4 Approaches for Preparing DNA for HLA Typing

[Genohub]

I'd like to hear about people's experiences using amplicons, long range PCR and exome-seq for HLA typing?

http://blog.genohub.com/4-approaches-to-hla-type-using-next-generation-sequencing/

[JackieBadger]

We use amplicons (MHC IIb). Many issues need to be taking into consideration for good quality genotype estimates. Our genotyping protocol paper has been accepted and will be published soon. My advice to people is to steer well clear of 454 and use Illumina.

I don't see how sequencing an entire genome could provide accurate haplotype reconstruction....?

[Genohub]

In your paper, with how much depth did you sequence those MHC amplicons ? Any recommendations on primer sets or is that described in your article ? Also curious to hear about the analysis software you used.

WGS is not ideal, it would require high coverage.

- Genohub

[Lj Lee]

We use amplicons (MHC IIb). Many issues need to be taking into consideration for good quality genotype estimates. Our genotyping protocol paper has been accepted and will be published soon. My advice to people is to steer well clear of 454 and use Illumina.

I don't see how sequencing an entire genome could provide accurate haplotype reconstruction....?

Hi, interested to read your paper as I'm using Illumina. Yes, which software to use for genotyping?