ArticleScientific reports2018
Discovering Genetic Factors for psoriasis through exhaustively searching for significant second order SNP-SNP interactions.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Multi-trait analysis characterizes the genetics of thyroid function and identifies causal associations with clinical implications.Nature communications · 2024Pooled it
- Exploring the genetic architecture of multiple long-term conditions using a genome-wide association study in the UK Biobank population.Scientific reports · 2025Article
- RNA-Based Antipsoriatic Gene Therapy: An Updated Review Focusing on Evidence from Animal Models.Drug design, development and therapy · 2024Review
- Deep learning captures the effect of epistasis in multifactorial diseases.Frontiers in medicine · 2024Article
- Perception and Assessment of Psoriasis Among the General Population in the Jazan Region, Saudi Arabia.Cureus · 2023Article
- Lineage-specific accelerated sequences underlying primate evolution.Science advances · 2023Article
- A multi-threaded approach to genotype pattern mining for detecting digenic disease genes.Frontiers in genetics · 2023Article
- Matrix Metalloproteinases and Glaucoma.Biomolecules · 2022Review
- Break on through: The role of innate immunity and barrier defence in atopic dermatitis and psoriasis.Skin health and disease · 2022Review
- Common and Rare 5'UTR Variants Altering Upstream Open Reading Frames in Cardiovascular Genomics.Frontiers in cardiovascular medicine · 2022Review
- Identifying Novel Psoriatic Disease Drug Targets Using a Genetics-Based Priority Index Pipeline.Journal of psoriasis and psoriatic arthritis · 2021Article
- Genetic Polymorphisms ofDisease markers · 2021Article
- Detecting Shared Genetic Architecture Among Multiple Phenotypes by Hierarchical Clustering of Gene-Level Association Statistics.Genetics · 2020Article
- Psoriasis and Genetics.Acta dermato-venereologica · 2020Review
- Genome-Wide Search for SNP Interactions in GWAS Data: Algorithm, Feasibility, Replication Using Schizophrenia Datasets.Frontiers in genetics · 2020Article
- Defining Early Life Stress as a Precursor for Autoimmune Disease.Critical reviews in immunology · 2019Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this paper, we aim at discovering genetic factors of psoriasis through searching for statistically significant SNP-SNP interactions exhaustively from two real psoriasis genome-wide association study datasets (phs000019.v1.p1 and phs000982.v1.p1) downloaded from the database of Genotypes and Phenotypes. To deal with the enormous search space, our search algorithm is accelerated with eight biological plausible interaction patterns and a pre-computed look-up table. After our search, we have discovered several SNPs having a stronger association to psoriasis when they are in combination with another SNP and these combinations may be non-linear interactions. Among the top 20 SNP-SNP interactions being found in terms of pairwise p-value and improvement metric value, we have discovered 27 novel potential psoriasis-associated SNPs where most of them are reported to be eQTLs of a number of known psoriasis-associated genes. On the other hand, we have inferred a gene network after selecting the top 10000 SNP-SNP interactions in terms of improvement metric value and we have discovered a novel long distance interaction between XXbac-BPG154L12.4 and RNU6-283P which is not a long distance haplotype and may be a new discovery. Finally, our experiments with the synthetic datasets have shown that our pre-computed look-up table technique can significantly speed up the search process.
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