tag:blogger.com,1999:blog-3162625598067227745.post2172037275617252978..comments2023-05-19T02:09:36.856-07:00Comments on Mendelian Disorder: Cliff Reid on CG vs IlluminaAnonymoushttp://www.blogger.com/profile/15925017686062610434noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-3162625598067227745.post-36694687222370656862012-03-15T14:07:03.547-07:002012-03-15T14:07:03.547-07:00Yea, I think 454 makes sense too. Not sure if Ion ...Yea, I think 454 makes sense too. Not sure if Ion Torrent and SOLiD are good for validation with their relatively higher error rates.Hugo 果言有理https://www.blogger.com/profile/01210924694199001194noreply@blogger.comtag:blogger.com,1999:blog-3162625598067227745.post-58414814791085537112012-03-14T15:35:43.879-07:002012-03-14T15:35:43.879-07:00Thanks Hugo.
I do think an alternative for this k...Thanks Hugo.<br /><br />I do think an alternative for this kind of comparison is to validate on a completely different technology. For example, 454 or Ion Torrent or even SOLiD.<br /><br />That said, I'm certain (from having a look at such data) that our conclusions will not change after doing so.Anonymoushttps://www.blogger.com/profile/15925017686062610434noreply@blogger.comtag:blogger.com,1999:blog-3162625598067227745.post-62778938862585910112012-03-13T17:30:48.857-07:002012-03-13T17:30:48.857-07:00A confidence level of 95% and a confidence interva...A confidence level of 95% and a confidence interval of 5% for each of the platform specific call set requires a minimum sample size of ~380. Any further estimation based on a statistically insignificant set is inconclusive. That's why we went on to SureSelect at a larger scale, which gives us a statistically significant result. <br /><br />As mentioned on the paper, the SureSelect may have potential bias since it was followed by Illumina sequencing. But if there is a strong bias towards Illumina due to systematic errors, probably the invalidation rate for Illumina itself wouldn't be as much as that for Complete.<br /><br />Let's take the existing Sanger numbers and calculate it once again with its possible errors. With the same confidence level of 95% aforementioned, the possibly best validation rate for Illumina is 30% and the worst for Complete is 83%, which convert into 104K and 83K true positives in their specific call sets, respectively. That said, Illumina is still having a higher sensitivity, whereas Complete is more accurate (less FDR).<br /><br />If it looks unfair, that's the problem of extrapolating on a set with big error bars. One thing that is true is that we can do a larger scale of Sanger sequencing on the specific calls, then we can have a better sense of the potential ground truth which will be less controversial.<br /><br />Until then, we gotta believe that they both have their goods and bads, and performed very well overall.Hugo 果言有理https://www.blogger.com/profile/01210924694199001194noreply@blogger.com