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International Research Team Demonstrates Dx Potential of Exome Sequencing

NEW YORK (GenomeWeb News) – In a paper scheduled to appear online this week in the Proceedings of the National Academy of Sciences, researchers from the US, Turkey, and Lebanon used whole-exome sequencing to diagnose a rare genetic condition in an infant with ambiguous symptoms.

Researchers from Yale University and elsewhere used Roche NimbleGen exome capture arrays and Illumina sequencing to assess DNA samples from a five-month-old Turkish boy with an unexplained medical condition characterized by dehydration and diarrhea. Among the numerous DNA variants they detected was a mutation in a gene called SLC26A3, which codes for a chloride anion exchanger.

Based on this finding — and a subsequent clinical follow-up — the team concluded that the infant has a rare genetic condition called congenital chloride diarrhea, which affects the way the gastrointestinal tract absorbs water and chloride anion.

"[W]e have demonstrated the utility of this technology, underscoring the potential for its broad use in the clinic," senior author Richard Lifton, a genetics researcher affiliated with Yale University and the Howard Hughes Medical Institute, said in a statement. "As the cost of DNA sequencing continues to plummet, it seems clear that this technology will be useful for clinical diagnosis in a number of settings."

Whole exome sequencing, limited to the one percent or so of the genome that contains exons, has been gaining momentum over the past few years. For instance, earlier this year, a team of researchers from the University of Washington and Agilent published a proof-of-principle study in which they sequenced a dozen exomes.

For the current paper, Lifton and his team adapted the Roche NimbleGen whole exome capture array for use with the Illumina Genome Analyzer sequencing platform. The array targets almost all of the protein and microRNA coding sequence in the human genome.

The team first validated their approach by sequencing the exomes of five Caucasian individuals and comparing the results with those generated by genotyping. They then turned their attention to DNA from one individual: a five-month-old Turkish boy suffering from dehydration and failure to thrive.

Based on the infant's clinical features, doctors suspected he had a rare disease called Bartter syndrome, caused by mutations affecting transporter genes in the kidney. Even so, the infant did not carry any known Bartter syndrome mutations.

To uncover the genetic underpinnings of his condition, the researchers extracted DNA from the baby's blood, captured exome sequences with the Roche NimbleGen array, and sequenced 34 million bases of exome DNA to about 40 times coverage using the Illumina Genome Analyzer.

After mapping the reads to the human reference genome and tossing out reads that didn't correspond to targeted sequence, the researchers looked for copy number variants and SNPs that might explain the boy's condition.

Because the infant's parents (and one set of grandparents) are first cousins, the researchers suspected he had inherited a recessive disease. Although his parents were healthy, the infant's sister, born prematurely, died a few days after birth, the team noted. His mother had also miscarried twice.

Among the many variants detected in the boy's DNA was a missense mutation in both copies of SLC26A3, a gene that's mutated in congenital chloride diarrhea. Indeed, doctors examining the child confirmed that his symptoms were consistent with a congenital chloride diarrhea, in which an individual's gastrointestinal tract doesn't take up water or electrolytes, such as chloride anions, properly.

The team also found SLC26A3 mutations in five other individuals when they re-sequenced SLC26A3 the exonic sequences for 39 other individuals suspected of having Bartter syndrome but lacking known Bartter-causing mutations.

"This example provides proof of concept of the use of whole-exome sequencing as a clinical tool in evaluation of patients with undiagnosed genetic illnesses," the researchers wrote. "These findings further underscore the ability to parse large quantities of sequence data to produce clinically useful information that combines clues from the clinical condition in conjunction with the genetic data to arrive at a correct diagnosis."

And while they conceded that non-coding portions of the genome probably contain rare variants missed by exon sequencing, the researchers argued that the approach has potential not only for diagnosing rare and common diseases but also for finding new genetic clues about complex traits and conditions.

"The ability to use comprehensive genetic diagnosis to clarify disease causation and to tailor treatment to the specific causes of disease in individual patients holds great potential to improve health," Lifton said.

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