Ani Manichaikul
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View article: Prediction of Polygenic Risks by Screening Thousands of Polygenic Scores
Prediction of Polygenic Risks by Screening Thousands of Polygenic Scores Open
Rationale: A polygenic score (PGS) summarizes the genetic information of a person in a single number for a trait, and its utility in genomic medicine is well-recognized. Although PGS models have been generated for many traits, they are not…
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
View article: Genetic mapping of complement system proteins for islet autoimmunity in children with high risk of T1D
Genetic mapping of complement system proteins for islet autoimmunity in children with high risk of T1D Open
View article: Associations of Immune Cell Subsets With Coronary Artery Calcium Incidence and Progression in the Multi‐Ethnic Study of Atherosclerosis
Associations of Immune Cell Subsets With Coronary Artery Calcium Incidence and Progression in the Multi‐Ethnic Study of Atherosclerosis Open
Background Limited data exist on associations of immune cell subsets with longitudinal changes in subclinical coronary artery disease. Methods In the MESA (Multi‐Ethnic Study of Atherosclerosis) study, we used a case‐cohort approach to exp…
View article: Whole genome sequence analysis of low-density lipoprotein cholesterol across 246 K individuals
Whole genome sequence analysis of low-density lipoprotein cholesterol across 246 K individuals Open
This study provides a meta-analysis framework for large-scale whole genome sequence association analyses from diverse population groups, yielding novel rare non-coding variant associations.
View article: Multi-Trait Polygenic Scores for COPD and COPD Exacerbations Implicate Druggable Proteins
Multi-Trait Polygenic Scores for COPD and COPD Exacerbations Implicate Druggable Proteins Open
Objectives. To construct multi-trait polygenic scores (PRS) predicting chronic obstructive pulmonary disease (COPD) and exacerbations, validate their performance in diverse cohorts, and identify PRS-related proteins for potential therapeut…
View article: Mosaic Loss of Y chromosome associates with lung function, emphysema and epigenetic aging
Mosaic Loss of Y chromosome associates with lung function, emphysema and epigenetic aging Open
Mosaic loss of Y chromosome (mLOY) in blood cells is an age-related somatic mutation, but its relationship with pulmonary health remains undercharacterized. Leveraging mLOY assessment in over 12,000 men, including 5,097 from the COPDGene S…
View article: Proteomic discovery analysis of quantitatively assessed emphysema in the general population. The MESA Lung Study
Proteomic discovery analysis of quantitatively assessed emphysema in the general population. The MESA Lung Study Open
Background Pulmonary emphysema occurs frequently in older adults, often without airflow limitation. Its presence predicts symptoms, respiratory hospitalizations and deaths, and all-cause mortality. Proteomics may provide further insights i…
View article: Multi-ancestry genome-wide association analyses incorporating SNP-by-psychosocial interactions identify novel loci for serum lipids
Multi-ancestry genome-wide association analyses incorporating SNP-by-psychosocial interactions identify novel loci for serum lipids Open
View article: Associations of interstitial lung disease subtype and CT pattern with lung function and survival
Associations of interstitial lung disease subtype and CT pattern with lung function and survival Open
Background Prior work suggests different interstitial lung diseases (ILDs) that share the radiological usual interstitial pneumonia (UIP) pattern have an overall worse prognosis. However, epidemiological data with longitudinal sampling and…
View article: Single-cell elderly blood–CSF atlas implicates peripherally influenced immune dysregulation in normal pressure hydrocephalus
Single-cell elderly blood–CSF atlas implicates peripherally influenced immune dysregulation in normal pressure hydrocephalus Open
We have generated a single-cell RNA sequencing atlas of peripheral blood and ventricular CSF in idiopathic normal pressure hydrocephalus (iNPH) patients totaling 140,207 single-cell transcriptomes. We found proinflammatory alterations in p…
View article: cellSTAAR: Incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of non-coding regions
cellSTAAR: Incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of non-coding regions Open
Whole genome sequencing (WGS) studies have identified hundreds of millions of rare variants (RVs) and have enabled RV association tests (RVATs) of these variants with complex traits and diseases. Analysis of non-coding variants is challeng…
View article: Trans-ancestry Mendelian Randomization Discovers Novel Causal Genes for Autoimmune Disease Traits
Trans-ancestry Mendelian Randomization Discovers Novel Causal Genes for Autoimmune Disease Traits Open
Mendelian randomization (MR) using summary statistics from genome-wide association studies (GWAS) has become a powerful tool for dissecting the causal relationships between exposure and outcomes. As GWAS begins to incorporate samples of di…
View article: Associations of albuminuria with interstitial lung abnormalities in older community-dwelling adults confounded by age
Associations of albuminuria with interstitial lung abnormalities in older community-dwelling adults confounded by age Open
In two population-based cohorts, we did not find an independent relationship between albuminuria and ILA, with age emerging as a key confounding factor. Our results suggest there may be a common systemic pathology of aging that underlies a…
View article: Sex Differences in Chronic Obstructive Pulmonary Disease: Implications for Pathogenesis, Diagnosis, and Treatment
Sex Differences in Chronic Obstructive Pulmonary Disease: Implications for Pathogenesis, Diagnosis, and Treatment Open
Chronic obstructive pulmonary disease (COPD) is a leading chronic disease worldwide, with significant healthcare utilization, morbidity, and mortality. Irreversible airflow obstruction identified on spirometry establishes the diagnosis of …
View article: Cross-cohort analysis of expression and splicing quantitative trait loci in TOPMed
Cross-cohort analysis of expression and splicing quantitative trait loci in TOPMed Open
Most genetic variants associated with complex traits and diseases occur in non-coding genomic regions and are hypothesized to regulate gene expression. To understand the genetics underlying gene expression variability, we characterize 14,3…
View article: Type 2 diabetes polygenic risk score demonstrates context-dependent effects and associations with type 2 diabetes-related risk factors and complications across diverse populations
Type 2 diabetes polygenic risk score demonstrates context-dependent effects and associations with type 2 diabetes-related risk factors and complications across diverse populations Open
Polygenic risk scores (PRS) hold prognostic value for identifying individuals at higher risk of type 2 diabetes (T2D). However, further characterization is needed to understand the generalizability of T2D PRS in diverse populations across …
View article: Cross-Ancestry Comparison of Aptamer and Antibody Proteomics Measures
Cross-Ancestry Comparison of Aptamer and Antibody Proteomics Measures Open
Measures from affinity-proteomics platforms often correlate poorly, challenging interpretation of protein associations with genetic variants (pQTL) and phenotypes. Here, we examined 2,157 proteins measured on both SomaScan 7k and Olink Exp…
View article: Genome-wide mapping of complement system proteins for islet autoimmunity in the DAISY and TEDDY children
Genome-wide mapping of complement system proteins for islet autoimmunity in the DAISY and TEDDY children Open
Background Type 1 diabetes (T1D) is characterized by the autoimmune destruction of the insulin-producing beta cells, and there is no cure yet for the disease. While islet autoantibodies are well-recognized biomarkers that mark the onset of…
View article: Soluble Immune Checkpoint Protein and Lipid Network Associations with All-Cause Mortality Risk: Trans-Omics for Precision Medicine (TOPMed) Program
Soluble Immune Checkpoint Protein and Lipid Network Associations with All-Cause Mortality Risk: Trans-Omics for Precision Medicine (TOPMed) Program Open
Adverse cardiovascular events are emerging with the use of immune checkpoint therapies in oncology. Using datasets in the Trans-Omics for Precision Medicine program (Multi-Ethnic Study of Atherosclerosis, Jackson Heart Study [JHS], and Fra…
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: Proteome-wide association studies for blood lipids and comparison with transcriptome-wide association studies
Proteome-wide association studies for blood lipids and comparison with transcriptome-wide association studies Open
View article: Genetics of Latin American Diversity Project: Insights into population genetics and association studies in admixed groups in the Americas
Genetics of Latin American Diversity Project: Insights into population genetics and association studies in admixed groups in the Americas Open
Latin Americans are underrepresented in genetic studies, increasing disparities in personalized genomic medicine. Despite available genetic data from thousands of Latin Americans, accessing and navigating the bureaucratic hurdles for conse…
View article: Whole Genome Sequence Analysis of Pulmonary Function and COPD in 44,287 Multi-ancestry Participants
Whole Genome Sequence Analysis of Pulmonary Function and COPD in 44,287 Multi-ancestry Participants Open
Background Whole genome sequence (WGS) data in multi-ancestry samples provide the opportunity to identify low-frequency or population-specific genetic variants associated with chronic obstructive pulmonary disease (COPD) and lung function.…
View article: Genetics of Latin American Diversity Project: Insights into population genetics and association studies in admixed groups in the Americas
Genetics of Latin American Diversity Project: Insights into population genetics and association studies in admixed groups in the Americas Open
View article: Proteogenomic analysis integrated with electronic health records data reveals disease-associated variants in Black Americans
Proteogenomic analysis integrated with electronic health records data reveals disease-associated variants in Black Americans Open
BACKGROUNDMost GWAS of plasma proteomics have focused on White individuals of European ancestry, limiting biological insight from other ancestry-enriched protein quantitative loci (pQTL).METHODSWe conducted a discovery GWAS of approximatel…
View article: Data from Predicted proteome association studies of breast, prostate, ovarian, and endometrial cancers implicate plasma protein regulation in cancer susceptibility
Data from Predicted proteome association studies of breast, prostate, ovarian, and endometrial cancers implicate plasma protein regulation in cancer susceptibility Open
Background: Predicting protein levels from genotypes for proteome-wide association studies (PWAS) may provide insight to the mechanisms underlying cancer susceptibility. Methods: We performed PWAS of breast, endometrial, ovarian, and prost…
View article: Supplementary Figure S1 from Predicted proteome association studies of breast, prostate, ovarian, and endometrial cancers implicate plasma protein regulation in cancer susceptibility
Supplementary Figure S1 from Predicted proteome association studies of breast, prostate, ovarian, and endometrial cancers implicate plasma protein regulation in cancer susceptibility Open
Supplementary Figure S1: Workflow illustrating the methods.
View article: Table S4 from Predicted proteome association studies of breast, prostate, ovarian, and endometrial cancers implicate plasma protein regulation in cancer susceptibility
Table S4 from Predicted proteome association studies of breast, prostate, ovarian, and endometrial cancers implicate plasma protein regulation in cancer susceptibility Open
Table S4. PWAS meta-FDR<0.05 proteins with endometrial cancer associations.
View article: Table S2 from Predicted proteome association studies of breast, prostate, ovarian, and endometrial cancers implicate plasma protein regulation in cancer susceptibility
Table S2 from Predicted proteome association studies of breast, prostate, ovarian, and endometrial cancers implicate plasma protein regulation in cancer susceptibility Open
Table S2. Replication of cancer PWAS results in independent cohort with meta-analysis FDR<0.05.