Not sure that it matters -- if you have a less accurate chip, you just resequence (run it) to greater depth. (If you can afford to, that is... and in all likel

Not sure that it matters -- if you have a less accurate chip, you just resequence (run it) to greater depth. (If you can afford to, that is... and in all likelihood, they can) That's effectively what Helicos et al. are doing anyways. Their call rate for whole-genome resequencing is on the order of 99.7% at a depth of 2; at a depth of 20-50 maybe it becomes useful. If you think of the chip (hybridization) methods being depth of 1, eg. a single scan per sample across however many probes there are for a given SNP, then you can probably see where the synthesis methods win. It's really cheap to re-run them. It's twice as expensive to run 2 chips... All of the sequencing-by-synthesis methods are less accurate but cheaper and ultimately more useful than anything based on the existing hybridization arrays (or beadarrays). If you look at eg. the Personal Genome Project, there is a good summary from the Church lab about how eg. padlock sequencing is different from Affy/Illumina/Nimblegene hybridization arrays. Also note that (1 - 0.999) * 550K still gives 550 miscalls. D'oh. (Another big win for sequencing by synthesis -- just do it again, and again, and again...) This is what I'm getting at when I bitch about 23andMe not advancing the state of the art. With the money they have, they could. But they're not.