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Is anyone doing HLA sequencing with the Nimblgene SeqCap EZ Human MHC design? Or are you doing HLA with your own custom pull-down kit? If so, I would really like to talk to you. I'm at a startup building a sequencing sample prep/analysis technology that will (among other things) significantly increase the performance of HLA sequencing, and we are looking for potential collaborators in this area.
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Hello mschnall,
Our lab has sequenced ~500 samples using NimbleGen's MHC design. For the most part, the sequencing worked quite well. Because of the high heterogeneity of several of the genes in this region (DQA1, DQB1, HLA-A, ect.), you will will have problems aligning reads to a single consensus sequence (hg19). Our bioinformatics core is currently helping us to resolve this problem.
DoubleA -
thanks a lot for the reply, doubleA. we are building a new technology that should help significantly with some of the alignment ambiguities as well as providing phasing information. if you think you might be interested in trying out our technology in the coming months, send me a private message and i can give you more details.Comment
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