Multivariate association between single-nucleotide polymorphisms in Alzgene linkage regions and structural changes in the brain: discovery, refinement and validation
Bibliographic record
Abstract
Abstract Both genetic variants and brain region abnormalities are recognized to play a role in cognitive decline. We explore the association between singlenucleotide polymorphisms (SNPs) in linkage regions for Alzheimer’s disease and rates of decline in brain structure using data from the Alzheimers Disease Neuroimaging Initiative (ADNI). In an initial discovery stage, we assessed the presence of linear association between the minor allele counts of 75,845 SNPs in the Alzgene linkage regions and predicted rates of change in structural MRI measurements for 56 brain regions using an RV test. In a second, refinement stage, we reduced the number of SNPs using a bootstrap-enhanced sparse canonical correlation analysis (SCCA) with a fixed tuning parameter. Each SNP was assigned an importance measure proportional to the number of times it was estimated to have a nonzero coefficient in repeated re-sampling from the ADNI-1 sample. We created refined lists of SNPs based on importance probabilities greater than 50% and 90%, respectively. In a third, validation stage, we assessed the multivariate association between these refined lists of SNPs and the rates of structural change in the independent ADNI-2 study dataset. There was strong statistical evidence for linear association between the SNPs in the Alzgene linkage regions and the 56 imaging phenotypes in both the ADNI-1 and ADNI-2 samples ( p < 0.0001). The bootstrap-enhanced SCCA identified 1,694 priority SNPs with importance probabilities > 50% and 22 SNPs with importance probabilities > 90%. The 1,694 prioritized SNPs in the ADNI-1 data were associated with imaging phenotypes in the ADNI-2 data ( p = 0.0021). This manuscript presents an analysis that addresses challenges in current imaging genetics studies such as biased sampling designs and highdimensional data with low-signal. Genes corresponding to priority SNPs having the highest contribution in the validation data have previously been implicated or hypothesized to be implicated in AD, including GCLC, IDE, and STAMBP1andFAS. We hypothesize that the effect sizes of the 1,694 SNPs in the priority set are likely small, but further investigation within this set may advance understanding of the missing heritability in late-onset Alzheimers disease. Multivariate analysis; Linkage regions; Imaging genetics; Endophenotypes; Inverse probability weighting; Variable importance probabilities
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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 | 0.050 | 0.067 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.003 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.001 | 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".