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Genome Sequencing Finds Unknown Cause of Epilepsy
Researchers pointed out that each
one of the roughly 3 billion base
pairs that make up the human
DNA alphabet was covered by
at least 50 reads; © University
Not only did they find the likely culprit – a previously unknown mutation in a gene coding for a sodium channel protein in the central nervous system – but their findings offer some emotional relief and explanation to the patient's family in the absence of a medical diagnosis and any family history of similar disease.
"If you have a small child with severe epilepsy, not knowing what is causing it is a big burden to carry for the family," said Michael Hammer of the UA's department of ecology and evolutionary biology. "It leaves a lot of open questions and sometimes even feelings of guilt."
Because the severity of the patient's condition, the absence of the disease in both parents and her younger sibling and no family history of epilepsy, Hammer and Krishna Veeramah ruled out an inherited genetic defect as the cause. Rather, they suspected a so-called de novo mutation, a "typo" in the genetic alphabet generated by pure happenstance, most likely in the paternal germ line.
"We were tasked with the search for the proverbial needle in a haystack," said Veeramah. "To find a de novo mutation, we have to comb through the entire genome. In the old days, we could have generated a list of candidate genes and sequenced them one gene at a time. Unfortunately that is a lot of work, especially in the brain where you have thousands of genes that could potentially be involved in a process leading to a neurological disorder."
"The development of Next Generation Sequencing Technology in recent years provides a much more powerful approach to actually analyse all the genes at the same time. So that is what we wanted to do. We are looking at the level of the entire genome something that was not possible until very recently", Hammer added.
In this case, the researchers did not find a smoking gun from looking at copy number variations, leaving point mutations or small insertions or deletions of DNA letters as a likely cause. Using the sequencing technology capabilities of Complete Genomics between 96 and 97 per cent of the patient's DNA sequence, as well as the genomes of her parents and her sibling, was deciphered within a few weeks.
Veeramah pointed out that each one of the roughly 3 billion base pairs that make up the human DNA alphabet was covered by at least 50 reads.
"This is important because whole genome sequencing still makes a lot of errors so you have to double up on your efforts to get the accuracy you need."
MEDICA.de; Source: University of Arizona