Longitudinal Data Analysis in Genome‐Wide Association Studies
Bibliographic record
Abstract
Genome-wide association studies have led to the discovery of thousands of susceptibility genetic variants (typically single-nucleotide polymorphisms [SNPs]) for a wide range of complex diseases and traits commonly measured at a single point in time. Although many novel genotype-phenotype associations have been identified and successfully replicated using cross-sectionally measured phenotypes, there is growing interest in the study of longitudinally measured phenotypes because these allow for the study of the natural trajectory of traits and disease progression. However, there are several challenges with analysis and interpretation of longitudinal data. Here, we summarize the methods and strategies proposed and applied in genome-wide association studies of blood pressure related phenotypes made available through Genetic Analysis Workshop 18 (GAW18). The investigators considered methods that incorporated correlation across time points and familial relatedness among the individuals into their studies and compared their approaches with single-time-point analysis using baseline data. Some of the studies used unrelated individuals; some also used the simulated data provided by the GAW18 organizers to assess type I error and power of their approach in detecting true associations.
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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 | 0.188 | 0.368 |
| Meta-epidemiology (narrow) | 0.001 | 0.002 |
| Meta-epidemiology (broad) | 0.003 | 0.003 |
| Bibliometrics | 0.005 | 0.009 |
| Science and technology studies | 0.002 | 0.002 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.003 | 0.004 |
| Research integrity | 0.002 | 0.005 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
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".