Aims: Elucidation of disease biology based on trans-omics analysis, GWAS in the Japanese and trans-ethnic populations, Elucidation of the mechanism of COVID-19 severity, Improving the performance of type 2 diabetes polygenic predictions, Elucidation of the genetic architecture of recurrent pregnancy loss, Elucidation of the association between Jomon component in the Japanese population and phenotypes and diseases, Elucidation of the entire HPV integration in HPV-associated Oropharyngeal Cancer, Elucidation of disease state regulation by gene-environment interactions through multi-layered omics analysis, Elucidation of male-specific genetic regulation through multi-layered omics analysis

Methods: Metagenome shotgun sequencing, genome-wide association study (GWAS), small RNA-seq and eQTL analyses, whole genome sequencing (WGS), single-cell RNA sequencing, proteomics

Targets: Metagenomic data of gut microbiome in the Japanese population (95 + 103 + 227 + 30 + 136 individuals) Autoimmune pulmonary alveolar proteinosis cases: 198, Control participants: 395 Populations: Biobank Japan (n = 179,000), UK biobank (n = 361,000), and FinnGen (n = 136,000), Phenotypes: 220 141 Japanese individuals Metagenomic data of gut microbiome in Inflammatory Bowel Disease (35 Ulcerative Colitis and 39 Crohn's disease) and 40 Healthy controls Intracranial germ cell tumors cases: 133, Control participants: 762 Populations: Biobank Japan (n = 161,801) and UK biobank (n = 377,583), Phenotypes: 9 Peripheral blood mononuclear cell (PBMC) from Japanese population (COVID-19: n = 30 + 43, Healthy controls: n = 31 + 44) Microbial genome: Metagenome-Assembled Genome (MAG), Viral genome, CRISPR spacers Metagenomic data of gut microbiome in the Japanese population (88 + 5 individuals) and healthy individuals (n = 73) BioBank Japan (n=180,215), UK Biobank (n=377,441), and large-scale meta-analysis including the summary statistics of other cohorts [FinnGen, Breast Cancer Association Consortium (BCAC), and Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome (PRACTICAL)] for breast and prostate cancer (n=648,746 and 482,080), Phenotypes: 15 Hunner-type interstitial cystitis cases: 144, Control participants: 41,516 524 Japanese individuals for gut microbiome-host genome association analysis, 362 Japanese individuals for plasma metabolite-host genome association analysis The weights of variants existing in the target cohorts, Tohoku Medical Megabank and the second cohort of BBJ, calculated from GWAS results on 27,642 type 2 diabetes cases and 70,242 controls from BioBank Japan and UK Biobank Recurrent pregnancy loss cases: 1,728, Control participants: 24,315 Autoimmune diseases cases: 2,238, Healthy controls: 2,919 The first cohort of BioBank Japan (n = 171,287) HPV-associated oropharyngeal cancer cases: 32, Non-HPV-associated oropharyngeal cancer cases: 17, Healthy controls: 2 Neuromyelitis optica spectrum disorders (NMOSD) cases: 240, Control participants: 50,578 Single-cell eQTL summary statistics of 40 immune cell types for Japanese population (COVID-19: n = 88, Healthy controls: n = 146) Plasma proteomics data from 83 COVID-19 patients and 144 healthy controls of Japanese Single-cell RNA-sequencing for PBMC from 15 COVID-19 patients and 72 healthy controls of Japanese Psoriasis cases: 1,415, Control participants: 3,968 Populations: Biobank Japan (n = 166,757) and UK biobank (n = 273,453), Phenotypes: 374 161,026 Japanese males (BBJ: 120,522, JCTF: 3,161, TMM: 26,544, COVC: 888, HERPACC: 6,636, JPHC: 3,275) Japanese male asthma patients: 3 cases, Japanese male COVID-19 patients: 4 cases Myasthenia gravis cases: 1,434 (Japan MG Registry), Control participants: 42,913 (BioBank Japan) 401 Moyamoya diseasepatients and 47,255 controls