Sequencing DNA/RNA of 4 genes of interest in multiple samples (n=50)?

[Thomas Hartjes]

I am looking for ideas for sub-genomic sequencing experiments and I realy can use some help:

I would like to use at least 50 normal/tumor samples and will extract genomic DNA or RNA from it.
I am looking for a way to sequence my regions of interest (four genes that are 50-500kb in length) in all these samples and look at the genetic variations.

I read about some capture arrays? Will this be the best option? Hope you guys can help me decicde which method suits best for this and referring to literature will be extremly helpfull.

Much obliged!

[Heisman]

Do you want to sequence the entire genes or just the exons?

[Thomas Hartjes]

Do you want to sequence the entire genes or just the exons?

I preferable go for sequencing the whole genes, but after that it is also interesting to just sequence only the exons, so actually both

[Heisman]

If you sequence the whole genes you will by definition sequence the exons.

I would look into earray.chem.agilent.com. Some sort of capture is probably going to be your best bet. Maybe others will chime in as well.

[Cofactor Genomics]

Here are the two links that I would explore for targeted capture.

http://www.genomics.agilent.com/Coll...ew&PageID=2094

http://www.nimblegen.com/products/seqcap/index.html

Best of luck.

[Chipper]

http://www.halogenomics.com/

[NextGenSeq]

Actually Illumina has just released their TruSeq Custom Amplicon kit which would be cheaper than NimbleGen or Agilent.