HLA genotyping in the clinical laboratory: comparison of next-generation sequencing methods

Implementation of human leukocyte antigen (HLA) genotyping by next‐generation sequencing (NGS) in the clinical lab brings new challenges to the laboratories performing this testing. With the advent of commercially available HLA‐NGS typing kits, labs must make numerous decisions concerning capital eq...

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Published inHLA Vol. 88; no. 1-2; pp. 14 - 24
Main Authors Profaizer, T., Lázár-Molnár, E., Close, D.W., Delgado, J. C., Kumánovics, A.
Format Journal Article
LanguageEnglish
Published Oxford, UK Blackwell Publishing Ltd 01.07.2016
Subjects
Alleles
Gene Library
Genotype
Genotyping Techniques - instrumentation
Genotyping Techniques - standards
High-Throughput Nucleotide Sequencing - methods
Histocompatibility Testing - instrumentation
Histocompatibility Testing - methods
Histocompatibility Testing - standards
HLA Antigens - classification
HLA Antigens - genetics
HLA Antigens - immunology
human leukocyte antigens (HLA)
Humans
Molecular Sequence Annotation - standards
next-generation sequencing (NGS)
paired-end sequencing
Polymerase Chain Reaction - methods
Reproducibility of Results
Sequence Analysis, DNA - statistics & numerical data
size selection
Time Factors
human leukocyte antigens (HLA)
size selection
next-generation sequencing (NGS)
paired-end sequencing
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Abstract Implementation of human leukocyte antigen (HLA) genotyping by next‐generation sequencing (NGS) in the clinical lab brings new challenges to the laboratories performing this testing. With the advent of commercially available HLA‐NGS typing kits, labs must make numerous decisions concerning capital equipment and address labor considerations. Therefore, careful and unbiased evaluation of available methods is imperative. In this report, we compared our in‐house developed HLA NGS typing with two commercially available kits from Illumina and Omixon using 10 International Histocompatibility Working Group (IHWG) and 36 clinical samples. Although all three methods employ long range polymerase chain reaction (PCR) and have been developed on the Illumina MiSeq platform, the methodologies for library preparation show significant variations. There was 100% typing concordance between all three methods at the first field when a HLA type could be assigned. Overall, HLA typing by NGS using in‐house or commercially available methods is now feasible in clinical laboratories. However, technical variables such as hands‐on time and indexing strategies are sufficiently different among these approaches to impact the workflow of the clinical laboratory.
AbstractList Abstract Implementation of human leukocyte antigen ( HLA ) genotyping by next‐generation sequencing ( NGS ) in the clinical lab brings new challenges to the laboratories performing this testing. With the advent of commercially available HLA‐NGS typing kits, labs must make numerous decisions concerning capital equipment and address labor considerations. Therefore, careful and unbiased evaluation of available methods is imperative. In this report, we compared our in‐house developed HLA NGS typing with two commercially available kits from Illumina and Omixon using 10 International Histocompatibility Working Group ( IHWG ) and 36 clinical samples. Although all three methods employ long range polymerase chain reaction ( PCR ) and have been developed on the Illumina MiSeq platform, the methodologies for library preparation show significant variations. There was 100% typing concordance between all three methods at the first field when a HLA type could be assigned. Overall, HLA typing by NGS using in‐house or commercially available methods is now feasible in clinical laboratories. However, technical variables such as hands‐on time and indexing strategies are sufficiently different among these approaches to impact the workflow of the clinical laboratory.
Implementation of human leukocyte antigen (HLA) genotyping by next‐generation sequencing (NGS) in the clinical lab brings new challenges to the laboratories performing this testing. With the advent of commercially available HLA‐NGS typing kits, labs must make numerous decisions concerning capital equipment and address labor considerations. Therefore, careful and unbiased evaluation of available methods is imperative. In this report, we compared our in‐house developed HLA NGS typing with two commercially available kits from Illumina and Omixon using 10 International Histocompatibility Working Group (IHWG) and 36 clinical samples. Although all three methods employ long range polymerase chain reaction (PCR) and have been developed on the Illumina MiSeq platform, the methodologies for library preparation show significant variations. There was 100% typing concordance between all three methods at the first field when a HLA type could be assigned. Overall, HLA typing by NGS using in‐house or commercially available methods is now feasible in clinical laboratories. However, technical variables such as hands‐on time and indexing strategies are sufficiently different among these approaches to impact the workflow of the clinical laboratory.
Author Close, D.W.
Profaizer, T.
Lázár-Molnár, E.
Delgado, J. C.
Kumánovics, A.
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Issue 1-2
Keywords human leukocyte antigens (HLA)
size selection
next-generation sequencing (NGS)
paired-end sequencing
Language English
License 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
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Table S1. Results of 10 International Histocompatibility Working Group (IHWG) samples.
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Snippet Implementation of human leukocyte antigen (HLA) genotyping by next‐generation sequencing (NGS) in the clinical lab brings new challenges to the laboratories...
Implementation of human leukocyte antigen (HLA) genotyping by next-generation sequencing (NGS) in the clinical lab brings new challenges to the laboratories...
Abstract Implementation of human leukocyte antigen ( HLA ) genotyping by next‐generation sequencing ( NGS ) in the clinical lab brings new challenges to the...
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SubjectTerms Alleles
Gene Library
Genotype
Genotyping Techniques - instrumentation
Genotyping Techniques - standards
High-Throughput Nucleotide Sequencing - methods
Histocompatibility Testing - instrumentation
Histocompatibility Testing - methods
Histocompatibility Testing - standards
HLA Antigens - classification
HLA Antigens - genetics
HLA Antigens - immunology
human leukocyte antigens (HLA)
Humans
Molecular Sequence Annotation - standards
next-generation sequencing (NGS)
paired-end sequencing
Polymerase Chain Reaction - methods
Reproducibility of Results
Sequence Analysis, DNA - statistics & numerical data
size selection
Time Factors
Title HLA genotyping in the clinical laboratory: comparison of next-generation sequencing methods
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https://onlinelibrary.wiley.com/doi/abs/10.1111%2Ftan.12850
https://www.ncbi.nlm.nih.gov/pubmed/27524804
Volume 88
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