Next-generation sequencing of 11 HLA loci in a large dengue vaccine cohort from the Philippines

Authors

Aviva Geretz, Walter Reed Army Institute of Research
Lauryn Cofer, Walter Reed Army Institute of Research
Philip K. Ehrenberg, Walter Reed Army Institute of Research
Jeffrey R. Currier, Walter Reed Army Institute of Research
In Kyu Yoon, Armed Forces Research Institute of Medical Sciences, Thailand
Marla T.P. Alera, Philippines-AFRIMS Virology Research Unit
Richard Jarman, Walter Reed Army Institute of Research
Alan L. Rothman, University of Rhode Island
Rasmi Thomas, Walter Reed Army Institute of Research

Document Type

Article

Date of Original Version

2020

Abstract

HLA genotyping by next-generation sequencing (NGS) has evolved with significant advancements in the last decade. Here we describe full-length HLA genotyping of 11 loci in 612 individuals comprising a dengue vaccine cohort from Cebu province in the Philippines. The multi-locus individual tagging NGS (MIT-NGS) method that we developed initially for genotyping 4–6 loci in one MiSeq run was expanded to 11 loci including HLA-A, B, C, DPA1, DPB1, DQA1, DQB1, DRB1, and DRB3/4/5. This change did not affect the overall coverage or depth of the sequencing reads. HLA alleles with frequencies greater than 10% were A*11:01:01, A*24:02:01, A*24:07:01, A*34:01:01, B*38:02:01, B*15:35, B*35:05:01, C*07:02:01, C*04:01:01, DPA1*02:02:02, DPB1*05:01:01, DPB1*01:01:01, DQA1*01:02:01, DQA1*06:01:01, DQB1*05:02:01, DQB1*03:01:01, DRB1*15:02:01, DRB1*12:02:01, DRB3*03:01:03, DRB4*01:03:01, and DRB5*01:01:01. Improvements in sequencing library preparation provide uniform and even coverage across all exons and introns. This has led to a marked reduction in allele imbalance and dropout. Furthermore, including more loci, such as DRB3/4/5, decreases cross-mapping and incorrect allele assignment at the DRB1 locus. The increased number of loci sequenced for each sample does not reduce the number of samples that can be multiplexed on a single MiSeq run and is therefore more cost-efficient. We believe that such improvements will help HLA genotyping by NGS to gain momentum over other conventional methods by increasing confidence in the calls.

Publication Title, e.g., Journal

Human Immunology

Volume

81

Issue

8

Citation/Publisher Attribution

Geretz, Aviva, Lauryn Cofer, Philip K. Ehrenberg, Jeffrey R. Currier, In Kyu Yoon, Marla T. Alera, Richard Jarman, Alan L. Rothman, and Rasmi Thomas. "Next-generation sequencing of 11 HLA loci in a large dengue vaccine cohort from the Philippines." Human Immunology 81, 8 (2020). doi: 10.1016/j.humimm.2020.06.010.