SynthesisGenome research2012
Ultrafast genome-wide scan for SNP-SNP interactions in common complex disease.
Synthesis in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
60 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Detecting fitness epistasis in recently admixed populations with genome-wide data.BMC genomics · 2020Pooled it
- Machine learning and statistical methods for molecular quantitative trait loci.Nature reviews. Genetics · 2026Review
- Article
- Empowering genetic discoveries and cardiovascular risk assessment by predicting electrocardiograms from genotype.NPJ digital medicine · 2026Article
- A biobank-scale test of marginal epistasis reveals genome-wide signals of polygenic interaction effects.Nature genetics · 2025Article
- Sparse modeling of interactions enables fast detection of genome-wide epistasis in biobank-scale studies.American journal of human genetics · 2025Article
- A global genetic interaction map of a human cell reveals conserved principles of genetic networks.bioRxiv : the preprint server for biology · 2025Article
- Resolving discrepancies between chimeric and multiplicative measures of higher-order epistasis.Nature communications · 2025Article
- A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits.Genome research · 2024Article
- Fast kernel-based association testing of non-linear genetic effects for biobank-scale data.Nature communications · 2023Article
- Leveraging the genetic correlation between traits improves the detection of epistasis in genome-wide association studies.G3 (Bethesda, Md.) · 2023Article
- Pathophysiological Roles of Auxiliary Calcium Channel αHandbook of experimental pharmacology · 2023Article
- Neuronal αPflugers Archiv : European journal of physiology · 2020Review
- Article
- SAMA: A Fast Self-Adaptive Memetic Algorithm for Detecting SNP-SNP Interactions Associated with Disease.BioMed research international · 2020Article
- Deep mixed model for marginal epistasis detection and population stratification correction in genome-wide association studies.BMC bioinformatics · 2019Article
- Association betweenNeural regeneration research · 2019Article
- Discovering genetic interactions bridging pathways in genome-wide association studies.Nature communications · 2019Article
- Genetic Associations between Voltage-Gated Calcium Channels and Psychiatric Disorders.International journal of molecular sciences · 2019Review
- VARIABLE PRIORITIZATION IN NONLINEAR BLACK BOX METHODS: A GENETIC ASSOCIATION CASE STUDYThe annals of applied statistics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Long-range gene-gene interactions are biologically compelling models for disease genetics and can provide insights on relevant mechanisms and pathways. Despite considerable effort, rigorous interaction mapping in humans has remained prohibitively difficult due to computational and statistical limitations. We introduce a novel algorithmic approach to find long-range interactions in common diseases using a standard two-locus test that contrasts the linkage disequilibrium between SNPs in cases and controls. Our ultrafast method overcomes the computational burden of a genome × genome scan by using a novel randomization technique that requires 10× to 100× fewer tests than a brute-force approach. By sampling small groups of cases and highlighting combinations of alleles carried by all individuals in the group, this algorithm drastically trims the universe of combinations while simultaneously guaranteeing that all statistically significant pairs are reported. Our implementation can comprehensively scan large data sets (2K cases, 3K controls, 500K SNPs) to find all candidate pairwise interactions (LD-contrast ) in a few hours-a task that typically took days or weeks to complete by methods running on equivalent desktop computers. We applied our method to the Wellcome Trust bipolar disorder data and found a significant interaction between SNPs located within genes encoding two calcium channel subunits: RYR2 on chr1q43 and CACNA2D4 on chr12p13 (LD-contrast test, ). We replicated this pattern of interchromosomal LD between the genes in a separate bipolar data set from the GAIN project, demonstrating an example of gene-gene interaction that plays a role in the largely uncharted genetic landscape of bipolar disorder.
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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.