Hsien points out that at the current going rates of the sole company offering commercial whole-genome sequencing, $2,500 would buy you only 0.71% of a whole genome. That sounds small, but it's still more than 20 million base pairs - twenty times the paltry one million sites interrogated by the Navigenics chip for the same price!
Of course, the Navigenics SNPs have been carefully selected to provide as much information as possible about common genetic variation, so they're still a better purchase right now than a random 0.71% of a genome sequence. Nonetheless, this comparison provides some insight into just how cheap sequencing technology is becoming; it certainly won't be long before it's commercially competitive.
As I've emphasised in recent posts, the chip technology currently used to analyse genetic variation by researchers and personal genomics companies (23andMe, deCODEme, SeqWright and now Navigenics) will only ever capture a fraction of your total genetic risk for common disease: the fraction that consists of common small-scale variants.
In contrast, whole-genome sequencing will give you information about the types of genetic variation - such as rare variants and large-scale structural variation - that are completely invisible to current chips. Since these variants probably constitute a substantial fraction of genetic risk for common diseases, sequencing (when it becomes affordable) is likely to give you a lot more useful information than current genome scans. And best of all, since whole-genome sequencing gives you information on every variation in your genome, it won't ever become obsolete - whereas chips will be periodically replaced by new, higher-resolution models that capture a larger (but still incomplete) snapshot of your genetic variation.
In other words, while genome scans are the best affordable technology we have right now, they have profound limitations and will become rapidly outdated as researchers begin to focus on the rare variants and structural variation that contribute to variation in complex traits and common disease risk. For those who care about value for money, my suggestion is that you put your $2,500 in a bank account with a good interest rate and don't take it out until whole-genome sequencing becomes cheap enough to buy that instead.
Of course, that's advice for those who are mainly interested in health prediction. For genetic genealogists current genome scans provide some powerful information about genetic ancestry; if that's your interest, you'd probably be best off investing in a deCODEme scan, which gives you the same number of SNPs as Navigenics for 40% of the price, and (unlike Navigenics) allows you to download your complete raw data.
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