Allele-specific plasmid MPRA in B-ALL patient-derived xenograft samples
Investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatmentThe same 1,696-variant plasmid MPRA library was tested in two pediatric B-ALL patient-derived xenograft samples, PDXMPRA1137 and PDXMPRA4420, with four transfections per sample. table.csv contains all variant-level count-supported results for both final GEO runs, plus the authors’ reported significant-hit annotations where available.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Perturbation & assay details
Basal / Untreated
Human B-ALL PDX cells were expanded in female NSG mice, transfected with the pMPRA1 library at 50–90 million cells per replicate by electroporation, incubated overnight for 24 h, and processed for reporter RNA sequencing. The library used 175-bp reference/alternative allele inserts with 28 unique 10-bp 3′-UTR barcodes per allele. GEO supplies four-reference and four-alternative aggregate DNA and RNA barcode-count columns for each PDX sample.
Processed data
50 rows per page. Click a cell to inspect its full value.
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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 21 definitions
- variant_id
- rsID of the regulatory variant tested.
- pdx_sample
- Final GEO PDX run identifier, PDXMPRA1137 or PDXMPRA4420.
- phenotypes
- Unique phenotype labels associated with the variant in the cell-line MPRA source table, joined with semicolons.
- sentinel_variant_ids
- Unique sentinel GWAS variant IDs associated with the variant, joined with semicolons.
- chromosome
- HG19 chromosome label from the cell-line MPRA source table.
- position_hg19
- HG19 1-based variant position; blank for positive controls without a coordinate.
- is_positive_control
- yes when the variant is a source ALL susceptibility positive control, otherwise no.
- ref_dna_count_sum
- Sum of four reference-allele plasmid DNA barcode counts from the GEO PDX-input file.
- alt_dna_count_sum
- Sum of four alternative-allele plasmid DNA barcode counts from the GEO PDX-input file.
- ref_rna_count_sum
- Sum of four reference-allele reporter RNA barcode counts for this PDX sample.
- alt_rna_count_sum
- Sum of four alternative-allele reporter RNA barcode counts for this PDX sample.
- ref_activity_log2_rna_dna
- Derived mean reference-allele log2 RNA/DNA activity across four replicates after per-library CPM normalization and a +1 CPM pseudocount.
- alt_activity_log2_rna_dna
- Derived mean alternative-allele log2 RNA/DNA activity across four replicates after per-library CPM normalization and a +1 CPM pseudocount.
- derived_allelic_log2_effect_alt_minus_ref
- Derived alternative-minus-reference difference between the two mean log2 RNA/DNA activities.
- author_reported_significant_hit
- yes when the variant/sample pair is present in Supplementary Data 3 as a significant PDX MPRA hit, otherwise no (not a newly recomputed p-value).
- author_pdx_log2_fold_change
- Author-reported PDX_logFC from Supplementary Data 3; blank for variants not listed as significant hits.
- author_mean_cell_line_log2_fold_change
- Author-reported mean cell-line log fold change used to compare the PDX hit with the cell-line MPRA; blank for variants not listed as significant hits.
- reproducible_concordant_in_cell_line_mpra
- yes when any associated variant–phenotype pair appears in Supplementary Data 4 as reproducible and concordant in at least three ALL cell lines.
- regulatory_context
- Unique Supplementary Data 4 context annotations joined across the variant’s phenotype associations.
- promoter_or_promoter_chic_gene
- Unique nearby-promoter or promoter-CHiC gene annotations joined across the variant’s phenotype associations.
- great_gene_associations
- Unique GREAT gene associations joined across the variant’s phenotype associations.
Quality control
The authors used exact barcode trimming without mismatches and mpralm on RNA and DNA counts merged across all barcodes for each allele. Package QC required a final GEO-supported PDX sample, complete positive reference/alternative DNA and RNA counts for all four replicates, and nonnegative finite values; all 3,392 rows for PDXMPRA1137 and PDXMPRA4420 passed. Derived activity values are four-replicate mean log2((allele RNA CPM + 1)/(allele DNA CPM + 1)) summaries. Supplementary Data 3 reports 26 significant hits for PDXMPRA1137 and 67 for PDXMPRA4420; because that sheet does not provide complete inferential statistics, no new significance calls are made here.
Curation notes
The processed table contains 3,392 rows: 1,696 variants in each of the two PDX runs named in the final GEO series. Supplementary Data 3 has 93 supported significant-hit rows (26 for PDXMPRA1137 and 67 for PDXMPRA4420) plus three rows labeled PDXMPRA4419. PDXMPRA4419 has no matching final GEO count file and is inconsistent with the paper’s two-PDX description, so those three supplemental-only rows are preserved in raw_data/SupplementaryData3_MPRA_PDX_hits.xlsx but omitted from the processed table.