hudson: A User-Friendly R Package to Extend Manhattan Plots

Lucas, Anastasia; Verma, Anurag; Ritchie, Marylyn D.

doi:10.1101/2022.01.25.474274

Cited by 9 publications

(6 citation statements)

References 17 publications

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“…In GWAS stratified by MF type (Supplemental Table 1), variants were filtered based on a more stringent control minor allele frequency (>5%) to remove potential spurious associations arising due to small sample size. Manhattan plots for results visualization were generated using the "qqman" and "hudson" R packages 66,67 .…”

Section: Genome-wide Association Studymentioning

confidence: 99%

Germline-somatic JAK2 interactions are associated with clonal expansion in myelofibrosis

et al. 2022

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Myelofibrosis is a rare myeloproliferative neoplasm (MPN) with high risk for progression to acute myeloid leukemia. Our integrated genomic analysis of up to 933 myelofibrosis cases identifies 6 germline susceptibility loci, 4 of which overlap with previously identified MPN loci. Virtual karyotyping identifies high frequencies of mosaic chromosomal alterations (mCAs), with enrichment at myelofibrosis GWAS susceptibility loci and recurrently somatically mutated MPN genes (e.g., JAK2). We replicate prior MPN associations showing germline variation at the 9p24.1 risk haplotype confers elevated risk of acquiring JAK2V617F mutations, demonstrating with long-read sequencing that this relationship occurs in cis. We also describe recurrent 9p24.1 large mCAs that selectively retained JAK2V617F mutations. Germline variation associated with longer telomeres is associated with increased myelofibrosis risk. Myelofibrosis cases with high-frequency JAK2 mCAs have marked reductions in measured telomere length – suggesting a relationship between telomere biology and myelofibrosis clonal expansion. Our results advance understanding of the germline-somatic interaction at JAK2 and implicate mCAs involving JAK2 as strong promoters of clonal expansion of those mutated clones.

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Section: Genome-wide Association Studymentioning

confidence: 99%

Germline-somatic JAK2 interactions are associated with clonal expansion in myelofibrosis

et al. 2022

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“…Miami plots were generated, to display signi cantly associated SNPs in associated regions, using the Hudson package in R 71 . Genomic control and quantile-quantile (Q-Q) plots were conducted as a QC check, to re-evaluate genetic in ation and confounding biases such as cryptic relatedness and population strati cation (with the assumption that the regional groupings will be independent of each other).…”

Section: Visualization and Interpretation Of Genetic Associationsmentioning

confidence: 99%

Genome-wide Association Study Meta-analysis of Blood Pressure Traits and Hypertension in Sub-Saharan African Populations: An AWI-Gen Study

Singh

Choudhury

Hazelhurst

et al. 2023

Preprint

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Most hypertension-related genome-wide association studies (GWAS) focus on non-African populations, despite hypertension (a major risk factor for cardiovascular disease) being highly prevalent in Africa. The AWI-Gen study GWAS meta-analysis for blood pressure-related traits (systolic and diastolic blood pressure, pulse pressure, mean-arterial pressure and hypertension) from three sub-Saharan African geographic regions (N=10,775), identified two genome-wide significant signals (p<5E-08): systolic blood pressure near P2RY1 (rs77846204; intergenic variant, p=4.25E-08) and pulse pressure near Linc01256 (rs80141533; intergenic variant, p=4.25E-08). No genome-wide signals were detected for the AWI-Gen GWAS meta-analysis with previous African-ancestry GWASs (UK Biobank (African), Uganda Genome Resource). Suggestive signals (p<5E-06) were observed for all traits, with 29 displaying pleiotropic effects and several replicating known associations. Polygenic risk scores developed from studies on different ancestries had limited transferability, with multi-ancestry models providing better prediction. This study provides insights into the genetics and physiology of blood pressure variation in African populations.

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“…The AUC quantified the models' ability to distinguish between presence and absence, while the Boyce index measured the agreement between observed and predicted values. We used several R packages, including "raster", "rgdal", "terra", "dismo", "modEvA", "dplyr", "gmp", "Metrics", "CalibratR", "caret", "ecospat" and "tidyr" 4,16,17,18,19,20,21,22,23,24,25,26 .…”

Section: Modelling Process Evaluation and Analysismentioning

confidence: 99%

MontObEO, Montesinho biodiversity observatory: an Earth observation tool for biodiversity conservation

Garcia,

Alírio,

Silva

et al. 2023

Earth Resources and Environmental Remote Sensing/Gis Applications XIV

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The Montesinho Natural Park (MNP) is one of the largest protected areas in Portugal, covering an area of 74,225 hectares in the extreme northeast of the country. MNP hosts a wide range of endemic and highly threatened species and priority habitats such as oak forests, meadows, grasslands, and bushlands. However, human activities continue to pose a significant challenge to conservation. To address this challenge, the MontObEO project aims to implement an early warning system to identify changes in habitat suitability and species extinction risk over time and space in the MNP, using a time series of satellite remote sensing data and ecological niche models (SRS-ENMs). Herein, we compiled biodiversity data for five major taxonomic groups (flora-vascular plants, amphibians, reptiles, birds, and mammals) and yearly remote sensing products from MODIS sensors between 2000 and 2021. We conducted all the satellite data processing and modelling procedures in Google Earth Engine (GEE) platform using the MaxEnt algorithm. We measured trends in species’ habitat suitability with the Mann-Kendall test, a non-parametric test for monotonic trend detection in a time series. Those species with stronger decreasing trends will have higher extinction risks. Additionally, we developed a ready-to-use web geographic information system (Web GIS) to map individual species distributions with a high spatial resolution (1 km). This project provides tools for biodiversity conservation in the MNP to help in the decision-making process for conservation planning and could serve as a model for other national or international protected areas.

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hudson: A User-Friendly R Package to Extend Manhattan Plots

Cited by 9 publications

References 17 publications

Germline-somatic JAK2 interactions are associated with clonal expansion in myelofibrosis

Germline-somatic JAK2 interactions are associated with clonal expansion in myelofibrosis

Genome-wide Association Study Meta-analysis of Blood Pressure Traits and Hypertension in Sub-Saharan African Populations: An AWI-Gen Study

MontObEO, Montesinho biodiversity observatory: an Earth observation tool for biodiversity conservation

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