction. This mutation has been seen before in CMT patients of particular ethnic groups. They also identified what they descirbed as a “missense” mutation in the other allele that results in the production of the wrong amino acid (so the associated protein can’t do its job properly inside cells).
The first mutation was found in one parent and two siblings who did not have CMT, and the other was found in the other parent and one grandparent, who also did not have the disease. Only siblings who inherited both genes had this particular form of CMT, including Lupski.
There are other ways of sequencing genomes which can for example look for particular variations, but in this case, because of the potential of different kinds of changes in different genes, some inherited recessively and some dominantly, the “whole shotgun” approach was thought to be a better option.
The authors wrote that experts struggling to understand diseases with these kind of genetic properties should also consider trying this approach:
“Clinical and genetics experts struggling with poorly understood high-penetrance genetic diseases must now seriously consider this approach for illuminating the molecular etiology of these cases, and ultimately providing better patient management for families living with such diseases,” they wrote.
Lupski said the study heralds a new era of clinical sequencing whereby a patient will one day be able to have his or her genome analysed in order to determine the best treatment for even quite common disorders.
“If you have hypertension, can we use your genome to figure out a better treatment for you? It will take a lot of time. We don’t know what 90 percent of the genes in the genome do,” said Lupski, explaining that his own genome contains 3.5 million differences to the reference genome that was sequenced in the Human Genome Project:
“I expect that to hold true for others. Everyone is truly unique,” said Lupski.
The study was funded by the National Human Genome Research Institute and the National Institute of Neurological Disorders and Stroke.
“Whole-Genome Sequencing in a Patient with Charcot-Marie-Tooth Neuropathy.”
Lupski, James R., Reid, Jeffrey G., Gonzaga-Jauregui, Claudia, Rio Deiros, David, Chen, David C.Y., Nazareth, Lynne, Bainbridge, Matthew, Dinh, Huyen, Jing, Chyn, Wheeler, David A., McGuire, Amy L., Zhang, Feng, Stankiewicz, Pawel, Halperin, John J., Yang, Chengyong, Gehman, Curtis, Guo, Danwei, Irikat, Rola K., Tom, Warren, Fantin, Nick J., Muzny, Donna M., Gibbs, Richard A.
Source: Baylor College of Medicine, National Institute of Neurological Disorders and Stroke.
Written by: Catharine Paddock, PhD