qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots

Turner, Stephen D.

doi:10.21105/joss.00731

Cited by 1,014 publications

(794 citation statements)

References 3 publications

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“…Genome‐wide association mapping across all groups was conducted using only SNPs with a minor allele frequency of >0.01, with population structure accounted for by using the respective fixed and random effects of γ and u . The qqman R package (Turner, 2014) was used to visualize quantile–quantile plots and the genomic inflation parameter Λ, a metric of the degree of inflation of p ‐values (Devlin and Roeder, 1999), was calculated.…”

Section: Methodsmentioning

confidence: 99%

Genome‐wide Association Mapping of Qualitatively Inherited Traits in a Germplasm Collection

et al. 2017

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Genome-wide association (GWA) has been used as a tool for dissecting the genetic architecture of quantitatively inherited traits. We demonstrate here that GWA can also be highly useful for detecting many major genes governing categorically defined phenotype variants that exist for qualitatively inherited traits in a germplasm collection. Genome-wide association mapping was applied to categorical phenotypic data available for 10 descriptive traits in a collection of ∼13,000 soybean [ (L.) Merr.] accessions that had been genotyped with a 50,000 single nucleotide polymorphism (SNP) chip. A GWA on a panel of accessions of this magnitude can offer substantial statistical power and mapping resolution, and we found that GWA mapping resulted in the identification of strong SNP signals for 24 classical genes as well as several heretofore unknown genes controlling the phenotypic variants in those traits. Because some of these genes had been cloned, we were able to show that the narrow GWA mapping SNP signal regions that we detected for the phenotypic variants had chromosomal bp spans that, with just one exception, overlapped the bp region of the cloned genes, despite local variation in SNP number and nonuniform SNP distribution in the chip set.

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Section: Methodsmentioning

confidence: 99%

Genome‐wide Association Mapping of Qualitatively Inherited Traits in a Germplasm Collection

et al. 2017

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“…The Manhattan plots in Figure 13 (generated using the qqman package (Turner, 2018)) show the magnitude of the univariate p-values and the size of the lasso coefficients for each gene for the two quantitative traits and two binary traits. The coefficients are plotted for the model with the optimal R 2 value on the validation set.…”

Section: A Manhattan Plotsmentioning

confidence: 99%

A Fast and Scalable Framework for Large-scale and Ultrahigh-dimensional Sparse Regression with Application to the UK Biobank

Qian

Tanigawa

et al. 2019

Preprint

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Since its first proposal in statistics (Tibshirani, 1996), the lasso has been an effective method for simultaneous variable selection and estimation. A number of packages have been developed to solve the lasso efficiently. However as large datasets become more prevalent, many algorithms are constrained by efficiency or memory bounds. In this paper, we propose a meta algorithm batch screening iterative lasso (BASIL) that can take advantage of any existing lasso solver and build a scalable lasso solution for large datasets. We also introduce snpnet, an R package that implements the proposed algorithm on top of glmnet (Friedman et al., 2010a) for largescale single nucleotide polymorphism (SNP) datasets that are widely studied in genetics. We demonstrate results on a large genotype-phenotype dataset from the UK Biobank, where we achieve state-of-the-art heritability estimation on quantitative and qualitative traits including height, body mass index, asthma and high cholesterol.

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“…A genome-wide association study (GWAS) based on sex was performed using plink v. 1.9b_5.2-x86_64 (Purcell et al, 2007) with the "fisher-midp" option. The -log(p-value) of each SNP was visualized on a manhattan plot created with the R software qqman v. 0.1.4 (Turner, 2018). Significance was assessed via Bonferonni correction at = 0.05.…”

Section: Genome-wide Association Studymentioning

confidence: 99%

Loss of genetic variation and sex determination system in North American northern pike characterized by whole-genome resequencing

Johnson

Rondeau

Minkley

et al. 2020

Preprint

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We present a chromosome-level, long-read genome assembly as a reference for northern pike (Esox lucius) where 97.5% of the genome is chromosome-anchored and N50 falls at 37.5 Mb. Whole-genome resequencing was genotyped using this assembly for 47 northern pike representing six North American populations from Alaska to New Jersey. We discovered that a disproportionate frequency of genetic polymorphism exists among populations east and west of the North American Continental Divide (NACD), indicating reproductive isolation across this barrier. Genome-wide analysis of heterozygous SNP density revealed a remarkable lack of genetic variation with 1 polymorphic site every 6.3kb in the Yukon River drainage and one every 16.5kb east of the NACD. Observed heterozygosity (H o ), nucleotide diversity (π), and Tajima's D are depressed in populations east of the NACD (east vs. west: H o : 0.092 vs 0.31; π : 0.092 vs 0.28; Tajima's D: -1.61 vs -0.47). We confirm the presence of the master sex determining (MSD) gene, amhby, in the Yukon River drainage and in an invasive population in British Columbia and confirm its absence in populations east of the NACD. We also describe an Alaskan populationwhere amhby is present but not associated with male gender determination. Our results support that northern pike originally colonized North America through Beringia, that Alaska provided an unglaciated refugium for northern pike during the last ice age, and southeast of the NACD was colonized by a small founding population(s) that lost amhby.

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qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots

Cited by 1,014 publications

References 3 publications

Genome‐wide Association Mapping of Qualitatively Inherited Traits in a Germplasm Collection

Genome‐wide Association Mapping of Qualitatively Inherited Traits in a Germplasm Collection

A Fast and Scalable Framework for Large-scale and Ultrahigh-dimensional Sparse Regression with Application to the UK Biobank

Loss of genetic variation and sex determination system in North American northern pike characterized by whole-genome resequencing

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