ArticleBMC bioinformatics2008
Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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57 citing papers in PubMed.
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- Large-Sample Genome-Wide Association Study of Resistance to Retained Placenta in U.S. Holstein Cows.International journal of molecular sciences · 2024Article
- A Million-Cow Validation of a Chromosome 14 Region Interacting with All Chromosomes for Fat Percentage in U.S. Holstein Cows.International journal of molecular sciences · 2024Article
- A Million-Cow Genome-Wide Association Study of Three Fertility Traits in U.S. Holstein Cows.International journal of molecular sciences · 2023Article
- Genome-Wide Association Study of Age at First Calving in U.S. Holstein Cows.International journal of molecular sciences · 2023Article
- Genome-Wide Association Study Reveals Additive and Non-Additive Effects on Growth Traits in Duroc Pigs.Genes · 2022Article
- Transcriptome and association mapping revealed functional genes respond to drought stress inFrontiers in plant science · 2022Article
- Genetic Architecture and Genome-Wide Adaptive Signatures Underlying Stem Lenticel Traits inInternational journal of molecular sciences · 2021Article
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- Multifactorial Landscape Parses to Reveal a Predictive Model for Knee Osteoarthritis.International journal of environmental research and public health · 2021Article
- Genetic Scores ofInternational journal of environmental research and public health · 2021Article
- Genetic Effects and Expression Patterns of the Nitrate Transporter (NRT) Gene Family inFrontiers in plant science · 2021Article
- Genetic dissection of the gene coexpression network underlying photosynthesis in Populus.Plant biotechnology journal · 2020Article
- A time-dependent genome-wide SNP-SNP interaction analysis of chicken body weight.BMC genomics · 2019Article
- Time-specific and pleiotropic quantitative trait loci coordinately modulate stem growth in Populus.Plant biotechnology journal · 2019Article
- A Large-Scale Genome-Wide Association Study in U.S. Holstein Cattle.Frontiers in genetics · 2019Article
- Genetic architecture underlying the lignin biosynthesis pathway involves noncoding RNAs and transcription factors for growth and wood properties in Populus.Plant biotechnology journal · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome-wide association studies (GWAS) using single nucleotide polymorphism (SNP) markers provide opportunities to detect epistatic SNPs associated with quantitative traits and to detect the exact mode of an epistasis effect. Computational difficulty is the main bottleneck for epistasis testing in large scale GWAS.
resultsThe EPISNPmpi and EPISNP computer programs were developed for testing single-locus and epistatic SNP effects on quantitative traits in GWAS, including tests of three single-locus effects for each SNP (SNP genotypic effect, additive and dominance effects) and five epistasis effects for each pair of SNPs (two-locus interaction, additive x additive, additive x dominance, dominance x additive, and dominance x dominance) based on the extended Kempthorne model. EPISNPmpi is the parallel computing program for epistasis testing in large scale GWAS and achieved excellent scalability for large scale analysis and portability for various parallel computing platforms. EPISNP is the serial computing program based on the EPISNPmpi code for epistasis testing in small scale GWAS using commonly available operating systems and computer hardware. Three serial computing utility programs were developed for graphical viewing of test results and epistasis networks, and for estimating CPU time and disk space requirements.
conclusionThe EPISNPmpi parallel computing program provides an effective computing tool for epistasis testing in large scale GWAS, and the epiSNP serial computing programs are convenient tools for epistasis analysis in small scale GWAS using commonly available computer hardware.
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