What is the difference between using genome build hg18 and hg19 in Genome-wide SNP arrays?

Question

[r.tor]

In CNV analysis, I would like to ask concerning on:

In Genome-wide SNP arrays via Affymetrix OncoScan FFPE Express, is there any limitation to choose genome build hg18 and hg19 for probe locations or any logical explanation for using hg18 instead of hg19? Thanks alot!

Answer 1

[WouterDeCoster]

Unless you need to compare your results with old data there is no real reason to choose an old genome build over a newer. An exception may be that the annotation you want to use is only available in the older build, which may be the case for datasets in hg19 not transferred to hg38. But there is also Liftover (which is imperfect).

[r.tor]

thank you for the reply. I am just looking for a logical answer because despite that we know there are some problem in using Liftover, but it supposed that we should exploit it instead of using an old genome build. I saw it in an credible article and it made me curious that is it possible to be a limitation in Affymetrix OncoScan FFPE Express approach or Nexus application to use hg19?

Answer 2

[r.tor]

thank you for the reply. I am just looking for a logical answer because despite that we know there are some problem in using Liftover, but it supposed that we should exploit it instead of using an old genome build. I saw it in an credible article and it made me curious that is it possible to be a limitation in Affymetrix OncoScan FFPE Express approach or Nexus application to use hg19?

[WouterDeCoster]

Please use ADD COMMENT to answer to earlier replies, as such this thread remains logically structured and easy to follow.

I don't understand what you try to say, so please rephrase.