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The author makes the comparison between the cost of 23andme's genotyping arrays and the cost of whole genome sequencing (WGS), but the comparison with whole exo

The author makes the comparison between the cost of 23andme's genotyping arrays and the cost of whole genome sequencing (WGS), but the comparison with whole exome sequencing (WES) is probably more appropriate. For the unfamiliar, exome sequencing specifically sequences the exons (which are the components of genes). I'm not sure how many SNPs 23andme genotypes outside of exomes. Since the exome is 1-2% of the whole genome. You can imagine the savings when doing WES vs WGS (although the prep for WES is more costly). WES can be done for under $300 at this point (I'm not sure of the actual price point on the latest Illumina systems, but my guess is it's lower than this).

coetzeesg 11y ago
Anything that is interrogating risk for complex disease must look outside of exons. Most genome wide association study (GWAS) index SNPs, in diseases such as cancer[1], autoimmune disorders and psychiatric disorders, fall in introns of genes and the large intergenic regions. This means that it's hard to pinpoint the gene that is being effected, and if you're only looking at the exons of genes, you're missing almost the whole picture of inherited risk. [1] from my paper in 2012: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467035/figure/gks542-F1/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467035/figure/g...
- adenadel 11y ago
  I agree with you completely, but comparing from a consumer standpoint the exome gives you a lot more information than the SNP chips for a potentially similar consumer price point.
  - coetzeesg 11y ago
    That's fair, but if you don't already present with a disease, I don't know how much WES can tell you. At least with a SNP chip, and the correct analysis, you can start speculating about what may happen down the road.
    - adenadel 11y ago
      I agree completely. The nice thing about the exome is that the knowledge is more extensible than the SNP chip. If we discover new variants within the exome you won't need to be genotyped a second time. That logic probably argues more for WGS though. It is also the problem with WGS and WES. You get a ton of variants of unknown significance that the patient/customer will be curious about but be able to obtain no answers.

coetzeesg 11y ago

Anything that is interrogating risk for complex disease must look outside of exons. Most genome wide association study (GWAS) index SNPs, in diseases such as cancer[1], autoimmune disorders and psychiatric disorders, fall in introns of genes and the large intergenic regions. This means that it's hard to pinpoint the gene that is being effected, and if you're only looking at the exons of genes, you're missing almost the whole picture of inherited risk. [1] from my paper in 2012: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467035/figure/gks542-F1/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467035/figure/g...

adenadel 11y ago
I agree with you completely, but comparing from a consumer standpoint the exome gives you a lot more information than the SNP chips for a potentially similar consumer price point.
- coetzeesg 11y ago
  That's fair, but if you don't already present with a disease, I don't know how much WES can tell you. At least with a SNP chip, and the correct analysis, you can start speculating about what may happen down the road.
  - adenadel 11y ago
    I agree completely. The nice thing about the exome is that the knowledge is more extensible than the SNP chip. If we discover new variants within the exome you won't need to be genotyped a second time. That logic probably argues more for WGS though. It is also the problem with WGS and WES. You get a ton of variants of unknown significance that the patient/customer will be curious about but be able to obtain no answers.