ArticleBioinformatics (Oxford, England)2016
LAMPLINK: detection of statistically significant SNP combinations from GWAS data.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 21 citations in OpenAlex.
- Detecting Interactions in High-Dimensional Data Using Cross Leverage Scores.Biometrical journal. Biometrische Zeitschrift · 2024Article
- Identification of epistatic SNP combinations in rheumatoid arthritis using LAMPLINK and Japanese cohorts.Journal of human genetics · 2024Article
- Refining the genetic risk of breast cancer with rare haplotypes and pattern mining.Life science alliance · 2023Article
- Pharmacogenetics of Praziquantel Metabolism: Evaluating the Cytochrome P450 Genes of Zimbabwean Patients During a Schistosomiasis Treatment.Frontiers in genetics · 2022Article
- Machine learning to reveal hidden risk combinations for the trajectory of posttraumatic stress disorder symptoms.Scientific reports · 2020Article
- A Fast and Scalable Workflow for SNPs Detection in Genome Sequences Using Hadoop Map-Reduce.Genes · 2020Article
- SAMA: A Fast Self-Adaptive Memetic Algorithm for Detecting SNP-SNP Interactions Associated with Disease.BioMed research international · 2020Article
- Self-Adjusting Ant Colony Optimization Based on Information Entropy for Detecting Epistatic Interactions.Genes · 2019Article
- MP-LAMP: parallel detection of statistically significant multi-loci markers on cloud platforms.Bioinformatics (Oxford, England) · 2018Article
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One of the major issues in genome-wide association studies is to solve the missing heritability problem. While considering epistatic interactions among multiple SNPs may contribute to solving this problem, existing software cannot detect statistically significant high-order interactions. We propose software named LAMPLINK, which employs a cutting-edge method to enumerate statistically significant SNP combinations from genome-wide case-control data. LAMPLINK is implemented as a set of additional functions to PLINK, and hence existing procedures with PLINK can be applicable. Applied to the 1000 Genomes Project data, LAMPLINK detected a combination of five SNPs that are statistically significantly accumulated in the Japanese population. AVAILABILITY AND IMPLEMENTATION: LAMPLINK is available at http://a-terada.github.io/lamplink/ CONTACT: terada@cbms.k.u-tokyo.ac.jp or sese.jun@aist.go.jpSupplementary information: Supplementary data are available at Bioinformatics online.
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