A study published in this month’s issue of Nature Genetics may provide insight into the future techniques of personalized medicine.
The articles deals with technical advancements and a proof-of-principle study in identifying the causes underlying rare Mendelian disorders.
The techniques involved re-sequencing (another name for next-generation sequencing and massively parallel sequencing) of the exome. That is defined as all protein-coding regions of the genome, which is a very small but significant part of the whole. Consider Illumina’s announcement last year to sequence your genome for $48,000. And of course all the hype since about ten years of having personal copies of our own genomes. The thing is, even if we could easily assemble all the little sequences of our own genome, it’s over-kill! Much of what we have is repeat DNA, that can be both difficult to sequence and assemble. It also provides little useful information in the way of medical genetics.
The exome is a way to get around that, by filtering out only the most useful information in the genome. The second step is to parse only the useful information in the exome to find the causative gene for a specific genetic disease.
The figure above describes the process. First the exomes of individuals with some genetic disease is filtered away from the rest of the genome and sequenced. Only genetic variations that cause coding changes (in the amino acid sequence, but also in splicing) are taken as being of particular interest (because they are more likely to be functional). Next, those variants are filtered by removing variants found in supposedly healthy controls (because they are probably not the disease-causing mutation) and common variants found already in databases (because the variant is probably rare and so not in those databases). What is left are the probable disease-causing mutations. In this case the researchers were able to identify the causative gene using only four individual cases.
Indeed, there is much chance in the process. The mutation has to be rare and present in the exome and it is supposed that it causes coding variation. An alternative would be the examination of the transcriptome. That is, all the transcribed DNA. However, that varies depending on when and where you look and mutations affecting splicing would be overlooked, so it much more likely to miss the causative mutation.
The exome filtering technique provides an exciting model for future studies of rare Mendelian disorders. It’s likely a key step in the long development of personalized medicine.
Image: Exome sequencing makes medical genomics a reality <link>
Citations:
Biesecker, L. (2010). Exome sequencing makes medical genomics a reality Nature Genetics, 42 (1), 13-14 DOI: 10.1038/ng0110-13
Biesecker, L. (2010). Exome sequencing makes medical genomics a reality Nature Genetics, 42 (1), 13-14 DOI: 10.1038/ng0110-13
Sample preparation costs could easily outweigh cost savings from exomic sequencing vs. whole genome sequencing if continued order-of-magnitude sequencing efficiencies are found. Because we don’t know what the non-exomic DNA always means does not mean that there is no information to be gained from the rest of the genome; indeed many of the important common variants so far have not been exomic.
Three comments.
First, on the pedantic side, is that “resequencing” is not synonymous with second generation sequencing. Resequencing is sequencing a target genome for which you already have one or more reference sequences. Contrast this with “de novo sequencing”, which generates such a reference sequence when none is available.
Second, a key bit of information is copy number, and while it is suggestive that at least some exome sequencing approaches preserve this, they may not do so fully (i.e. introduce some distortion).
Third, it may soon be a moot point. Exome sequencing adds additional steps, whose cost is worth it if you save money on everything else. The cost of whole genome sequencing is coming down very rapidly, whereas the cost of various exome selection methods is not on such a trend. If the added cost of selection outweighs downstream efficiencies, then targeted sequencing won’t be competitive. For whole exome sequencing — barring some major improvements in the cost — that point of lost economy is probably less than 2 years away.
Hi Keith,
Thanks for the useful comments, especially wrt to the clear definition of resequencing.