I wanted to know if anyone has experience sequencing the human MHC region (~4 Mb). My plan is capture the region using a custom Agilent SureSelect kit (exons, intron, 5' and 3' UTRs). After masking the repetitive regions, I found that ~30,000 baits will cover the remaining 2 Mb of sequence at 1X tiling. We would like to generate libraries for both the 454 and GAIIX machines.
Our next-generation core facility beta-tested Agilent's Human All-Exon SureSelect kit with good results except for the MHC region. Unfortunately, ~70% of the genes in this region were lacking sequence in one or more exons. I'm getting the feeling that it is probably impossible to sequence this region using a hybridization sequence capture approach. Any thoughts?
Thanks,
Double A
Our next-generation core facility beta-tested Agilent's Human All-Exon SureSelect kit with good results except for the MHC region. Unfortunately, ~70% of the genes in this region were lacking sequence in one or more exons. I'm getting the feeling that it is probably impossible to sequence this region using a hybridization sequence capture approach. Any thoughts?
Thanks,
Double A
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