LDpop: an interactive online tool to calculate and visualize geographic LD patterns

Alexander, Theresa A; Machiela, Mitchell J.

doi:10.1186/s12859-020-3340-1

Cited by 59 publications

(46 citation statements)

References 7 publications

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“…Manhattan plots were used to plot p -values for all SNP associations across chromosomes, and regional association plots (Locus Zoom) [ 87 ] were used to provide detail on genetic regions of interest, providing gene annotations and pairwise correlations between the surrounding SNPs and the SNP of interest. Additionally, Ldlink [ 88 , 89 ], a suite of web-based applications, was used to efficiently interrogate linkage disequilibrium (LD) for SNPs.…”

Section: Methodsmentioning

confidence: 99%

Genetic Variations and Health-Related Quality of Life (HRQOL): A Genome-Wide Study Approach

Adjei

Lopez

Schaid

et al. 2021

Cancers

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Health-related quality of life (HRQOL) is an important prognostic patient-reported outcome in oncology. Because prior studies suggest that HRQOL is, in part, heritable, we performed a GWAS to elucidate genetic factors associated with HRQOL in breast cancer survivors. Physical and mental HRQOL were measured via paper surveys that included the PROMIS-10 physical and mental health domain scales in 1442 breast cancer survivors participating in the Mayo Clinic Breast Disease Registry (MCBDR). In multivariable regression analyses, age and financial concerns were significantly associated with global physical health (age: p = 1.6 × 10−23; financial concerns: p = 4.8 × 10−40) and mental health (age: p = 3.5 × 10−7; financial concerns: p = 2.0 × 10−69). Chemotherapy was associated with worse global mental health (p = 0.01). In the GWAS, none of the SNPs reached the genome-wide association significance threshold of 5 × 10−8 for associations with either global physical or global mental health, however, a cluster of SNPs in SCN10A, particularly rs112718371, appeared to be linked to worse global physical health (p = 5.21 × 10−8). Additionally, SNPs in LMX1B, SGCD, PARP12 and SEMA5A were also moderately associated with worse physical and mental health (p < 10−6). These biologically plausible candidate SNPs warrant further study as possible predictors of HRQOL.

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Section: Methodsmentioning

confidence: 99%

Genetic Variations and Health-Related Quality of Life (HRQOL): A Genome-Wide Study Approach

Adjei

Lopez

Schaid

et al. 2021

Cancers

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“…Of note, Shrine et al 68 have discovered 279 lung functions signals in the meta-analysis of UK Biobank and the SpiroMeta Consortium. We looked up the nearest GWAS hits to the eQTL, and calculated LD between the variants in the African and European populations using LDpop 69 web tool.…”

Section: Methodsmentioning

confidence: 99%

Genetic and non-genetic factors affecting the expression of COVID-19 relevant genes in the large airway epithelium

Kasela

Ortega

Martorella

et al. 2020

Preprint

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Particular host and environmental factors influence susceptibility to severe COVID-19. We analyzed RNA-sequencing data from bronchial epithelial brushings - a relevant tissue for SARS-CoV-2 infection - obtained from three cohorts of uninfected individuals, and investigated how non-genetic and genetic factors affect the regulation of host genes implicated in COVID-19. We found that ACE2 expression was higher in relation to active smoking, obesity, and hypertension that are known risk factors of COVID-19 severity, while an association with interferon-related inflammation was driven by the truncated, non-binding ACE2 isoform. We discovered that expression patterns of a suppressed airway immune response to early SARS-CoV-2 infection, compared to other viruses, are similar to patterns associated with obesity, hypertension, and cardiovascular disease, which may thus contribute to a COVID-19-susceptible airway environment. eQTL mapping identified regulatory variants for genes implicated in COVID-19, some of which had pheWAS evidence for their potential role in respiratory infections. These data provide evidence that clinically relevant variation in the expression of COVID-19-related genes is associated with host factors, environmental exposures, and likely host genetic variation.

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“…One SNP on chromosome 11 (rs10769096), two SNPs on the X chromosome (rs4969675 and rs73538805), and 11 SNPs located within the same intergenic 2q22 chromosome region (a gene desert) had p -values < 1.0 × 10 −6 . Using LDlink [ 59 , 60 ], a suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups, all of the chromosome 2 SNPs were determined to be in strong linkage disequilibrium (LD) (r 2 = 0.913–1.0 and D’ = 0.977–1.0), as observed from the Caucasian population. D’ (D prime) values range from 0 to 1 with higher values indicating tight linkage of alleles.…”

Section: Resultsmentioning

confidence: 99%

“…Two SNPs on chromosome 5 and eight other SNPs on chromosome 12 were also associated with CIPN at a marginal significance level of p < 1.0 × 10 −6 . In the Caucasian population, all the chromosome 12 SNPs ( Table 6 ) were found to be in strong LD with one another (r 2 and D’ = 1) [ 59 , 60 ]. SNP positions on chromosomes were based on the GRCh37 (Genome Reference Consortium Human Build 37) assembly in National Center for Biotechnology Information (NCBI).…”

Section: Resultsmentioning

confidence: 99%

Genetic Predictors of Chemotherapy-Induced Peripheral Neuropathy from Paclitaxel, Carboplatin and Oxaliplatin: NCCTG/Alliance N08C1, N08CA and N08CB Study

Adjei

Lopez

Schaid

et al. 2021

Cancers

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Chemotherapy-induced peripheral neuropathy (CIPN) is a common and potentially permanent adverse effect of chemotherapeutic agents including taxanes such as paclitaxel and platinum-based compounds such as oxaliplatin and carboplatin. Previous studies have suggested that genetics may impact the risk of CIPN. We conducted genome-wide association studies (GWASs) for CIPN in two independent populations who had completed European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ)-CIPN20 assessments (a CIPN-specific 20-item questionnaire which includes three scales that evaluate sensory, autonomic, and motor symptoms). The study population N08Cx included 692 participants from three clinical trials (North Central Cancer Treatment Group (NCCTG) N08C1, N08CA, and N08CB) who had been treated with paclitaxel, paclitaxel plus carboplatin, or oxaliplatin. The primary endpoint for the GWAS was the change from pre-chemotherapy CIPN20 sensory score to the worse score over the following 18 weeks. Study population The Mayo Clinic Breast Disease Registry (MCBDR) consisted of 381 Mayo Clinic Breast Disease Registry enrollees who had been treated with taxane or platinum-based chemotherapy. The primary endpoint for the GWAS assessed was the earliest CIPN20 sensory score available after the completion of chemotherapy. In multivariate model analyses, chemotherapy regimen (p = 3.0 × 10−8) and genetic ancestry (p = 0.007) were significantly associated with CIPN in the N08Cx population. Only age (p = 0.0004) was significantly associated with CIPN in the MCBDR population. The SNP most associated with CIPN was rs56360211 near PDE6C (p =7.92 × 10−8) in N08Cx and rs113807868 near TMEM150C in the MCBDR (p = 1.27 × 10−8). Due to a lack of replication, we cannot conclude that we identified any genetic predictors of CIPN.

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LDpop: an interactive online tool to calculate and visualize geographic LD patterns

Cited by 59 publications

References 7 publications

Genetic Variations and Health-Related Quality of Life (HRQOL): A Genome-Wide Study Approach

Genetic Variations and Health-Related Quality of Life (HRQOL): A Genome-Wide Study Approach

Genetic and non-genetic factors affecting the expression of COVID-19 relevant genes in the large airway epithelium

Genetic Predictors of Chemotherapy-Induced Peripheral Neuropathy from Paclitaxel, Carboplatin and Oxaliplatin: NCCTG/Alliance N08C1, N08CA and N08CB Study

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