Publications by authors named "Karen M Funderburk"

Article Synopsis
  • Lung adenocarcinoma is the most prevalent form of lung cancer, and existing known genetic risk factors account for only a small portion of its heritability.
  • A comprehensive genome-wide association study involving nearly 22,000 cases and over 150,000 controls identified 12 new genetic variants linked to the disease, raising the count to 28 variants across 25 distinct locations in the genome.
  • The study emphasized that these genetic markers are particularly significant in East Asian populations, especially among never-smokers, and indicates that further research could inform better prevention and treatment strategies tailored to these populations.
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The most recent genome-wide association study (GWAS) of cutaneous melanoma identified 54 risk-associated loci, but functional variants and their target genes for most have not been established. Here, we performed massively parallel reporter assays (MPRAs) by using malignant melanoma and normal melanocyte cells and further integrated multi-layer annotation to systematically prioritize functional variants and susceptibility genes from these GWAS loci. Of 1,992 risk-associated variants tested in MPRAs, we identified 285 from 42 loci (78% of the known loci) displaying significant allelic transcriptional activities in either cell type (FDR < 1%).

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Genome-wide association studies (GWAS) have identified ~20 melanoma susceptibility loci, most of which are not functionally characterized. Here we report an approach integrating massively-parallel reporter assays (MPRA) with cell-type-specific epigenome and expression quantitative trait loci (eQTL) to identify susceptibility genes/variants from multiple GWAS loci. From 832 high-LD variants, we identify 39 candidate functional variants from 14 loci displaying allelic transcriptional activity, a subset of which corroborates four colocalizing melanocyte cis-eQTL genes.

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Chemicals, toxicants, and environmental stressors mediate their biologic effect through specific modes of action (MOAs). These encompass key molecular events that lead to changes in the expression of genes within regulatory pathways. Elucidating shared biologic processes and overlapping gene networks will help to better understand the toxicologic effects on biological systems.

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