Correction: Correcting for Population Structure and Kinship Using the Linear Mixed Model: Theory and Extensions
Bibliographic record
Abstract
Population structure and kinship are widespread confounding factors in genome-wide association studies (GWAS).It has been standard practice to include principal components of the genotypes in a regression model in order to account for population structure.More recently, the linear mixed model (LMM) has emerged as a powerful method for simultaneously accounting for population structure and kinship.The statistical theory underlying the differences in empirical performance between modeling principal components as fixed versus random effects has not been thoroughly examined.We undertake an analysis to formalize the relationship between these widely used methods and elucidate the statistical properties of each.Moreover, we introduce a new statistic, effective degrees of freedom, that serves as a metric of model complexity and a novel low rank linear mixed model (LRLMM) to learn the dimensionality of the correction for population structure and kinship, and we assess its performance through simulations.A comparison of the results of LRLMM and a standard LMM analysis applied to GWAS data from the Multi-Ethnic Study of Atherosclerosis (MESA) illustrates how our theoretical results translate into empirical properties of the mixed model.Finally, the analysis demonstrates the ability of the LRLMM to substantially boost the strength of an association for HDL cholesterol in Europeans.
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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 | 0.024 | 0.178 |
| Meta-epidemiology (narrow) | 0.003 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.003 |
| Bibliometrics | 0.003 | 0.006 |
| Science and technology studies | 0.002 | 0.002 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.006 | 0.003 |
| Research integrity | 0.004 | 0.007 |
| Insufficient payload (model declined to judge) | 0.058 | 0.015 |
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".