Despite recent claims by Illumina, the $1000 genome is still a myth – companies benchmark the bare bone cost of sequencing, not including the cost of sample collection, shipping, DNA purification and most importantly, the cost of genome data analysis, annotation and reporting which eclipses the cost of sequencing the genome. In post sequencing analysis increases the cost of meaningful and actionable genomic data two to three-fold.
$1000 genome – is it complete?
Current shotgun sequencing technologies provide an incomplete picture of the genome sequence, impeding the analysis of genomic architecture – without the essential knowledge of repeated elements, gene duplication or deletion, inversion and other chromosomal rearrangement, the genome is incomplete. Much longer read-length (3-10Kb instead of 150bp) sequencing approaches could provide the “true” genome. Imagine, you are trying to build a pyramid using loose sand instead of blocks – possible, but insanely difficult and inefficient process.
Too much noise
Another significant challenge posed by sequencing the whole genome, is the excess of data. Over 99.9% of variations identified in whole genome sequencing have no impact or only an insignificant impact on your health. Filtering out the 4 million variants is a problem in genome analysis, as it is not always clear which variations are sand grains and which are the golden nuggets – imagine the efficiency of a gold prospector working at night armed with an underpowered flashlight. Typically, the first step in genome analysis is to discount most of the variations that fall outside the protein coding regions, because most of the “action” happens within the protein coding region, the exome. Panning for those gold nuggets under a lamppost might not seem very clever, but when surrounded by darkness, this may be the only way to actually find something.
Too many unknowns
The other challenge is too many unknowns. Even after extensive data annotation and filtering you will find thousands of novel mutations that might, or might not, have a substantial impact on your health. Imagine finding a novel mutation in a known disease-causing gene that may lead to fatal disease, a potential gemstone, that you are trying to evaluate. There are many in-silico models for assessing disease liability of a mutation, but these are as reliable as merchants in pawnshops: to find the true value you shop around – one merchant tells you it is a worthless rock, another tells you it just might be a diamond.
But you do not have any tools to probe further or even polish the stone, so the only thing you can do, is to keep it in your pocket. To know what a mutation is really worth, someone has to report it and provide clinical annotation (i.e. a price tag). Novel mutations in disease causing genes can be properly assessed only if they were found in several other people afflicted by illness, and rarely identified in healthy individuals – the odds of finding the mutation in each group are indicative of disease liability.
Why get my genome sequenced?
If you are wondering ‘why bother?’, genome sequencing can truly save lives. Genome sequencing may indicate that you have a predisposition to colon cancer -but you may have been ignoring the reminders about colonoscopy. Some people may not realize that they have a brain aneurysm, which can be identified by genome sequencing and could be surgically repaired. Like it or not, genome sequencing can be a rude awaking call that can put you on the right track. So my advice would be, get your genome sequenced.
Why exome sequencing is the most effective solution?
You are firm in your decision to get control over your future genomic health and are wondering ‘where I can get my genome sequenced? Should I pay $5000 for whole genome, buy an exome based test, or wait out for a $1000 genome?’ Buying exome sequencing is like buying a shovel and good sift and heading to the river for some prospecting, which may be a more efficient way to go. Best is if you can follow an experienced prospector who does not mind sharing his trade secrets, that way you can save a lot of time and effort. Genome analysis, as well as gold prospecting, may bring you just sand and sediments, but sometimes you may find a nugget of gold that may save someone’s life. In the end, the gold is there, you just need to find it.