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Open AccessStatistical Learning of Large-Scale Genetic Data: How to Run a Genome-Wide Association Study of Gene-Expression Data Using the 1000 Genomes Project Data
Teaching statistics through engaging applications to contemporary large-scale datasets is essential to attracting students to the field. To this end, we developed a hands-on, week-long workshop for senior high...
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Open AccessAuthor Correction: GWAS for the composite traits of hematuria and albuminuria
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Open AccessA genome-wide association, polygenic risk score and sex study on opioid use disorder treatment outcomes
Opioid use disorder continues to be a health concern with a high rate of opioid related deaths occurring worldwide. Medication Assisted Treatments (MAT) have been shown to reduce opioid withdrawal, cravings an...
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Article
Open AccessGWAS for the composite traits of hematuria and albuminuria
Our GWAS of hematuria in the UK Biobank identified 6 loci, some of which overlap with loci for albuminuria suggesting pleiotropy. Since clinical syndromes are often defined by combinations of traits, generatin...
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Article
Open AccessGenome-wide association study identifies novel loci associated with skin autofluorescence in individuals without diabetes
Skin autofluorescence (SAF) is a non-invasive measure reflecting accumulation of advanced glycation endproducts (AGEs) in the skin. Higher SAF levels are associated with an increased risk of develo** type 2 ...
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Article
Open AccessIntegrating variant functional annotation scores have varied abilities to improve power of genome-wide association studies
Functional annotations have the potential to increase power of genome-wide association studies (GWAS) by prioritizing variants according to their biological function, but this potential has not been well studi...
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Article
Population-based studies reveal an additive role of type IV collagen variants in hematuria and albuminuria
Specific variants in genes that encode the α3α4α5 chains of type IV collagen cause Alport syndrome (AS), which encompass a clinical spectrum from isolated hematuria to multisystem disease affecting sight, hear...
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Genetic Anticipation: Fact or Artifact, Genetics or Epigenetics?
F. Clarke Fraser in his Aug 16 commentary.
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Open AccessLAMA2 and LOXL4 are candidate FSGS genes
Focal and segmental glomerulosclerosis (FSGS) is a histologic pattern of injury that characterizes a wide spectrum of diseases. Many genetic causes have been identified in FSGS but even in families with compre...
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Article
Open AccessGenome-wide association study of pediatric obsessive-compulsive traits: shared genetic risk between traits and disorder
Using a novel trait-based measure, we examined genetic variants associated with obsessive-compulsive (OC) traits and tested whether OC traits and obsessive-compulsive disorder (OCD) shared genetic risk. We con...
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Large-scale association analyses identify host factors influencing human gut microbiome composition
To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microb...
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Open AccessSkin autofluorescence predicts new cardiovascular disease and mortality in people with type 2 diabetes
Skin autofluorescence (SAF) is a non-invasive marker of tissue accumulation of advanced glycation endproducts (AGE). Recently, we demonstrated in the general population that elevated SAF levels predict the dev...
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Article
Open AccessStatistical power in COVID-19 case-control host genomic study design
The identification of genetic variation that directly impacts infection susceptibility to SARS-CoV-2 and disease severity of COVID-19 is an important step towards risk stratification, personalized treatment pl...
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Article
Open AccessAssociations of NOD2 polymorphisms with Erysipelotrichaceae in stool of in healthy first degree relatives of Crohn’s disease subjects
Genetic analyses have identified many variants associated with the risk of inflammatory bowel disease (IBD) development. Among these variants, the ones located within the NOD2 gene have the highest odds ratio of ...
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Article
DNA methylation mediates development of HbA1c-associated complications in type 1 diabetes
Metabolic memory, the persistent benefits of early glycaemic control on preventing and/or delaying the development of diabetic complications, has been observed in the Diabetes Control and Complications Trial (...
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Open AccessDNA methylation age calculators reveal association with diabetic neuropathy in type 1 diabetes
Many CpGs become hyper or hypo-methylated with age. Multiple methods have been developed by Horvath et al. to estimate DNA methylation (DNAm) age including Pan-tissue, Skin & Blood, PhenoAge, and GrimAge. Pan-...
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Association of IGF1 and VEGFA polymorphisms with diabetic retinopathy in Pakistani population
The incidence of microvascular complications, including diabetic retinopathy (DR), increases with duration of type 2 diabetes (T2D). Meta-GWAS have reported numerous single-nucleotide polymorphisms (SNPs) asso...
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Article
Phenotypic and genetic analysis of an adult cohort with extreme obesity
Adult extreme obesity (EO) is a growing health concern. The prevalence of known obesity associated co-morbidities namely cardio-metabolic and neuro-psychiatric disease in EO is not fully established. The contr...
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Open AccessSkin autofluorescence predicts incident type 2 diabetes, cardiovascular disease and mortality in the general population
Earlier studies have shown that skin autofluorescence measured with an AGE reader estimates the accumulation of AGEs in the skin, which increases with ageing and is associated with the metabolic syndrome and t...
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Article
Open AccessEvidence of batch effects masking treatment effect in GAW20 methylation data
Using the real data set from GAW20, we examined changes in the distribution of DNA methylation before and after treatment. Paired analysis of differences in both mean and variance had grossly inflated type 1 e...
