Cohort-scale extension of Hunter et al. (2023) "Transcription dosage compensation does not occur in Down syndrome" (BMC Biology 21:228), applied to the Human Trisome Project (HTP): 304 T21 + 95 Control whole-blood RNA-seq samples, 302 of the T21 subjects with paired chr21 genotypes.
The pipeline asks, for each chromosome 21 protein-coding gene whose ploidy-corrected expression deviates from the 1.5x trisomy expectation by more than typical genome-wide cohort noise: can the deviation be explained by a common cis-acting eQTL in GTEx whole blood that reproduces in our T21 cohort, or does it remain a candidate for true regulatory dosage compensation?
Of the 160 chr21 protein-coding genes tested:
| Lane | Count |
|---|---|
| Expected dosage (within cohort noise) | 119 |
| DE_high, eQTL-supported | 6 |
| DE_low, eQTL-supported | 9 |
| DE_low, eQTL-tested but unsupported | 3 (BACE2, ADARB1, NRIP1) |
| DE_low, no GTEx cis-eQTL coverage | 3 (LTN1, RUNX1, ZBTB21) |
| High repeats / Low expression / Not DE | 20 |
All higher-than-expected genes (DE_high) are eQTL-supported - acting as a positive control. Among lower-than-expected genes that could be tested against GTEx, 9 of 12 (75%) are eQTL-supported; the remaining 3 (BACE2, ADARB1, NRIP1) plus the 3 untestable ones are the residual compensation candidates.
Rscript install_packages.R # one-time
Rscript scripts/00_preprocess_data.R # long -> wide counts
Rscript scripts/01_deseq2_analysis.R # trisomy-aware DESeq2
Rscript scripts/02_filter_genotypes.R # gene + variant universe
Rscript scripts/03_t21_dosage_boxplots.R # within-T21 fits
Rscript scripts/04_chr21_lane_assignment.R # MAIN per-gene table + SankeyMATIC
Rscript scripts/05_chr21_distribution_panel.R # population viewThe full 00-05 chain runs in ~30 minutes.
This project utilized the AI assistant Claude, developed by Anthropic, during the development process. Its assistance included generating initial code snippets and improving documentation. All AI-generated content was reviewed, tested, and validated by human developers.
See CLAUDE.md for the canonical project documentation: methodology, pipeline walkthrough, data inputs, full script catalog, and output file inventory.
Hunter, S., Hendrix, J., Freeman, J., Dowell, R.D., & Allen, M.A. (2023). Transcription dosage compensation does not occur in Down syndrome. BMC Biology 21:228. https://doi.org/10.1186/s12915-023-01700-4
BSD 3-Clause License — see LICENSE.