PMID- 31844174
OWN - NLM
STAT- MEDLINE
DCOM- 20210525
LR  - 20210525
IS  - 1476-5438 (Electronic)
IS  - 1018-4813 (Print)
IS  - 1018-4813 (Linking)
VI  - 28
IP  - 5
DP  - 2020 May
TI  - SweHLA: the high confidence HLA typing bio-resource drawn from 1000 Swedish 
      genomes.
PG  - 627-635
LID - 10.1038/s41431-019-0559-2 [doi]
AB  - There is a need to accurately call human leukocyte antigen (HLA) genes from 
      existing short-read sequencing data, however there is no single solution that 
      matches the gold standard of Sanger sequenced lab typing. Here we aimed to 
      combine results from available software programs, minimizing the biases of 
      applied algorithm and HLA reference. The result is a robust HLA population 
      resource for the published 1000 Swedish genomes, and a framework for future HLA 
      interrogation. HLA 2nd-field alleles were called using four imputation and 
      inference methods for the classical eight genes (class I: HLA-A, HLA-B, HLA-C; 
      class II: HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1). A high confidence 
      population set (SweHLA) was determined using an n-1 concordance rule for class I 
      (four software) and class II (three software) alleles. Results were compared 
      across populations and individual programs benchmarked to SweHLA. Per gene, 875 
      to 988 of the 1000 samples were genotyped in SweHLA; 920 samples had at least 
      seven loci called. While a small fraction of reference alleles were common to all 
      software (class I = 1.9% and class II = 4.1%), this did not affect the overall 
      call rate. Gene-level concordance was high compared to European populations 
      (>0.83%), with COX and PGF the dominant SweHLA haplotypes. We noted that 15/18 
      discordant alleles (delta allele frequency >2) were previously reported as 
      disease-associated. These differences could in part explain across-study genetic 
      replication failures, reinforcing the need to use multiple software solutions. 
      SweHLA demonstrates a way to use existing NGS data to generate a population 
      resource agnostic to individual HLA software biases.
FAU - Nordin, Jessika
AU  - Nordin J
AUID- ORCID: 0000-0002-8414-2190
AD  - Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, 
      Uppsala University, Uppsala, Sweden. jessika.nordin@imbim.uu.se.
FAU - Ameur, Adam
AU  - Ameur A
AUID- ORCID: 0000-0001-6085-6749
AD  - Science for Life Laboratory, Department of Immunology, Genetics and Pathology, 
      Uppsala University, Uppsala, Sweden.
FAU - Lindblad-Toh, Kerstin
AU  - Lindblad-Toh K
AD  - Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, 
      Uppsala University, Uppsala, Sweden.
AD  - Broad Institute of MIT and Harvard, Cambridge, MA, USA.
FAU - Gyllensten, Ulf
AU  - Gyllensten U
AD  - Science for Life Laboratory, Department of Immunology, Genetics and Pathology, 
      Uppsala University, Uppsala, Sweden.
FAU - Meadows, Jennifer R S
AU  - Meadows JRS
AD  - Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, 
      Uppsala University, Uppsala, Sweden.
LA  - eng
GR  - 2018.0101/Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg 
      Foundation)/International
GR  - 541-2013-8161/Vetenskapsradet (Swedish Research Council)/International
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20191216
PL  - England
TA  - Eur J Hum Genet
JT  - European journal of human genetics : EJHG
JID - 9302235
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Histocompatibility Antigens Class II)
SB  - IM
MH  - *Databases, Genetic
MH  - Gene Frequency
MH  - Genome, Human
MH  - Histocompatibility Antigens Class I/*genetics
MH  - Histocompatibility Antigens Class II/*genetics
MH  - Histocompatibility Testing/*methods/standards
MH  - Humans
MH  - Software
MH  - Sweden
PMC - PMC7170882
COIS- The authors declare that they have no conflict of interest.
EDAT- 2019/12/18 06:00
MHDA- 2021/05/26 06:00
PMCR- 2019/12/16
CRDT- 2019/12/18 06:00
PHST- 2019/05/20 00:00 [received]
PHST- 2019/11/26 00:00 [accepted]
PHST- 2019/11/12 00:00 [revised]
PHST- 2019/12/18 06:00 [pubmed]
PHST- 2021/05/26 06:00 [medline]
PHST- 2019/12/18 06:00 [entrez]
PHST- 2019/12/16 00:00 [pmc-release]
AID - 10.1038/s41431-019-0559-2 [pii]
AID - 559 [pii]
AID - 10.1038/s41431-019-0559-2 [doi]
PST - ppublish
SO  - Eur J Hum Genet. 2020 May;28(5):627-635. doi: 10.1038/s41431-019-0559-2. Epub 
      2019 Dec 16.