Genome-wide association study of chlamydia reinfection in African American women
Bibliographic record
Abstract
Background Chlamydia trachomatis (Ct) is a bacterium that causes chlamydia, the most diagnosed bacterial sexually transmitted infection (STI) in the world. In the U.S., chlamydia is most prevalent among non-Hispanic African American (AA) individuals, implying substantial racial disparity. Despite prevention and control efforts, reinfection is common, suggesting that some individuals have insufficient protective immunity to Ct. To better understand the genetically mediated risks of chlamydia reinfection, we sought to identify genetic loci associated with reinfection using a Genome-Wide Association Study (GWAS) approach. Method We performed GWAS in 300 AA women with versus without chlamydia reinfection based on Ct testing done about 3 months after chlamydia treatment. We conducted logistic regression models to test the additive genetic effect and used Firth regression to confirm the association results. Furthermore, we performed post-GWAS analysis to determine the functional consequences of GWAS hits, including fine-mapping, expression quantitative loci (eQTL) and chromatin interaction analyses, tissue and cell-type expression, and pathway analysis. Results GWAS identified 17 suggestive genomic regions of interest. Five genomic regions out of 17 were identified as strongly associated with reinfection, using linkage disequilibrium and fine mapping. The positional mapping, eQTL, and chromatin interactions (CIs) analyses further identified 12 gene targets. Among the 12 gene targets, CHIT1, ADORA1, and CHI3L1 in chromosome 1 (chr. 1); TDRP, FBXO25, and SULF1 in chr. 8; and the SOCS6 gene in chr. 18, were functionally relevant to reinfection. Conclusions This GWAS study in AA women identified multiple novel genes associated with chlamydia reinfection, including CHIT1, CHI3L1, ADORA1, ALK, TDRP, FBXO25, LINC01592, SULF1, and SOCS6, which are involved in the immune response. CHIT1, ADORA1, CHI3L1, TDRP, FBOXO25, SULF1, and SOCS6 were identified using CI/eQTL mapping.
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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 | 0.003 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 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".