Longitudinal Blood DNA Methylation Changes During Weight-Loss Intervention and Dementia Progression Risk
David Lukacsovich, Juan I. Young, Lissette Gomez, Wei Zhang1, Brian W. Kunkle, X. Steven Chen, Eden R. Martin, Lily Wang
This GitHub repository includes scripts used for the analyses in the above manuscript and the resulting summary statistics.
Weight loss improves metabolic health, but the DNA methylation (DNAm) changes induced by the lifestyle intervention and their relevance to dementia outcomes remain unclear. We studied longitudinal blood DNAm changes during an 18-month weight-loss intervention in the CENTRAL clinical trial and evaluated their relevance to dementia progression in an external cohort.
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| code/preprocessing/01a_get_phenotype.Rmd | Link to the script |
| code/preprocessing/01b_get_data.Rmd | Link to the script |
| code/preprocessing/01c_filter_probes.Rmd | Link to the script |
| code/preprocessing/01d_impute_autosomal.Rmd | Link to the script |
| code/preprocessing/01e_normalize_autosomal.Rmd | Link to the script |
| code/preprocessing/01f_batch.Rmd | Link to the script |
| code/preprocessing/01g_pca.Rmd | Link to the script |
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| code/preprocessing/02a_time_correlation.Rmd | Link to the script |
| code/preprocessing/02b_bacon_correct.Rmd | Link to the script |
| code/preprocessing/02c_pathway_analysis.Rmd | Link to the script |
| code/preprocessing/02d_compare_correlation.Rmd | Link to the script |
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| code/preprocessing/03a_get_sample_statistics.Rmd | Link to the script |
| code/preprocessing/03b_prepare_combp.Rmd | Link to the script |
| code/preprocessing/03c_summarize_combp.Rmd | Link to the script |
| code/preprocessing/03d_eQTM_association.Rmd | Link to the script |
| code/preprocessing/03e_brain_blood_correlation.Rmd | Link to the script |
| code/preprocessing/03f_miami_ad_comparison.Rmd | Link to the script |
| code/preprocessing/03g_ewas_association.Rmd | Link to the script |
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| code/markdown/04a_miami_plot.Rmd | Link to the script |
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| code/ADNI_repeated_measures/01a_get_phenotype.Rmd | Link to the script |
| code/ADNI_repeated_measures/01b_get_data.Rmd | Link to the script |
| code/ADNI_repeated_measures/01c_filter_probes.Rmd | Link to the script |
| code/ADNI_repeated_measures/01d_impute_autosomal.Rmd | Link to the script |
| code/ADNI_repeated_measures/01e_normalize_autosomal.Rmd | Link to the script |
| code/ADNI_repeated_measures/01f_batch.Rmd | Link to the script |
| code/ADNI_repeated_measures/01g_pca.Rmd | Link to the script |
| code/ADNI_repeated_measures/01h_get_sample_statistics.Rmd | Link to the script |
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| code/MRS_model/01a_correlation_score_diet_only.Rmd | Link to the script |
| code/MRS_model/01b_correlation_score_diet_plus_pa.Rmd | Link to the script |