I am wondering if people are still resequencing regions flanking an associated SNP, in order to identify hitherto undiscovered common variants which may be the causative SNP? Or is this a bit of an out-of-date strategy after the release of 1000G data?
No fine mapping is not out-of-date strategy yet. It depends what kind of project and how much budget you/your lab is dealing with.
The answer is: it depends. If the goal is to identify hitherto undiscovered *common* variants and your study participants come from one of the population groups represented in the 1000 Genomes Project, resequencing the region flanking an associated SNP is unlikely to find novel variants. However, if the population is not well represented in the 1000G, then resequencing is indicated.
It depends. If your region of interest is adequately covered by 1000 Genomes. For some regions such as those in recent segmental duplications the 1000 Genomes database also contains "false" SNPs (differences between homologous gene sequences, otherwise known as paralogous sequence variant or PSVs).
Even for those regions which are adequately covered you are limited by the populations sampled. So no, fine mapping by resequencing is definitely not dead.
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