The new post-doc's plans

I've been reading over the fellowship application our new post-doc submitted to NIH. NIH didn't fund it, but the comments were quite supportive so we want to fix it up and send it in for the next deadline (June sometime?). For me this is also an opportunity to think carefully about the immediate and long-term experiments we're planning. The immediate experiments will provide preliminary data that should make the proposal more compelling, and will also be a foundation for the full NIH R01 proposal we hope to submit in the fall. The medium-term is the experiments the proposals actually propose to do, and the long-term is where they'll lead, both for the post-doc's career (an issue raised in the reviews of his application) and for my lab's ongoing research.

One preliminary analysis we should do is comparison of the two genomes he'll use. Both are sequenced, and it would be good to provide table and/or a figure giving specific numbers of SNPs (is it called a polymorphism when you're only comparing two individuals?), numbers and lengths of indels, and information about specific differences relevant to the proposed analysis. This could be an appendix if such are allowed, or a small table in the text.

Another thing the proposal needs is a more explicit description of the calculations that underlie its claims that the scope of the sequencing is sufficient for the information desired. He'll be creating pools of DNA from different stages and sequencing these. Depending on the source of the pool of DNA, this will require a lot of sequencing, a ton of sequencing, and what until recently would have been an absurd amount of sequencing. We can afford to do some sequencing on our present budget, and the R01 proposal is mainly to get funding for the massive sequencing. I don't understand the sequencing methods he's proposing as well as I need to, and I haven't seen any of the calculations yet. We need to lay them out in enough detail that the reviewers will have confidence in us. Perhaps we can also create some simple diagrams illustrating how the different pools will be analyzed.