Experiment / E2EY1H87REpisomal Plasmid MPRA

UACC903 melanoma-cell episomal allelic MPRA

Massively parallel reporter assays and variant scoring identified functional variants and target genes for melanoma loci and highlighted cell-type specificity

The 191,232-oligo library tested 1,992 melanoma-GWAS variants as 145-bp reference and alternative sequences in both orientations with barcode tags. The library was transfected into UACC903 human melanoma cells in 8 biological transfections, normalized to MPRA DNA Inputs 1 or 2.

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Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:4052
Reference genome: hg19
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated; harvested 48 h after transfection

Episomal pMPRA1/pMPRAdonor2 luc2 reporter with a minimal promoter; each allele was represented by forward and reverse-complement 145-bp test sequences and 20 12-bp random barcode tags per unique sequence (with a 2-bp AC spacer). UACC903 cells were transfected with Lipofectamine 3000 in 8 biological transfections; T1-T3 used DNA Input 1 and T4-T8 used DNA Input 2.

Processed data

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Column dictionary · 41 definitions

variant_id: Variant identifier as chromosome:position on hg19; multiallelic variants use the S2 A/B suffix.
rsid: dbSNP rs identifier, or NA for variants without an rs identifier.
gwas_locus: Melanoma GWAS locus label assigned by the authors.
ref_allele: Reference allele used in the MPRA oligo.
alt_allele: Alternative allele used in the MPRA oligo.
ref_sequence_145bp: 145-bp forward-strand reference test sequence from Table S3.
alt_sequence_145bp: 145-bp forward-strand alternative test sequence from Table S3.
n_qc_tags: Number of unique reference plus alternative barcode tags with DNA TPM >=2 in at least one input library used for this experiment.
n_ref_qc_tags: Unique reference-allele barcode tags passing the DNA TPM >=2 filter.
n_alt_qc_tags: Unique alternative-allele barcode tags passing the DNA TPM >=2 filter.
n_qc_observations: Number of allele-tag by transfection observations retained after DNA TPM QC; RNA-nondetected tags are represented as zero TPM.
n_ref_qc_observations: Reference-allele tag by transfection observations passing DNA TPM QC.
n_alt_qc_observations: Alternative-allele tag by transfection observations passing DNA TPM QC.
n_ref_rna_detected_observations: QC-passing reference observations with a detected RNA tag in the deposited RNA count table.
n_alt_rna_detected_observations: QC-passing alternative observations with a detected RNA tag in the deposited RNA count table.
mean_ref_log2_rna_dna: Mean log2((RNA TPM + 1)/(DNA TPM + 1)) across QC-passing reference observations.
mean_alt_log2_rna_dna: Mean log2((RNA TPM + 1)/(DNA TPM + 1)) across QC-passing alternative observations.
raw_log2_fc_alt: Raw-derived alternative-minus-reference difference between the two mean log2 RNA/DNA ratios.
author_log2_fc_alt: Authors' reported log2 fold difference for alternative versus reference allelic activity from the current MPRA regression (Table S6 or S7).
author_fdr: Authors' BH-adjusted FDR for the current MPRA allelic regression (Table S6 or S7); 0 is reported as 0 in the source workbook.
author_mtsa_log2_fc_alt: Authors' MTSA-corrected log2 fold difference for alternative versus reference allelic activity (Table S8).
author_mtsa_fdr: Authors' MTSA-corrected BH-adjusted FDR (Table S8).
author_mpra_significant: Y when the authors' current-MPRA FDR is <0.01; otherwise N or NA.
ref_effect: Authors' melanoma-risk/protective classification of the reference allele.
risk_direction: Authors' direction of the melanoma-risk allele relative to the protective allele in this MPRA.
activator: Authors' putative activator/repressor annotation from MPRA activity inference (Table S12).
open_chromatin_annotation: Authors' number/category of open-chromatin datasets overlapping the variant (Table S12).
histone_annotation: Authors' enhancer/promoter histone annotation (Table S12).
motif_sig_count: Number of significant motifBreakR predictions for the variant (Table S12).
motif_strong_count: Number of strong motifBreakR effects for the variant (Table S12).
integrative_score: Authors' combined variant-prioritization score across MPRA, chromatin, motif, and fine-mapping features (Table S12).
tier: Authors' within-locus prioritization tier (Table S12).
prioritized: Y when the authors prioritized the variant based on Tier 1 or Tier 2 (Table S12).
SKCM_eGenes: Semicolon-separated significant eGenes linked in the TCGA skin cutaneous melanoma QTL dataset.
melanocyte_eGenes: Semicolon-separated significant eGenes linked in the primary melanocyte QTL dataset.
SKCM_meGenes: Semicolon-separated significant meGenes linked in the TCGA skin cutaneous melanoma methylation-QTL dataset.
melanocyte_meGenes: Semicolon-separated significant meGenes linked in the primary melanocyte methylation-QTL dataset.
cell_type_specific: Authors' cell-type-specific designation for this experiment; NA means it was not in the corresponding S16/S17 subset.
cell_type_score: Authors' corresponding cell-type specificity score from S16 or S17.
cell_type_fdr: Authors' FDR for the allelic-effect by cell-type interaction from S16 or S17.
cell_type_TFs: Authors' transcription factors predicted to explain the corresponding cell-type specificity.

Quality control

The authors reported high recovery and replicate reproducibility in Table S4. For this package (UACC903 melanoma; 8 transfections.), each GEO barcode TPM table was joined to Table S3, and the authors' normalization log2((RNA TPM + 1)/(DNA TPM + 1)) was calculated using the input assignment recorded in GEO. Barcode observations with DNA input TPM <2 were removed as specified in the paper; RNA tags absent from a deposited RNA table were treated as zero TPM after the pseudocount. Scrambled control oligos were excluded from the variant table. Variants without at least one QC-passing reference and alternative observation were excluded (15 excluded; 1977 retained). The table retains all QC-passing tested variants, not only significant hits; author MPRA significance is FDR <0.01. Author FDR/effect fields are copied from Table S6/S7 and MTSA-corrected fields from Table S8.

Curation notes

Raw-derived mean ratios use all input-qualified mapped reference/alternative tag observations, with missing RNA tags represented by zero TPM; the simple raw mean is expected to differ from the authors’ strand- and transfection-adjusted robust regression coefficient. For validation, the mean absolute difference between raw-derived and author log2 effects for variants with both values was 0.0245.

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