Benchmarking NGS-Based HLA Typing Algorithms

Nikolas Hallberg Thuesen; Michael Schantz Klausen

doi:10.1007/978-1-0716-3874-3_6

Benchmarking NGS-Based HLA Typing Algorithms

Methods Mol Biol. 2024:2809:87-99. doi: 10.1007/978-1-0716-3874-3_6.

Authors

Nikolas Hallberg Thuesen¹, Michael Schantz Klausen²

Affiliations

¹ Evaxion Biotech, Copenhagen, Denmark. [email protected].
² Evaxion Biotech, Copenhagen, Denmark.

PMID: 38907892
DOI: 10.1007/978-1-0716-3874-3_6

Abstract

Knowledge of the expected accuracy of HLA typing algorithms is important when choosing between algorithms and when evaluating the HLA typing predictions of an algorithm. This chapter guides the reader through an example benchmarking study that evaluates the performances of four NGS-based HLA typing algorithms as well as outlining factors to consider, when designing and running such a benchmarking study. The code related to this benchmarking workflow can be found at https://github.com/nikolasthuesen/springers-hla-benchmark/ .

Keywords: Algorithm; Benchmark; Depth of coverage; Human leukocyte antigen; Next-generation sequencing (NGS); Typing resolution; Whole exome sequencing; Workflow management.

MeSH terms

Algorithms*
Benchmarking* / methods
HLA Antigens / genetics
High-Throughput Nucleotide Sequencing* / methods
High-Throughput Nucleotide Sequencing* / standards
Histocompatibility Testing* / methods
Histocompatibility Testing* / standards
Humans
Software

Substances

HLA Antigens