NBDC Research ID: hum0505.v1
SUMMARY
Aims: Genetic factors play an important role for the development of allergic diseases such as bronchial asthma, hay fever, atopic dermatitis, and food allergy. This study aims to identify genes involved in the pathogenesis of allergic diseases.
Methods: DNA was extracted from blood or saliva and genotyped using the Infinium Asian Screening Array (illumina).
Participants/Materials: Five hundred and sixty-four children who participated in T-Child study (a birth cohort study) with ImmunoCAP ISAC sIgE 112 data available at age 9 years.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0505.v1.gwas.v1 | GWAS for 564 children who participated in the adult cohort study | Unrestricted-access | 2025/05/30 |
*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials |
564 children who participated in T-child study (a birth cohort study) with ImmunoCAP ISAC sIgE 112 data available at age 9 years 562 children for total serum IgE data |
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| Targets | Genome wide SNPs | ||
| Target Loci for Capture Methods | - | ||
| Platform | Illumina [Infinium Asian Screening Array] | ||
| Source | DNAs extracted from peripheral blood cells or saliva | ||
| Cell Lines | - | ||
| Reagents (Kit, Version) | - | ||
| Genotype Call Methods (software) |
SHAPEIT2 software and Minimac4 software Imputation reference：JGAS000114 reference panel (GRCh37) |
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| Association Analysis (software) | SAIGE | ||
| Filtering Methods |
Sample QC: We excluded samples based on the following criteria (1) a call rate of < 98% (2) outliers from the Japanese ancestry estimated by use of principal-component (PC) analysis using the 1000 Genome Project Phase 3 (3) PI_HAT > 0.1875 (4) phenotype-genotype sex discordance Genotyping QC: We selected the genotyped variants based on the following criteria (1) Gentrain score of >= 0.7 (2) minor allele frequency > 1% (3) variant genotyping call rate > 95% (4) Hardy–Weinberg-equilibrium P value > 1.0 × 10^-5. Imputation QC: Rsq > 0.7 and minor allele count >= 20. |
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| Marker Number (after QC) |
ImmunoCAP ISAC sIgE data: 6,471,740 variants Total IgE data: 7,099,279 variants |
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| NBDC Dataset ID | hum0505.v1.gwas.v1 | 2S albumin | |
| 7S globulin | |||
| Aln g 1 | |||
| Alt a 1 | |||
| Amb a 1 | |||
| Ara h 8 | |||
| Arginine kinase | |||
| Berberine bridge enzyme | |||
| Beta expansin | |||
| Bet v 1 | |||
| Bet v 2 | |||
| Blo t 5 | |||
| Can f 1 | |||
| Cor a 1.0101 | |||
| Cor a 1.0401 | |||
| Cry j 1 | |||
| Cup a 1 | |||
| Cyn d 1 | |||
| Cystein protease | |||
| Der f 1 | |||
| Der f 2 | |||
| Der p 1 | |||
| Der p 2 | |||
| Fel d 1 | |||
| Fel d 4 | |||
| Gly m 4 | |||
| Grass group 5 | |||
| Hev b 8 | |||
| Jug r 2 | |||
| Lep d 2 | |||
| Lipocalin | |||
| Mal d 1 | |||
| Mer a 1 | |||
| Mite group 5/21 | |||
| NPC2 family | |||
| Pectate lyase | |||
| Pen m 2 | |||
| Phl p 1 | |||
| Phl p 12 | |||
| Phl p 4 | |||
| Phl p 5 | |||
| Pla a 2 | |||
| Polygalacturonase | |||
| PR-10 Protein | |||
| Profilin | |||
| total_IgE.txt | |||
| Tropomyosin | |||
| Uteroglobin | |||
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（Click the allergen components/protein groups to download the gwas summary statistics） |
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| Total Data Volume |
GWAS: 342 MB (txt) on average hum0505.v1.gwas.v1: 5.9 GB (txt) |
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| Comments (Policies) | NBDC policy | ||
DATA PROVIDER
Principal Investigator: Emiko Noguchi
Affiliation: Faculty of Medicine, Department of Medical Genetics, University of Tsukuba
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (B) | Elucidation of Genetic and Environmental Factors in Allergic Disease using Birth Cohort Study | 16H03269 |
| Practical Research Project for Allergic Diseases and Immunology, Japan Agency for Medical Research and Development (AMED) | Development of a prediction method for allergic diseases and allergen responsiveness using patients cohorts and general population cohorts | JP20ek0410076 |
| National Center for Child Health and Development (NCCHD) | A birth cohort study on the establishment of long-term follow-up data with genetic information and the elucidation of disease etiology in perinatal and pediatric medicine | 26-18 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | A genome-wide association study for allergen component sensitizations identifies allergen component–specific and allergen protein group–specific associations | doi: 10.1016/j.jacig.2023.100086 | hum0505.v1.gwas.v1 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
