P822 Genetic analysis of ulcerative colitis in Japanese individuals using population-specific SNP array
Bibliographic record
Abstract
Abstract Background Previous genome wide association studies (GWASs) have identified over 200 susceptibility loci for inflammatory bowel diseases (IBD), but studies in non-European population are limited. To clarify the genetic background of ulcerative colitis (UC) in the Japanese population, we conducted GWAS using a population specific SNP array (Japonica Array). Methods Discovery GWAS included 624 UC patients and 2004 healthy controls (HC) and replication study included 1075 UC patients and 419 HCs. We performed GWAS using a Japonica Array and the subsequent imputation with a Japanese population reference panel (referred to as 2KJPN). After GWAS, significant and candidate loci were identified and the representative top SNPs of each region were analysed in replication study and combined analysis. The probability of colectomy between genotypes of rs117506082, the top hit SNP at HLA loci, was analysed using the Kaplan–Meier method. Results In the GWAS, only the HLA loci showed genome wide significant association [rs117506082, p = 6.69E−28, OR=1.29, 95%CI=1.23–1.35]. 7 regions with nominal significance included 2 known loci: IL23R [rs76418789, p = 6.29E−7, OR=0.89, 95%CI=0.85–0.93], IRF8 [rs16940202, p = 1.03E−6, OR=1.07, 95%CI=1.04–1.10] and 5 novel loci: miR-622 [rs9560575, p = 8.23E−7, OR=1.06, 95%CI=1.04–1.09], 14q31 [rs117618617, p = 1.53E−6, OR=1.13, 95%CI=1.09–1.19], KAT6B [rs12260609, p = 1.81E−6, OR=1.06, 95%CI=1.04–1.09], PAX3-CCDC140-SGPP2 [rs7589797, p = 2.87E−6, OR=0.94, 95%CI=0.93–0.97], KCNA2 [rs118020656, p = 4.01E−6, OR=1.12, 95%CI=1.07–1.18]. Combined analysis revealed that the HLA loci [rs117506082, p = 1.10E−23, OR=3.43, 95%CI=2.99–3.83] and IL23R p.G149R [rs76418789, p = 9.03E−11, OR=0.51, 95%CI=0.42–0.63] had a genome wide significant association. The GG genotype of rs117506082 had a significantly lower probability for total colectomy compared with the GA+AA genotype (p = 1.72E−2). Conclusion IL23R p.G149R is a susceptibility locus for UC in Japanese individuals. The GG genotype of rs117506082 at HLA loci, a risk genotype for UC susceptibility, may predict a better clinical course.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".