The family's DNA sequences turned out to stray from the human reference genome in about 5 million places. This may sound like a lot, but in light of the fact that only about 2 percent of the human DNA sequence contains actual genes, most of those variations fall into non-coding regions of the genetic material.
In the next step, Hammer's team had to figure out what those variations meant. Using databases of known genes, they checked which were located in actual gene sequences and which would change the amino acid sequence of the respective protein they encoded. In the end, they were left with about 13,000 mutations.
They hoped that somewhere in that pool of candidates was that one mutation that had caused the girl's epilepsy and possibly led to her death.
To whittle down the number of possibilities, the team then screened for mutations that seemed to violate the laws of Mendelian inheritance.
"De novo mutations will look like they don't obey the rules by which we know genetic material is inherited," Veeramah explained. "The patient will have a variant that is not found in the parents or the sibling. We found 34 sites that fit this pattern."
On average, in one individual, only one spontaneous mutation springs up within the coding region of a gene. Therefore, finding 34 told the team that most of those mutations most likely were sequencing errors.
Veeramah said: "Ten of them had already been listed in public databases, meaning they occur in normal individuals and should not be disease-causing. They're probably just systematic artifacts of the sequencing process, so we could eliminate them."
The team sequenced the remaining 24 variations by standard methods, and as expected, only one turned out to be a real mutation. The variant, which was not previously associated with any human epilepsy disorders, consisted of a wrong letter in a gene that serves as the
|Contact: Daniel Stolte|
University of Arizona