Question: Training dataset for NGS HLA typing (reads >200bp from PCR amplicons)
gravatar for Alvaro Sebastian
3.4 years ago by
Alvaro Sebastian50 wrote:

I'm looking for a training set from human HLA typing with long reads (454, IonTorrent or MiSeq 300bp) obtained by PCR (amplicon sequencing). I don't mind about MHC loci or if it's genomic or transcriptomic, but I need a dataset that contains:

- NGS reads
- Sequences of used primers
- Sequences of barcodes used to tag samples
- Reference genotypes of the samples to validate predictions (by Sanger sequencing or another well established method)

It's very hard to find any public data from literature. There a lot of papers about the topic, but most of them are from companies (for ex. Roche) and they don't publish the data.

Thanks in advance.

PD: HapMap and 1000 Genomes reads are not valid, they are not from PCR and they are too short ;)

amplicon typing hla ngs • 1.2k views
ADD COMMENTlink modified 6 weeks ago by bounlu130 • written 3.4 years ago by Alvaro Sebastian50
gravatar for bounlu
6 weeks ago by
bounlu130 wrote:

The references to HLA typing tools might help as they usually train their software on public datasets:

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by bounlu130
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1129 users visited in the last hour