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Individual Genome Sequence Reveals New Charcot-Marie-Tooth Disease Culprits

By Andrea Anderson

NEW YORK (GenomeWeb News) – A Baylor College of Medicine-led research team has used whole-genome sequencing of an affected individual to find two new recessive mutations behind the inherited peripheral nerve condition called Charcot-Marie-Tooth disease.

The researchers used whole-genome sequencing and array-based comparative genomic hybridization to find SNPs and copy number variants in the genome of James Lupski, vice chair of molecular and human genetics at the Baylor College of Medicine. Their search yielded two causative alleles for the condition, affecting a gene called SH3TC2.

Those involved say the research, which appeared online last night in the New England Journal of Medicine, represents a shift from whole-genome sequencing as a method for assessing normal human variation to a means of finding disease-related variants in the human genome.

"We now are at a point where we are no longer describing people's variation as an intellectual exercise," lead author Lupski told GenomeWeb Daily News.

The researchers used mate-pair sequencing with the Applied Biosystems SOLiD platform to sequence Lupski's genome to an average of 30 times coverage. They also used array-based comparative genomic hybridization with Agilent and Nimblegen arrays to look for CNVs in the genome and did neurophysiological and electrophysiological assessments of Lupski and several family members, including his parents, three affected siblings, and four unaffected siblings.

Once they had Lupski's genome sequenced, the researchers were faced with the task of trying to distinguish between normal variants and those related to Charcot-Marie-Tooth disease. "This is a real challenge, a real daunting task," Lupski said, explaining that bioinformatic analyses increasingly represent the bottleneck in sequencing studies.

They found 3,420,306 SNPs — 1,165,204 in protein-coding regions and 2,255,102 in non-gene regions — as well as 234 CNVs in the genome.

The researchers were able to narrow down this list by comparing the variants with those found in databases such as the Human Gene Mutation, Online Mendelian Inheritance in Man, and Polyphen databases.

They also incorporated information from studies of Charcot-Marie-Tooth disease spanning a couple decades, Lupski said, which have implicated about 40 loci to the condition.

Having an idea of some of the genes and pathways involved in the condition allowed the team to focus in on a pair of missense and nonsense mutations in the SH3TC2 gene.

Through their subsequent analyses of Lupski's family, they found that his father carries the same missense mutation in SH3TC2, while his mother carries the nonsense mutation, which appears to increase the risk of carpal tunnel syndrome.

Although the most common form of Charcot-Marie-Tooth neuropathy is due to a duplication affecting a myelin gene, Lupski noted, none of the CNVs in his own genome seem to contribute to the condition.

While it will likely take many years for such findings to translate into new Charcot-Marie-Tooth treatments, if at all, Lupski explained, understanding the biology of the condition will be important down the road. "You can't make any kind of a treatment plan until you make a diagnosis," he said.

And, Lupski added, given the role of the nonsense mutation in complex conditions such as carpal tunnel syndrome, the current findings also hint at the possibility of a yet unappreciated relationship between Mendelian and complex conditions.

In an editorial appearing in the same issue of NEJM, Yale University geneticist Richard Lifton discussed the role of genome sequencing in understanding, diagnosing, and treating human disease.

While questions remain about the utility of whole-genome sequencing in a clinical setting and the interpretation and application of data in the genome, Lifton explained, the new study heralds the advent of genome sequencing as a more widely used tool in medicine and disease research.

"It is increasingly clear that the cost is fast approaching a threshold at which DNA sequencing will become a routine part of the diagnostic armamentarium," Lifton wrote. "Lupski and colleagues provide a glimpse of the future for which we need to prepare."

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