imputeqc: an R package for assessing imputation quality of genotypes and optimizing imputation parameters

Khvorykh, Gennady V.; Khrunin, Andrey

doi:10.1186/s12859-020-03589-0

Cited by 11 publications

(8 citation statements)

References 18 publications

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“…The R software (Version 4.0.5) was applied for data processing and DEGs identification. The Linear Models for Microarray Analysis (LIMMA) package and impute package were used to preprocess the 3 raw datasets, matching probe ID and gene names, removing missing values, normalizing data, and performing log2 conversions (16,17). The LIMMA package was used to merge the 3 datasets into an integrated dataset.…”

Section: Data Processing and Identification Of Degsmentioning

confidence: 99%

Integrative bioinformatics analysis of potential therapeutic targets and immune infiltration characteristics in dilated cardiomyopathy

et al. 2022

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Background: Dilated cardiomyopathy (DCM) is currently the major cause of systolic heart failure. This study explored potential therapeutic targets and investigated the role of immune cell infiltration in DCM.Methods: Three DCM datasets (GSE3585, GSE9800, and GSE84796) from the Gene Expression Omnibus (GEO) database were merged into an integrated dataset, and batch effects were removed.Differentially expressed genes (DEGs) were screened and the associations between gene co-expression modules and clinical traits were assessed by weighted gene co-expression network analysis (WGCNA) in R software. Any DEGs from the integrated dataset overlapped with the significant module genes were defined as common genes (CGs). Enrichment analysis of the CGs was performed. The protein-protein interaction (PPI) network of the CGs was visualized and the hub gene was identified by using Cytoscape 3.8.2 software.The miRNA-transcription factor-mRNA (miRNA-TF-mRNA) network was constructed using Cytoscape to unveil the regulatory relationships in DCM. Finally, the CIBERSORT method (https://cibersort.stanford. edu/) was used to investigate immune cell infiltration in DCM.Results: A total of 53 DEGs were identified, and 5 gene co-expression modules were detected by WGCNA of the DCM and control group samples of cardiac tissue. Genes such as FRZB, ASPN, and PHLDA1were significantly upregulated, whereas IDH2 and ENDOG were significantly downregulated. Functional enrichment analysis showed that CGs were mainly enriched in the extracellular matrix (ECM) signaling pathway. ASPN was the hub gene in the PPI network. The miRNA-TF-mRNA network revealed that FRZB and ASPN were targeted by paired related homeobox 2 (Prrx2). We also found that miR-129-5p could regulate ASPN, PHLDA1, and IDH2 simultaneously. The immune infiltration analysis revealed higher levels of M1 macrophages in DCM samples than in the control samples. Conclusions:In conclusion, we speculate that miR-129-5p might target ASPN in regulating DCM via the ECM signaling pathway. Macrophage infiltration may be involved in ECM remodeling and eventually lead to DCM.

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Section: Data Processing and Identification Of Degsmentioning

confidence: 99%

Integrative bioinformatics analysis of potential therapeutic targets and immune infiltration characteristics in dilated cardiomyopathy

et al. 2022

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“…The hapFLK package v1.2 was used to detect selection signatures based on differences in haplotype frequencies between all the Merino-derived breeds included in this study ( Fariello et al, 2014 ). The number of haplotype clusters ( K ) was calculated using the imputeqc R package and accompanied scripts ( Khvorykh and Khrunin, 2020 ). Using the number of haplotype clusters, the hapFLK values and the kinship matrix were calculated in the fastPHASE model (- K 40).…”

Section: Methodsmentioning

confidence: 99%

Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders

et al. 2023

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Merino sheep are a breed of choice across the world, popularly kept for their wool and mutton value. They are often reared as a pure breed or used in crossbreeding and are a common component in synthetic breed development. This study evaluated genetic diversity, population structure, and breed divergence in 279 animals of Merino and Merino-based sheep breeds in South Africa using the Illumina Ovine SNP 50K BeadChip. The sheep breeds analysed included the three Merino-derived breeds of Dohne Merino (n = 50); Meatmaster (n = 47); and Afrino (n = 52) and five presumed ancestral populations of Merinos (Merino (n = 46); South African Merino (n = 10); and South African Mutton Merino (n = 8)); and the non-Merino founding breeds of Damara (n = 20); Ronderib Afrikaner (n = 17); and Nguni (n = 29). Highest genetic diversity values were observed in the Dohne Merino (DM), with Ho = 0.39 ± 0.01, followed by the Meatmaster and South African Merino (SAM), with Ho = 0.37 ± 0.03. The level of inbreeding ranged from 0.0 ± 0.02 (DM) to 0.27 ± 0.05 (Nguni). Analysis of molecular variance (AMOVA) showed high within-population variance (>80%) across all population categories. The first principal component (PC1) separated the Merino, South African Mutton Merino (SAMM), DM, and Afrino (AFR) from the Meatmaster, Damara, Nguni, and Ronderib Afrikaner (RDA). PC2 aligned each Merino-derived breed with its presumed ancestors and separated the SAMM from the Merino and SAM. The iHS analysis yielded selection sweeps across the AFR (12 sweeps), Meatmaster (four sweeps), and DM (29 sweeps). Hair/wool trait genes such as FGF12; metabolic genes of ICA1, NXPH1, and GPR171; and immune response genes of IL22, IL26, IFNAR1, and IL10RB were reported. Other genes include HMGA, which was observed as selection signatures in other populations; WNT5A, important in the development of the skeleton and mammary glands; ANTXR2, associated with adaptation to variation in climatic conditions; and BMP2, which has been reported as strongly selected in both fat-tailed and thin-tailed sheep. The DM vs. SAMM shared all six sweep regions on chromosomes 1, 10, and 11 with AFR vs. SAMM. Genes such as FGF12 on OAR 1:191.3–194.7 Mb and MAP2K4 on OAR 11:28.6–31.3 Mb were observed. The selection sweep on chromosome 10 region 28.6–30.3 Mb harbouring the RXFP2 for polledness was shared between the DM vs. Merino, the Meatmaster vs. Merino, and the Meatmaster vs. Nguni. The DM vs. Merino and the Meatmaster vs. Merino also shared an Rsb-based selection sweep on chromosome 1 region 268.5–269.9 Mb associated with the Calpain gene, CAPN7. The study demonstrated some genetic similarities between the Merino and Merino-derived breeds emanating from common founding populations and some divergence driven by breed-specific selection goals. Overall, information regarding the evolution of these composite breeds from their founding population will guide future breed improvement programs and management and conservation efforts.

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“…H ap FLK takes the number of cluster of haplotypes as a parameter (K). To determine the number of clusters of haplotypes K, we ran FASTPHASE v1.4 (Scheet & Stephens 2006) and R package IMPUTEQ (Khvorykh & Khrunin 2020) on polymorphism data for the largest chromosome BCIN01. For each population, we used IMPUTEQ to generate five datasets with 10% of polymorphic positions masked, and for each masked dataset we used FASTPHASE for imputing masked positions assuming clusters of K=2,3…10 haplotypes and the following parameters: -T10 -C25 -H-1 -n -Z.…”

Section: Methodsmentioning

confidence: 99%

Population Genomics Reveals Molecular Determinants of Specialization to Tomato in the Polyphagous Fungal PathogenBotrytis cinereain France

Mercier

Simon

Lapalu

et al. 2020

Preprint

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Many fungal plant pathogens encompass multiple populations specialized on different plant species. Understanding the factors underlying pathogen adaptation to their hosts is a major challenge of evolutionary microbiology, and it should help preventing the emergence of new specialized pathogens on novel hosts. Previous studies have shown that French populations of the grey mould pathogen Botrytis cinerea parasitizing tomato and grapevine are differentiated from each other, and have higher aggressiveness on their host-of-origin than on other hosts, indicating some degree of host specialization in this polyphagous pathogen. Here, we aimed at identifying the genomic features underlying the specialization of B. cinerea populations to tomato and grapevine. Based on whole genome sequences of 32 isolates, we confirmed the subdivision of B. cinerea pathogens into two genetic clusters on grapevine and another, single cluster on tomato. Levels of genetic variation in the different clusters were similar, suggesting that the tomato-specific cluster has not recently emerged following a bottleneck. Using genome scans for selective sweeps and divergent selection, tests of positive selection based on polymorphism and divergence at synonymous and non-synonymous sites and analyses of presence/absence variation, we identified several candidate genes that represent possible determinants of host specialization in the tomato-associated population. This work deepens our understanding of the genomic changes underlying the specialization of fungal pathogen populations.

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imputeqc: an R package for assessing imputation quality of genotypes and optimizing imputation parameters

Cited by 11 publications

References 18 publications

Integrative bioinformatics analysis of potential therapeutic targets and immune infiltration characteristics in dilated cardiomyopathy

Integrative bioinformatics analysis of potential therapeutic targets and immune infiltration characteristics in dilated cardiomyopathy

Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders

Population Genomics Reveals Molecular Determinants of Specialization to Tomato in the Polyphagous Fungal PathogenBotrytis cinereain France

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