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A comment on When sequencing makes genotyping obsolete (soon). Parent comment

Re:When sequencing makes genotyping obsolete (soon) by coetzeesg on Friday October 23, 2015 @03:13PM (#10440688)
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/g...

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Re:When sequencing makes genotyping obsolete (soon) by adenadel on Friday October 23, 2015 @03:14PM (#10440701)
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.
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Re:When sequencing makes genotyping obsolete (soon) by coetzeesg on Friday October 23, 2015 @03:21PM (#10440740)
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.
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Re:When sequencing makes genotyping obsolete (soon) by adenadel on Friday October 23, 2015 @03:48PM (#10440893)
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.
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