Capture design

One project that I'm working on is to map the genetic factors that cause parent-of-origin growth in dwarf hamsters. This project will end up being the final chapter in my dissertation and has a number of angles that hopefully will all come together in the end to forma  complete story. One of these angles is a mapping panel made out of ~200 backcrossed hamster individuals. I'm using a RAD-seq approach which has recently been sent for sequencing. This will use anonymous markers across the genome to find regions associated with growth. The shortcoming of this approach is that the markers are anonymous and not necessarily associated with known genes. In order to place known genes on the map I am designing a capture.

The capture will pull out ~10,000 gene regions (parts of exons) that are known to contain snps from each individual. I will be able to sequence those specific regions in a subset of individuals and then place those genes on the genetic map. In the end I will have actual genes that associate with growth.

I've never designed a custom capture before but J~ has and so with some guidance I'm figuring it out. My goal is to have a list of sequences, each around 200bp long (I should check that length - it needs to be long enough to sequence on Illumina) that have a diagnostic snp in the middle somewhere.

The first step is to find genes that have snps in them and I have done this earlier for my F1 placental transcriptome project.
Now that I have a set of genes with known snps, I need to make sure that none of these fall near exon boundaries. To do this I am using a Blat approach. Blat is nice because it will align my transcriptome to the Mesocricetus auratus genome and split up the genes into different exons. The output of a blat gives me the exact breakpoints in each gene so that I can choose snps that are far from those areas.

Then, once I have the list of genes that have snps far from breakpoints, we send that in to agilent (I think we're using agilent) who will actually design the capture for me. Then it just remains to do the labwork and sequence it.

Parent-of-Origin Effect paper was just accepted!!

My very first first-author paper has just been accepted by the journal Evolution!

It's now going through the typesetting process. They publish the pre-formated articles here and while it's not up now, it should appear soon.

They said expect ~12 weeks for the final proofs to be ready and then I expect there is a queue before it shows up in print.

Generally, it's a description of the parent-of-origin growth effects in dwarf hamsters and the first dalliances of mine to understand the genetic basis and answer the question: is imprinting involved or not?

I'm really excited. Now on to the writing of my second paper...