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.jpg): Failed to open stream: No such file or directory in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 117 J+Hum+Genet
2017 ; 62
(3
): 397-405
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Comparison of exome-based HLA class I genotyping tools: identification of
platform-specific genotyping errors
#MMPMID27881843
Kiyotani K
; Mai TH
; Nakamura Y
J Hum Genet
2017[Mar]; 62
(3
): 397-405
PMID27881843
show ga
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.
|*Algorithms
[MESH]
|*Exome
[MESH]
|Alleles
[MESH]
|Artifacts
[MESH]
|Genotype
[MESH]
|Genotyping Techniques/*standards
[MESH]
|High-Throughput Nucleotide Sequencing
[MESH]
|Histocompatibility Antigens Class I/classification/*genetics/immunology
[MESH]
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