PMID- 27881843
OWN - NLM
STAT- MEDLINE
DCOM- 20170515
LR  - 20181113
IS  - 1435-232X (Electronic)
IS  - 1434-5161 (Print)
IS  - 1434-5161 (Linking)
VI  - 62
IP  - 3
DP  - 2017 Mar
TI  - Comparison of exome-based HLA class I genotyping tools: identification of 
      platform-specific genotyping errors.
PG  - 397-405
LID - 10.1038/jhg.2016.141 [doi]
AB  - Accurate human leukocyte antigen (HLA) genotyping is critical in studies 
      involving the immune system. Several algorithms to estimate HLA genotypes from 
      whole-exome data were developed. We compared the accuracy of seven algorithms, 
      including Optitype, Polysolver and PHLAT, as well as investigated patterns and 
      possible causes of miscalls using 12 clinical samples and 961 individuals from 
      the 1000 Genomes Project. Optitype showed the highest accuracy of 97.2% for HLA 
      class I alleles at the second field resolution, followed by 94.0% in Polysolver 
      and 85.6% in PHLAT. In Optitype, 34 (21.1%) of 161 miscalls were across different 
      serological types, and common miscalls were HLA-A*26:01 to HLA-A*25:01, 
      HLA-B*45:01 to HLA-B*44:15 and HLA-C*08:02 to HLA-C*05:01 with error rates of 
      4.1%, 10.0% and 4.1%, respectively. In Polysolver, 193 (55.9%) of 345 miscalls 
      occurred across different serological alleles, and a specific pattern of 
      genotyping error from HLA-A*25:01 to HLA-A*26:01 was observed in 93.3% of 
      HLA-A*25:01 carriers, due to dropping of HLA-A*25:01 sequence reads during the 
      extraction process of HLA reads. In PHLAT, 147 (59.8%) of 246 miscalls in HLA-A 
      were due to erroneous assignment of multiple alleles to either HLA-A*01:22 or 
      HLA-A*01:81. These results suggest that careful considerations needed to be taken 
      when using exome-based HLA class I genotyping data and applying these results in 
      clinical settings.
FAU - Kiyotani, Kazuma
AU  - Kiyotani K
AD  - Section of Hematology/Oncology, Department of Medicine, The University of 
      Chicago, Chicago, IL, USA.
FAU - Mai, Tu H
AU  - Mai TH
AD  - Section of Hematology/Oncology, Department of Medicine, The University of 
      Chicago, Chicago, IL, USA.
AD  - Committee on Clinical Pharmacology and Pharmacogenomics, The University of 
      Chicago, Chicago, IL, USA.
FAU - Nakamura, Yusuke
AU  - Nakamura Y
AD  - Section of Hematology/Oncology, Department of Medicine, The University of 
      Chicago, Chicago, IL, USA.
AD  - Department of Surgery, The University of Chicago, Chicago, IL, USA.
LA  - eng
PT  - Comparative Study
PT  - Journal Article
DEP - 20161124
PL  - England
TA  - J Hum Genet
JT  - Journal of human genetics
JID - 9808008
RN  - 0 (Histocompatibility Antigens Class I)
SB  - IM
MH  - *Algorithms
MH  - Alleles
MH  - Artifacts
MH  - *Exome
MH  - Genotype
MH  - Genotyping Techniques/*standards
MH  - High-Throughput Nucleotide Sequencing
MH  - Histocompatibility Antigens Class I/classification/*genetics/immunology
MH  - Histocompatibility Testing
MH  - Humans
MH  - Mesothelioma/diagnosis/*genetics/immunology
MH  - Reproducibility of Results
MH  - Sensitivity and Specificity
MH  - Sequence Analysis, DNA/*standards
PMC - PMC5334549
COIS- The authors declare no conflict of interest.
EDAT- 2016/11/25 06:00
MHDA- 2017/05/16 06:00
PMCR- 2017/03/03
CRDT- 2016/11/25 06:00
PHST- 2016/07/14 00:00 [received]
PHST- 2016/09/26 00:00 [revised]
PHST- 2016/10/14 00:00 [accepted]
PHST- 2016/11/25 06:00 [pubmed]
PHST- 2017/05/16 06:00 [medline]
PHST- 2016/11/25 06:00 [entrez]
PHST- 2017/03/03 00:00 [pmc-release]
AID - jhg2016141 [pii]
AID - 10.1038/jhg.2016.141 [doi]
PST - ppublish
SO  - J Hum Genet. 2017 Mar;62(3):397-405. doi: 10.1038/jhg.2016.141. Epub 2016 Nov 24.