Christopher R. Gignoux
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View article: Genetic underpinnings of the heterogeneous impact of obesity on lipid levels and cardiovascular disease
Genetic underpinnings of the heterogeneous impact of obesity on lipid levels and cardiovascular disease Open
Background Obesity is thought to increase cardiovascular disease (CVD) risk partly through dyslipidemia. Yet, obesity’s effects on dyslipidemia are not uniform. Understanding the shared genetic basis between obesity and lipid traits can pr…
View article: Genome-wide association study provides novel insight into the genetic architecture of severe obesity
Genome-wide association study provides novel insight into the genetic architecture of severe obesity Open
Severe obesity (SevO) is a primary driver of cardiovascular diseases (CVD), cardiometabolic diseases (CMD) and several cancers, with a disproportionate impact on marginalized populations. SevO is an understudied global health disease, limi…
View article: Genetic underpinnings of the heterogeneous impact of obesity on lipid levels and cardiovascular disease
Genetic underpinnings of the heterogeneous impact of obesity on lipid levels and cardiovascular disease Open
Background Obesity is thought to increase cardiovascular disease (CVD) risk partly through dyslipidemia. Yet, obesity’s effects on dyslipidemia are not uniform. Understanding the shared genetic basis between obesity and lipid traits can pr…
View article: Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin analyses
Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin analyses Open
View article: Polygenic risk score for type 2 diabetes shows context-dependent effects across populations
Polygenic risk score for type 2 diabetes shows context-dependent effects across populations Open
Polygenic risk scores hold prognostic value for identifying individuals at higher risk of type 2 diabetes. However, further characterization is needed to understand the generalizability of type 2 diabetes polygenic risk scores in diverse p…
View article: Genome-wide association study provides novel insight into the genetic architecture of severe obesity
Genome-wide association study provides novel insight into the genetic architecture of severe obesity Open
Severe obesity (SevO) is a primary driver of cardiovascular diseases (CVD), cardiometabolic diseases (CMD) and several cancers, with a disproportionate impact on marginalized populations. SevO is an understudied global health disease, limi…
View article: Present-day admixed genomes reveal prehistoric adaptation to cold, maritime diet, and local pathogens in Patagonia
Present-day admixed genomes reveal prehistoric adaptation to cold, maritime diet, and local pathogens in Patagonia Open
Patagonia, the last region settled by humans after the out-of-Africa migration, provides a unique case for studying genetic adaptations to extreme environments. Despite archaeological evidence of human occupation for at least 13,500 years,…
View article: Modeling the genomic architecture of adiposity and anthropometrics across the lifespan
Modeling the genomic architecture of adiposity and anthropometrics across the lifespan Open
Obesity-related conditions are among the leading causes of preventable death and are increasing in prevalence worldwide. Body size and composition are complex traits that are challenging to characterize due to environmental and genetic inf…
View article: Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin analyses
Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin analyses Open
Haplotype phasing, the process of determining which genetic variants are physically located on the same chromosome, is crucial for genetic analyses. Here, we benchmark SHAPEIT and Beagle, two state-of-the-art phasing methods, on two large …
View article: Enabling reproducible type 1 diabetes polygenic risk scoring for clinical and translational applications
Enabling reproducible type 1 diabetes polygenic risk scoring for clinical and translational applications Open
Objective Type 1 diabetes polygenic risk scores (PRS) offer a promising tool for identifying diabetes subtypes in adults with new-onset disease. We aimed to develop a pipeline for the clinical translation of type 1 diabetes PRS to support …
View article: Demographic Factors, Attitudes, and Pre-Existing Conditions Impacting COVID-19 Vaccine Hesitancy
Demographic Factors, Attitudes, and Pre-Existing Conditions Impacting COVID-19 Vaccine Hesitancy Open
We aimed to understand factors that distinguish vaccine hesitancy from early uptake or refusal to inform public health strategies for the next emergent infectious disease pandemic and clinician-patient communication around vaccine decision…
View article: SPC: a SPectral Component approach leveraging Identity-by-Descent graphs to address recent population structure in genomic analysis
SPC: a SPectral Component approach leveraging Identity-by-Descent graphs to address recent population structure in genomic analysis Open
Population structure is a well-known confounder in statistical genetics, particularly in genome-wide association studies (GWAS), where it can lead to inflated test statistics and spurious associations. Traditional methods, such as principa…
View article: A rapid accurate approach to inferring pedigrees in endogamous populations
A rapid accurate approach to inferring pedigrees in endogamous populations Open
Accurate reconstruction of pedigrees from genetic data remains a challenging problem. Many relationship categories (e.g. half-sibships vs avuncular) can be difficult to distinguish without external information. Pedigree inference algorithm…
View article: Genetic drivers of etiologic heterogeneity in thyroid cancer
Genetic drivers of etiologic heterogeneity in thyroid cancer Open
Thyroid cancer is the most common endocrine malignancy, yet its biological underpinnings remain incompletely understood. We conducted a multi-ancestry genome-wide association study meta-analysis of thyroid cancer (16,167 cases and 2,430,37…
View article: Global multi-ancestry genetic study elucidates genes and biological pathways associated with thyroid cancer and benign thyroid diseases
Global multi-ancestry genetic study elucidates genes and biological pathways associated with thyroid cancer and benign thyroid diseases Open
Thyroid diseases are common and highly heritable. Under the Global Biobank Meta-analysis Initiative, we performed a meta-analysis of genome-wide association studies from 19 biobanks for five thyroid diseases: thyroid cancer, benign nodular…
View article: Alterations in DNA Methylation, Proteomic, and Metabolomic Profiles in African Ancestry Populations with APOL1 Risk Alleles
Alterations in DNA Methylation, Proteomic, and Metabolomic Profiles in African Ancestry Populations with APOL1 Risk Alleles Open
Key Points We aimed to elucidate potential methylation, proteomic, and metabolomic mechanisms by which APOL1 variants may be linked to kidney disease. We report distinct methylation profiling between APOL1 risk allele carriers and noncarri…
View article: Can AI reveal the next generation of high-impact bone genomics targets?
Can AI reveal the next generation of high-impact bone genomics targets? Open
Genetic studies have revealed hundreds of loci associated with bone-related phenotypes, including bone mineral density (BMD) and fracture risk. However, translating discovered loci into effective new therapies remains challenging. We revie…
View article: Prediction and Characterization of Genetically Regulated Expression of Target Tissues in Asthma
Prediction and Characterization of Genetically Regulated Expression of Target Tissues in Asthma Open
Background Genetic control of gene expression in asthma-related tissues is not well-characterized, particularly for African-ancestry populations, limiting advancement in our understanding of the increased prevalence and severity of asthma …
View article: Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants Open
Kidney dysfunction is a major cause of mortality, but its genetic architecture remains elusive. In this study, we conducted a multiancestry genome-wide association study in 2.2 million individuals and identified 1026 (97 previously unknown…
View article: Pharmacogenomics of the Etonogestrel Contraceptive Implant
Pharmacogenomics of the Etonogestrel Contraceptive Implant Open
OBJECTIVE: To identify novel genetic loci associated with differences in serum etonogestrel concentrations among contraceptive implant users. METHODS: We conducted a cross-sectional analysis in which we enrolled healthy, reproductive-aged …
View article: Epigenome-wide association study meta-analysis of BMI in African American Adults
Epigenome-wide association study meta-analysis of BMI in African American Adults Open
Despite considerable advances in identifying risk factors for obesity development, there remains substantial gaps in our knowledge about its etiology. Variation in obesity (defined by BMI) is thought to be due in part to heritable factors;…
View article: Characterizing substructure via mixture modeling in large-scale genetic summary statistics
Characterizing substructure via mixture modeling in large-scale genetic summary statistics Open
View article: Multi-Ancestry Transcriptome Prediction with Functionally Informed Variants in TOPMed MESA Improves Performance of Transcriptome-Wide Association Studies
Multi-Ancestry Transcriptome Prediction with Functionally Informed Variants in TOPMed MESA Improves Performance of Transcriptome-Wide Association Studies Open
View article: Prevalence of the major thyroid cancer-associated syndromes in the United States
Prevalence of the major thyroid cancer-associated syndromes in the United States Open
Importance A subset of thyroid cancers develops in a setting of a known hereditary cancerassociated syndrome. Understanding the population prevalence of thyroid cancer-associated syndromes is important to guide germline genetic testing and…
View article: Uncovering hidden gene-trait patterns through biclustering analysis of the UK Biobank
Uncovering hidden gene-trait patterns through biclustering analysis of the UK Biobank Open
The growing availability of genome-wide association studies (GWAS) and large-scale biobanks provides an unprecedented opportunity to explore the genetic basis of complex traits and diseases. However, with this vast amount of data comes the…
View article: MUSSEL: Enhanced Bayesian polygenic risk prediction leveraging information across multiple ancestry groups
MUSSEL: Enhanced Bayesian polygenic risk prediction leveraging information across multiple ancestry groups Open
View article: Improving GWAS performance in underrepresented groups by appropriate modeling of genetics, environment, and sociocultural factors
Improving GWAS performance in underrepresented groups by appropriate modeling of genetics, environment, and sociocultural factors Open
Genome-wide association studies (GWAS) and polygenic score (PGS) development are typically constrained by the data available in biobank repositories in which European cohorts are vastly overrepresented. Here, we increase the utility of non…
View article: CCAFE: Estimating Case and Control Allele Frequencies from GWAS Summary Statistics
CCAFE: Estimating Case and Control Allele Frequencies from GWAS Summary Statistics Open
Methods involving summary statistics in genetics can be quite powerful but can be limited in utility. For instance, many post-hoc analyses of disease studies require case and control allele frequencies (AFs), which are not always published…
View article: Identification of proteins associated with type 2 diabetes risk in diverse racial and ethnic populations
Identification of proteins associated with type 2 diabetes risk in diverse racial and ethnic populations Open
View article: Modeling the genomic architecture of adiposity and anthropometrics across the lifespan
Modeling the genomic architecture of adiposity and anthropometrics across the lifespan Open
Obesity-related conditions are among the leading causes of preventable death and are increasing in prevalence worldwide. Body size and composition are complex traits that are challenging to characterize due to environmental and genetic inf…