ArticleFrontiers in genetics2018
PASSPORT-seq: A Novel High-Throughput Bioassay to Functionally Test Polymorphisms in Micro-RNA Target Sites.
Article in Frontiers in genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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Who cites it
10 citing papers in PubMed, 12 citations in OpenAlex.
- Regulatory mechanisms driven by functional 3'-UTR variants in alcohol use disorder and related traits.Genome biology · 2026Article
- Decoding biology with massively parallel reporter assays and machine learning.Genes & development · 2024Review
- Massively parallel screen uncovers many rare 3' UTR variants regulating mRNA abundance of cancer driver genes.Nature communications · 2024Article
- The Search for and Functional Analysis of Genetic Variants in microRNA-Binding Sites using Massively Parallel Reporter Assay.Bulletin of experimental biology and medicine · 2024Article
- 5. Collaborative Study on the Genetics of Alcoholism: Functional genomics.Genes, brain, and behavior · 2023Review
- SNPs in 3'UTR miRNA Target Sequences Associated with Individual Drug Susceptibility.International journal of molecular sciences · 2022Review
- Mapping the miRNA-mRNA Interactome in Human Hepatocytes and Identification of Functional mirSNPs in Pharmacogenes.Clinical pharmacology and therapeutics · 2021Article
- Allele-specific expression and high-throughput reporter assay reveal functional genetic variants associated with alcohol use disorders.Molecular psychiatry · 2021Article
- Identification of Functional Genetic Variants Associated With Alcohol Dependence and Related Phenotypes Using a High-Throughput Assay.Alcoholism, clinical and experimental research · 2020Article
- The Impact of Population Variation in the Analysis of microRNA Target Sites.Non-coding RNA · 2019Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
Next-generation sequencing (NGS) studies have identified large numbers of genetic variants that are predicted to alter miRNA-mRNA interactions. We developed a novel high-throughput bioassay, PASSPORT-seq, that can functionally test in parallel 100s of these variants in miRNA binding sites (mirSNPs). The results are highly reproducible across both technical and biological replicates. The utility of the bioassay was demonstrated by testing 100 mirSNPs in HEK293, HepG2, and HeLa cells. The results of several of the variants were validated in all three cell lines using traditional individual luciferase assays. Fifty-five mirSNPs were functional in at least one of three cell lines (FDR ≤ 0.05); 11, 36, and 27 of them were functional in HEK293, HepG2, and HeLa cells, respectively. Only four of the variants were functional in all three cell lines, which demonstrates the cell-type specific effects of mirSNPs and the importance of testing the mirSNPs in multiple cell lines. Using PASSPORT-seq, we functionally tested 111 variants in the 3' UTR of 17 pharmacogenes that are predicted to alter miRNA regulation. Thirty-three of the variants tested were functional in at least one cell line.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.