This directory contains the HLA types are generated for the paper

HLA Diversity in the 1000 Genomes Dataset
Pierre-Antoine Gourraud, Pouya Khankhanian, Nezih Cereb, Soo Young Yang,
Michael Feolo, Martin Maiers, John D. Rioux, Stephen Hauser, Jorge Oksenberg

Published: July 02, 2014 DOI: 10.1371/journal.pone.0097282

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0097282

Columns in the File

 "id"       : Coriell ID
 "sbgroup"  : Sub population
 "A" "A.1"  : HLA-A genotype
 "B" "B.1"  : HLA-B genotype
 "C" "C.1"  : HLA-C genotype
"DRB1" "DRB1.1": HLA-DRB1 genotype
"DQB1""DQB1.1" : HLA-DQB1 genotype
   The sample  "NA06985" at Coriell belongs to the "CEPH" sub-population  and his HLA genotype is  
HLA-A* ("03:01" "02:01") HLA-C*( "07:02" "06:02:01:01") HLA-B*("07:02:01" "57:01")  in the MHC class I 
region and HLA-DRB1*("15:01" "15:01")HLA-DQB1*("06:02:01" "06:02:01") in the MHC class II region.

From the paper supplementary info

The HLA typing data of 1,267 individuals related to the 1000 Genomes Project (Table 1) covers 14 populations 
encompassing 4 major ancestral groups. After specific PCR amplification, exons were sequenced by Sanger technique. 
The sequences were compared to available sequence information in the HLA allele database on exons 2 and 3 for 
class I and on exon 2 class II genes, therefore any polymorphism occurring in exon 4 of class I allele or exon 3 
of class II gene was not investigated. Typing ambiguities between alleles were allowed since HLA-A, HLA-B, HLA-C 
gene products have identical sequences in exon 2 and exon 3 antigen recognition sites. Similarly, for class II genes, 
typing ambiguities occur if HLA-DRB1, HLA-DQB1 gene products have identical sequences in exon 2 antigen recognition sites. 
(See Appendix S1 in supplemental material for further details). The Allele Database version used in the report is 
IMGT 2.26.0 (Jul 2009), effective Feb 2010. 

Sequence-based typing (SBT) was used for typing HLA class I (HLA-A, -B, -C) and class II (DRB1 and DQB1) genes.  
Sequencing templates were produced by locus- or group-specific pairs of oligonucleotide primers from genomic 
DNA by Polymerase Chain Reaction (PCR). A total of 40 locus- and group- specific primers were used to amplify the 
target sequences.   Sanger cycle sequencing was carried out using BigDye V3.1 (Applied Biosystems) chemistry and 
ABI 3730xl capillary sequencer for base calling. The PCR product was treated with Exonuclease, and ethanol precipitation 
was used to clean-up post-sequencing reaction extension products. Class I sequencing primers were those locus-specific 
sequences for each locus in the intron/exon boundary regions to sequence the entire exons. All Class II PCR primers were 
tailed with M13 forward and T7 reverse sequences. Sequencing was performed on both strands.    When further resolution is 
required for the ambiguous combinations that were not distinguished by these groups, additional group-specific amplifications 
or group-specific sequencing primers were used.

The HLA genotype data of the present study is available online: The full specification of HLA alleles in the specified release 
of the HLA nomenclature [17] is provided on the dbMHC portal (See on-line resources) at NCBI [30]. In addition, allele frequencies 
can be viewed online using tools developed in the anthropology and cell line components of the Histocompatibility Workshops [31]
(Figure S2, screen capture of the display [32]). Allele frequency tables are extremely sparse, reflecting the high diversity of 
HLA alleles for all loci and the limited sampling of the HLA alleles in 1000 Genome Project sample sets (Supplementary Data Tables S2; 
S3 for HLA allele naming convention used, also available online at dbMHC [32]).

Additional data formats can be obtained contacting pierreantoine.gourraud@ucsf.edu

