Evidence map›Paper›PMID 32654962›Full record

ArticleHuman immunology2020

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

Aviva Geretz, Lauryn Cofer, Philip K Ehrenberg, Jeffrey R Currier, In-Kyu Yoon, Maria T P Alera, Richard Jarman, Alan L Rothman, Rasmi Thomas

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Human immunology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.4field-weighted citation impact, top 34% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed, 6 citations in OpenAlex.

  1. Trial
  2. Article
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  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 4 institutions in 2 countries.

Aviva GeretzU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
Lauryn CoferU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
Philip K EhrenbergU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
Jeffrey R CurrierViral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
In-Kyu YoonDepartment of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
Maria T P AleraPhilippines-AFRIMS Virology Research Unit, Cebu City, Philippines.
Richard JarmanViral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
Alan L RothmanInstitute for Immunology and Informatics and Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA.
Rasmi ThomasU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA. Electronic address: rthomas@hivresearch.org.
Henry M. Jackson Foundation · USWalter Reed Army Institute of Research · USArmed Forces Research Institute of Medical Science · THUniversity of Rhode Island · US

Funding

VIRAL DETERMINANTS OF SEVERE DENGUE DISEASEP01AI034533 · NIAID · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI ROTHMAN, ALAN L · 1994 to 2022
$42.0M
NIAID NIH HHS P01 AI034533
6 · The paper itself

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.

Indexed as

AllelesClinical Trials, Phase III as TopicDengueDengue VaccinesExonsGene FrequencyGenetic LociGenotypeGenotyping TechniquesHigh-Throughput Nucleotide SequencingHLA AntigensHumansIntronsPhilippinesProspective StudiesDengue VaccinesHLA AntigensDengueHLA allelesIlluminaNext-generation sequencingPhilippines

Identifiers

PMID32654962
PMCPMC7442730
OpenAlexW3041736366

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.