Genetic sequencing has gone through several advances. A major breakthrough came when scientists began breaking the billions of letters that compose DNA up into relatively small bits of a few hundred base pairs. Once the sequences of all of those bits were known, they were reassembled with a computer. This has allowed researchers to easily sequence entire genomes, and has revealed the causes of many genetic diseases. But there are inherent limitations to this method. For example, it cannot handle highly repetitive sequences and some kinds of mutations, like large inversions or rearrangements of DNA sequences.
Scientists have now used the more recent, long read technology to sequence far longer pieces of DNA. PacBio's HiFi sequencing can read about 20,000 bases, instead of a few hundred at a time. A new study reported in the American Journal of Human Genetics has shown that long read sequencing is an excellent technique for finding the causes of rarer genetic diseases. In one hundred cases, the investigators were able to "immediately" find causes for 83 of the cases. The causes of another ten cases were found with additional work, said co-corresponding study author Christian Gilissen, a Professor at Radboud University Medical Center. More refinement of this tool may be needed to find the cause of the last seven cases.
"Initially, this technique was less accurate and quite expensive, but it has now become reliable and much more affordable," noted co-corresponding study author Lisenka Vissers, a Professor at Radboud University Medical Center. "Therefore, we asked ourselves: could we replace the short reads and all the additional tests with long reads?"
This work suggested that long read sequencing can find 93 percent of the causes of genetic diseases. "Causes that cannot, or are very difficult to detect with current short read techniques. For less difficult causes, this percentage is likely even higher," said Vissers.
Unlike short read sequencing, this technique can also map an epigenetic feature called methylation, which can affect gene expression.
Vissers added that this is the first direct comparison of the long read sequencing technique to existing tools, using one hundred known cases. Long read sequencing may soon be the preferred option as it continues to be less expensive and reveal even more about DNA. This is particularly true for rare diseases, the study authors noted.
Sources: Radboud University, American Journal of Human Genetics
