H520 episomal MPRA — benzo(a)pyrene exposure
High-throughput characterization of functional variants highlights heterogeneity and polygenicity underlying lung cancer susceptibilityThe shared allele-specific episomal MPRA library of 2,245 lung-cancer GWAS candidate variants plus positive and negative controls was transfected into H520 human lung squamous cell carcinoma cells and assayed after benzo(a)pyrene exposure. Five independent transfections were summarized by the published variant-level allele-versus-reference reporter activity results.
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
10 μM benzo(a)pyrene for 42 h
H520 cells were transfected with an episomal luc2 reporter library carrying 145-bp (123–145 bp for indels) reference and alternative allele sequences in both orientations. Each variant sequence was assigned 25 unique 12-bp tags, producing 100 oligos per variant and a 239,800-oligo pooled library including scrambled controls; expressed tags were placed in the luc2 3′ UTR. Five H520 RNA output samples (GSM7847067, GSM7847069, GSM7847071, GSM7847073, GSM7847075) were normalized to H520 input DNA GSM7847065. After 6 h of transfection, media containing 10 μM benzo(a)pyrene was added; cells were harvested 48 h after transfection, corresponding to a 42 h exposure. Tag counts were converted to TPM, pseudocount-adjusted RNA/DNA ratios were used for the MPRA allele comparison, and the published table reports the condition-specific FDR and log2 fold change.
Processed data
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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 · 15 definitions
- variant_id_hg19
- Unique variant coordinate identifier reported by the source table using hg19 coordinates.
- rsid
- dbSNP rs identifier, or NA when the source does not provide one.
- chromosome
- Chromosome parsed from variant_id_hg19.
- position_hg19
- Base position parsed from variant_id_hg19 on hg19.
- variant_class
- Package classification as GWAS_candidate, Positive_control, or Negative_control.
- gwas_locus_or_control_status
- Source GWAS locus identifier or positive/negative control label.
- reference_allele
- Reference allele in the tested MPRA oligo pair.
- alternate_allele
- Alternative allele in the tested MPRA oligo pair.
- risk_allele
- GWAS risk allele reported by the source; NA for control variants or unavailable values.
- alt_vs_ref_fdr
- Published BH-adjusted FDR for the alternative-versus-reference allelic transcriptional activity test in H520_BaP.
- alt_vs_ref_log2fc
- Published log2 fold change of mean (RNA TPM + 1)/(DNA TPM + 1) for alternative versus reference alleles in H520_BaP.
- risk_direction
- Source direction of the risk allele's mean TPM ratio relative to the protective allele; NA when not reported.
- activator
- Source putative activator call (Y/N/NA) for the H520 condition.
- mpra_significant_fdr_lt_0_01
- Boolean derived from the published H520_BaP FDR using the paper's FDR <0.01 significance threshold.
- source_table
- Supplementary workbook table and cell line used to obtain the published result.
Quality control
The paper removed tags with input-DNA TPM <1.6 and retained tags detected in RNA output across all transfections; the remaining tags represented 86.01% of detected DNA-input tags. Library/sample QC reported >95% designed-tag detection in RNA, >98% recovery of DNA-input tags in RNA, and median inter-transfection Pearson correlation of 0.9. The published two-sided robust-sandwich Wald tests were BH-adjusted, with FDR <0.01 defining MPRA significance. Package QC excluded 24 of 2,312 variant records whose H520_BaP FDR or log2FC was unavailable after the paper's QC, retaining 2,288 records including nonsignificant variants.
Curation notes
H520/NCI-H520 is the human lung squamous cell carcinoma line (Cellosaurus CVCL:1566). BaP was applied after the transfection media change and the paper reports a 42 h exposure for H520. The same library was also measured in H520 with DMSO and in A549 cells; those are separate child experiments. Oligo design used GRCh38, while the source result table labels its variant IDs as hg19. The processed table is a cleaned projection of Data S1 Table S8; 24 rows with unavailable post-QC results were omitted.