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Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Research ID

hum0343-v4Release info

This page is a past version (v4). The latest version is v5.
Latest version (v5)

Research title

Development of COVID19 vaccine and evaluation system based on genetics of COVID-19

Research overview

Aims
To construct a prediction system for severe disease through whole genome sequencing, RNA sequencing, and ultra-high-precision HLA analysis of patients with COVID-19, asymptomatic infected patients, and patients suspected of having novel coronavirus infection. In addition, we will use anonymized data to analyze the prediction of severity of COVID-19 using mathematical models. To elucidate the association between viruses and autoimmune diseases and COVID-19.
Methods
Genome-wide association study (GWAS), RNA-seq, Protein expression analysis, eQTL/sQTL/pQTL study, whole genome sequencing
Participants/materials
GWAS: 5,682 Japanese individuals (2,393 COVID-19 infected patients and 3,289 controls)
RNA-seq: Maximum 1,019 COVID-19 infected patients
Protein expression: 1,384 COVID-19 infected patients
Whole genome sequencing: 1,164 COVID-19 infected patients
URL
N/A

Datasets

The list is the one this version published; each dataset's content is shown as it is now.

CartDataset IDType of dataAnalysis methodAccess criteriaDate published
NHA000169GWAS for COVID-19
  • Genome wide SNPs
Unrestricted-access2022-05-26
NHA000168NGS (RNA-seq) for COVID-19
  • RNA-seq
Unrestricted-access2022-05-26
NHA000172eQTL/sQTL summary statistics for COVID-19
  • eQTL/sQTL summary statistics
Unrestricted-access2022-06-14
E-GEAD-759NGS (RNA-seq) for COVID-19
Protein expression for COVID-19
  • RNA-seq
  • Protein expression (2932 proteins)
Unrestricted-access2024-06-28
NHA000193eQTL/pQTL summary statistics for COVID-19
  • eQTL/pQTL summary statistics
Unrestricted-access2024-06-21
JGAD000874The presence or absence of endogenous herpesvirus 6 and anellovirus load calculated from NGS (WGS) for COVID-19
  • WGS
Controlled-access (Type I)2024-10-04

Data provider

Principal investigator
Koichi Fukunaga
Affiliation
Department of Medicine, Pulmonary Division, Keio University School of Medicine

Research projects

No research projects.

Grants

NameTitleProject number
Project Promoting Support for Drug Discovery, Japan Agency for Medical Research and Development (AMED)
Development of genetically-designed COVID19 mucosal immune vaccine with molecular needle platform
  • JP20nk0101612
Research Program on Emerging and Re-emerging Infectious Diseases, Japan Agency for Medical Research and Development (AMED)
Promotion of genetic, immunological, and metabolic research necessary for the development of next-generation vaccines and drugs aiming to prevent the aggravation of coronavirus disease 2019
  • JP20fk0108415
Research Program on Emerging and Re-emerging Infectious Diseases, Japan Agency for Medical Research and Development (AMED)
Elucidation of pathogenesis and development of therapeutic strategies using genetic, immunological, and metabolic studies against SARS-CoV-2 variants
  • JP20fk0108452
Japan Program for Infectious Diseases Research and Infrastructure, Japan Agency for Medical Research and Development (AMED)
Elucidation of the pathophysiology of the sequelae of coronavirus disease 2019 using a multidisciplinary approach
  • JP21wm0325031
Core Research and Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST)
Research on Conquering Coronavirus Disease by Advanced Genomic Analysis and Artificial Intelligence
  • JPMJCR20H2
Practical Research Project for Allergic Diseases and Immunology, Japan Agency for Medical Research and Development (AMED)
Genomic prediction medicine of rheumatoid arthritis based on comprehensive immune-omics resources
  • 20ek0410075h0001
KAKENHI Grant-in-Aid for Scientific Research (A)
Elucidation of tissue-specificity of disease biology using trans-layer omics analysis and whole-genome sequencing
  • 19H01021
Program for Promoting Platform of Genomics based Drug Discovery, Japan Agency for Medical Research and Development (AMED)
Systematic evaluation of variant of uncertain significance (VUS) pathogenicity through population genomics data analysis and massively parallel reporter assay
  • JP22kk0305022
Fusion Oriented REsearch for disruptive Science and Technology (FOREST) program, Japan Science and Technology Agency (JST)
Towards a generalized and interpretable model for comprehensive understanding of human gene regulatory mechanisms
  • JPMJFR225Y
Promoting Individual Research to Nurture the Seeds of Future Innovation and Organizing Unique, Innovative Network (PRESTO), Japan Science and Technology Agency (JST)
Fundamental research to build an academic system resilient to pandemics
  • JPMJPR21R7

Related publications

TitleDOIDataset ID
DOCK2 is involved in the host genetics and biology of severe COVID-19
https://doi.org/10.1038/s41586-022-05163-5 (opens in a new tab)
The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force
https://doi.org/10.1038/s41467-022-32276-2 (opens in a new tab)
Statistically and functionally fine-mapped blood eQTLs and pQTLs from 1,405 humans reveal their distinct regulation patterns and disease relevance
https://doi.org/10.1038/s41588-024-01896-3 (opens in a new tab)
Blood DNA virome associates with autoimmune diseases and COVID-19.
https://doi.org/10.1038/s41588-024-02022-z (opens in a new tab)

Controlled access users

Principal investigatorAffiliationCountry/RegionResearch titlePeriod of data useDataset ID
Michiaki HamadaHamada Laboratory, Faculty of Science and Engineering, Waseda UniversityJapanConstruction of RNA-targeted Drug Discovery Database2023-01-05 – 2027-10-31