Fasta Sequence For Each Hla Alleles

Question

[J.F.Jiang]

Hi all,

Since it is a new question for HLA typing, I post this question as new.

After trying several public tools, such as HLAminer and ATHLATES for HLA typing, it seems that the two tools are developed for whole-exome seq for the HLA genes. If we only seq some specific exons, it will not worked.

For example, we use Miseq to ONLY sequence the exon 2 and 3 for HLA-A gene, till now, my idea is to directly match the reads to the exon reference, because our reads length is 300bp while the exon length is ~270bp, in other words, one reads stand for a round of exon.

However, I am confused about the HLA database, for example, for HLA-A gene, it provides 2579 alleles. I can get the whole fasta file for each allele, but can not directly get the exon fasta data for each alleles.

The only similar file is the alignment file, A_nuc.txt, but I did not find any comments for this file. The HLA-A gene supposed to have 8 exons, does the file seperate these exons by "|"？If there is anyone know how to get the exon fasta data for alleles, plz let me know. HLA Class I Gene A B C E F G
Alleles 2,579 3,285 2,133 15 22 50 Proteins 1,833 2,459 1,507 6 4 16 Nulls 121 109 63 0 0 2

Thanks

[Hamish]

You can try looking at the EMBL format IMGT/HLA data file which include the exon data (see ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/hla.dat).

For more information about the data provided by IPD (including IMGT/HLA) I suggest you contact the IPD folks via their contact forms:

• IMGT/HLA: http://www.ebi.ac.uk/support/hla.php
• IPD: http://www.ebi.ac.uk/support/ipd.php

[J.F.Jiang]

Thanks, I actually build a script to extract all the exon seq from the alignment file in IMGT

[GouthamAtla]

Hi jing, which tool did you use finally for the data analysis ?

[demolidd77]

This is useful !!! others who wana extract HLA exomes information , I suggest you can use hla.dat to build your database.

[greeshmathulasi1]

Hi, Did you got the answer?

Answer 1

[zam.iqbal.genome]

I think the resource you want does not exist yet. IMGT contains information on the HLA classical genes restricted to 2 exons for class I, and 1 for class II (I think - don't quote me on class II). The _nuc files are from CDS (so with introns spliced out) and the _gen files are from genomic sequence (so have the introns). But I don't think there is available full sequence of the entire gene (all exons).

You might be interested in this paper:

Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing Vinzenz Lange1†, Irina Böhme1*†, Jan Hofmann2, Kathrin Lang1, Jürgen Sauter2, Bianca Schöne1, Patrick Paul1, Viviane Albrecht1, Johanna M Andreas1, Daniel M Baier2, Jochen Nething3, Ulf Ehninger2,3, Carmen Schwarzelt1, Julia Pingel2, Gerhard Ehninger4 and Alexander H Schmidt1,2

in BMC Genomics, this year.

[J.F.Jiang]

Thanks, I actually build a script to extract all the exon seq from the alignment file in IMGT

[GouthamAtla]

Hi Jiang, which tool you are using for the data generated for only exon 2 and exon 3 ?

[demolidd77]

HI,geek_y, You can write a script to deal with hla.dat ,just to extract any HLA allele exons that you need .