Another explanation for apparent epistasis

doi:10.1038/nature13691

Comment

. 2014 Oct 2;514(7520):E3-5.

doi: 10.1038/nature13691.

Another explanation for apparent epistasis

Affiliations

¹ Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter EX2 5DW, UK.
² Laboratory of Neurogenetics, National Institute of Aging, Bethesda, Maryland 20892, USA.
³ 1] Laboratory of Neurogenetics, National Institute of Aging, Bethesda, Maryland 20892, USA [2] Department of Molecular Neuroscience and Reta Lila Laboratories, Institute of Neurology, UCL, London WC1N IPJ, UK.
⁴ 1] Tuscany Regional Health Agency, Florence, Italy, I.O.T. and Department of Medical and Surgical Critical Care, University of Florence, Florence, Italy [2] Geriatric Unit, Azienda Sanitaria di Firenze, Florence, Italy.
⁵ Longitudinal Studies Section, Clinical Research Branch, Gerontology Research Center, National Institute on Aging, Baltimore, Maryland 21225, USA.

PMID: 25279928
PMCID: PMC6478385
DOI: 10.1038/nature13691

Comment

Another explanation for apparent epistasis

Andrew R Wood et al. Nature. 2014.

. 2014 Oct 2;514(7520):E3-5.

doi: 10.1038/nature13691.

Affiliations

¹ Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter EX2 5DW, UK.
² Laboratory of Neurogenetics, National Institute of Aging, Bethesda, Maryland 20892, USA.
³ 1] Laboratory of Neurogenetics, National Institute of Aging, Bethesda, Maryland 20892, USA [2] Department of Molecular Neuroscience and Reta Lila Laboratories, Institute of Neurology, UCL, London WC1N IPJ, UK.
⁴ 1] Tuscany Regional Health Agency, Florence, Italy, I.O.T. and Department of Medical and Surgical Critical Care, University of Florence, Florence, Italy [2] Geriatric Unit, Azienda Sanitaria di Firenze, Florence, Italy.
⁵ Longitudinal Studies Section, Clinical Research Branch, Gerontology Research Center, National Institute on Aging, Baltimore, Maryland 21225, USA.

PMID: 25279928
PMCID: PMC6478385
DOI: 10.1038/nature13691

No abstract available

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Conflict of interest statement

Competing Financial Interests Declared none.

Figures

**Figure 1 |. Haplotype and linkage disequilibrium structure.**
**a, b**, Haplotype and LD structure are shown at the *ADK* locus of two proposed epistatic SNPs from Hemani *et al.* (a) and when adding a third SNP captured by sequencing in 450 Italian individuals (b). The two “epistatic” SNPs form all four of the possible haplotypes. When adding the third SNP no new haplotypes are formed at >.2.4% frequency. Haplotypes were estimated using Haploview.

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Comment in

Hemani et al. reply.
Hemani G, Shakhbazov K, Westra HJ, Esko T, Henders AK, McRae AF, Yang J, Gibson G, Martin NG, Metspalu A, Franke L, Montgomery GW, Visscher PM, Powell JE. Hemani G, et al. Nature. 2014 Oct 2;514(7520):E5-6. doi: 10.1038/nature13692. Nature. 2014. PMID: 25279929 Free PMC article. No abstract available.

Comment on

Detection and replication of epistasis influencing transcription in humans.
Hemani G, Shakhbazov K, Westra HJ, Esko T, Henders AK, McRae AF, Yang J, Gibson G, Martin NG, Metspalu A, Franke L, Montgomery GW, Visscher PM, Powell JE. Hemani G, et al. Nature. 2014 Apr 10;508(7495):249-53. doi: 10.1038/nature13005. Epub 2014 Feb 26. Nature. 2014. Retraction in: Nature. 2021 Aug;596(7871):306. doi: 10.1038/s41586-021-03766-y PMID: 24572353 Free PMC article. Retracted.

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References

1. Hemani G et al. Detection and replication of epistasis influencing transcription humans. Nature 508, 249–253 (2014). - PMC - PubMed
1. Wood AR et al. Allelic heterogeneity and more detailed analyses of known loci explain additional phenotypic variation and reveal complex patterns of association. Hum. Mol. Genet 20, 4082–4092 (2011). - PMC - PubMed
1. Hemani G, Theocharidis A, Wei W & Haley C EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards. Bioinformatics 27, 1462–1465 (2011). - PubMed
1. Nielsen DM, Ehm MG, Zaykin DV & Weir BS Effect of two- and three-locus linkage disequilibrium on the power to detect marker/phenotype associations. Genetics 168, 1029–1040 (2004). - PMC - PubMed
1. DePristo MA et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet. 43, 491–498 (2011). - PMC - PubMed

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[1] Hemani G et al. Detection and replication of epistasis influencing transcription humans. Nature 508, 249–253 (2014). - PMC - PubMed

[2] Hemani G et al. Detection and replication of epistasis influencing transcription humans. Nature 508, 249–253 (2014). - PMC - PubMed

[3] Wood AR et al. Allelic heterogeneity and more detailed analyses of known loci explain additional phenotypic variation and reveal complex patterns of association. Hum. Mol. Genet 20, 4082–4092 (2011). - PMC - PubMed

[4] Wood AR et al. Allelic heterogeneity and more detailed analyses of known loci explain additional phenotypic variation and reveal complex patterns of association. Hum. Mol. Genet 20, 4082–4092 (2011). - PMC - PubMed

[5] Hemani G, Theocharidis A, Wei W & Haley C EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards. Bioinformatics 27, 1462–1465 (2011). - PubMed

[6] Hemani G, Theocharidis A, Wei W & Haley C EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards. Bioinformatics 27, 1462–1465 (2011). - PubMed

[7] Nielsen DM, Ehm MG, Zaykin DV & Weir BS Effect of two- and three-locus linkage disequilibrium on the power to detect marker/phenotype associations. Genetics 168, 1029–1040 (2004). - PMC - PubMed

[8] Nielsen DM, Ehm MG, Zaykin DV & Weir BS Effect of two- and three-locus linkage disequilibrium on the power to detect marker/phenotype associations. Genetics 168, 1029–1040 (2004). - PMC - PubMed

[9] DePristo MA et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet. 43, 491–498 (2011). - PMC - PubMed

[10] DePristo MA et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet. 43, 491–498 (2011). - PMC - PubMed

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Another explanation for apparent epistasis

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Another explanation for apparent epistasis

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