HLA typing by next-generation sequencing - getting closer to reality

Area of Science:

• Genomics and Bioinformatics
• Immunogenetics
• Molecular Biology

Background:

• Next generation sequencing (NGS) technologies generate large volumes of clonal sequences rapidly.
• NGS has applications in whole genome sequencing, mutation detection, and increasingly, high-resolution human leukocyte antigen (HLA) typing.
• The complexity of the HLA system presents significant bioinformatics challenges for NGS applications.

Purpose of the Study:

• To review the application of different NGS platforms for human leukocyte antigen (HLA) typing.
• To highlight the advantages and limitations of using NGS for HLA typing.
• To discuss the economic attractiveness of NGS for HLA typing laboratories.

Main Methods:

• Review of HLA typing data generated using Roche 454, Illumina MiSeq, and Ion Torrent NGS platforms.
• Analysis of bioinformatics challenges associated with NGS-based HLA typing.
• Comparison of NGS with traditional Sanger-based sequencing methods.

Main Results:

• NGS platforms are becoming increasingly cost-effective for HLA typing laboratories.
• Specific bioinformatics strategies and software algorithms are required to optimize NGS for HLA typing.
• Early adopters of NGS for HLA typing have identified distinct advantages and limitations across different platforms.

Conclusions:

• NGS presents a promising, economically viable approach for high-throughput HLA typing.
• Overcoming bioinformatics complexities is crucial for the widespread adoption and full potential of NGS in HLA typing.
• Further development of tailored typing strategies and algorithms will enhance NGS utility in immunogenetics.