Hélène Choquet, PhD

People

Kaiser Permanente Division of Research
2000 Broadway
Oakland, CA 94612

(510) 891-5972 (phone)
helene.choquet@kp.org

Hélène Choquet, PhD, is a Research Scientist II at the Kaiser Permanente Northern California Division of Research. Her research interests are in human genetics and genomics, with a focus on identifying genetic factors which influence complex traits, diseases and their treatments. Dr. Choquet received doctoral training in Human Genetics from the Lille 2 University of Health and Law in France. Prior to joining the faculty at the Division of Research, she was a Postdoctoral Research Fellow at the University of California, San Francisco (UCSF), where she received training in genetic epidemiology and statistical genetics and where she was a recipient of an American Heart Association award.

Dr. Choquet has broad expertise in Human Genetics, having worked on diverse complex traits and disorders, including obesity, alcohol and tobacco use, and brain vascular malformation. Dr. Choquet's research interests currently focus on the genetics of eye diseases, and the genetic factors underlying nonmelanoma skin cancers and other skin conditions. She is also interested in understanding the genetic mechanisms that drive the development of abdominal hernias.

Current Position(s):

Research Scientist II, Division of Research, Kaiser Permanente Northern California

Section Affiliations:

Behavioral Health and Aging

Primary Research Interests:

Genetic epidemiology and pharmacogenomics
Genetic factors influencing alcohol, and tobacco use
Genetics of vision disorders including myopia, refractive error, cataract, glaucoma, intraocular pressure, and response to treatments
Genetic determinants of metabolic diseases, including obesity and type 2 diabetes
Genetic epidemiology of cerebrovascular diseases
Genetics of hernia susceptibility
Genetic disparities among race/ethnicity in disease risk and treatment outcomes
Genetic epidemioilogy of nonmelanoma skin cancers

Related Website(s):

Research Program on Genes, Environment and Health

Studies

Prioritizing diversity in polygenic risk prediction of primary open-angle glaucoma

Primary open-angle glaucoma (POAG) is a leading cause of irreversible vision loss, yet much of the genetic risk remains unaccounted for, especially in African-Americans, who have a higher risk for developing POAG. This proposal aims to bring together the largest African-descent glaucoma datasets in the world to identify novel POAG loci that may be specific to people of African descent through both genome-wide association studies and admixture mapping. We will also develop and test ancestry-specific polygenic risk scores in African-descent populations.
Investigator: Choquet, Helene
Funder: National Eye Institute

The Role of Genetic and Non-Genetic Factors and Causal Mechanisms Underlying Cataract Susceptibility For Risk Prediction

Cataract is a leading cause of blindness and a major cause of impaired vision worldwide. The overall objective of this study is to better understand the role of genetic and non-genetic factors and causal mechanisms underlying the etiology of cataract and develop a prediction tool to facilitate risk-stratified screening for cataract. This study has 3 major aims: 1) to evaluate whether glaucoma, myopic refractive error, diabetes, high blood pressure, high BMI, cigarette smoking, or alcohol consumption, and other non-genetic factors are causal risk factors of cataract; 2) to develop risk prediction models of cataract susceptibility based on genetic and non-genetic risk factors; and 3) to determine the function (in the lens tissue) of novel candidate genes prioritized within genetic loci associated with cataract.
Investigator: Choquet, Helene
Funder: National Eye Institute

Genetic and non-genetic factors affecting weight loss variability after bariatric surgery

Bariatric surgery is currently the most effective long-term treatment for severe obesity. However, inter-individual variability in surgery outcomes has been observed, particularly in relation to postoperative weight loss. This study aims to assess the contribution of genetic and non-genetic factors to such inter-individual variability by leveraging a large and ethnically diverse cohort with longitudinal electronic health record data. Study findings could help to develop predictive risk scores for outcomes of bariatric surgery based on genetic information along with other demographic and clinical factors. In future clinical practice, predictive risk scores could help patients be realistic about the outcomes of bariatric surgery and guide treatment strategies for patients with severe obesity.
Investigator: Choquet, Helene
Funder: Northern California Community Benefit Programs

Identification of genetic loci and pathways underlying hidradenitis suppurativa risk

Hidradenitis suppurativa (also named: acne inversa) is a chronic inflammatory skin condition that causes painful lumps to form under the skin usually in areas where skin rubs together such as in the armpits, groin, buttocks and under breasts. The overall scientific objective of this study is to identify and validate genetic factors associated with the risk of hidradenitis suppurativa, with the long-term goal of uncovering new therapeutic targets.
Investigator: Choquet, Helene
Funder: National Institute of Arthritis and Musculoskeletal and Skin Diseases

The Role of Genetic Risk Factors in Keratinocyte Carcinoma Susceptibility

The goal of this proposal is to identify genetic loci that affect the risk of keratinocyte carcinoma, examine how environmental risk factors influence genetic risk, and determine whether these loci act to influence the risk of basal cell carcinoma, squamous cell carcinoma, or both.
Investigator: Choquet, Helene; Asgari, Maryam
Funder: National Cancer Institute

Genetic Etiology of Abdominal Hernia Susceptibility

The objective of this project is to investigate the genetic mechanisms that drive the development of abdominal hernias. This study has three major aims: 1) to investigate the shared and individual genetic risks of different types of abdominal hernia, 2) to examine the genetic risk factors underlying recurrence of hernias in individual patients, and 3) to investigate the genetic pathways and biological mechanisms through which abdominal hernia risk loci act.
Investigator: Choquet, Helene
Funder: National Institute of Diabetes and Digestive and Kidney Diseases

The Role of Refractive Error in the Etiology of Glaucoma

The specific aims of this study are to: 1) Determine whether refractive error predicts the development of glaucoma due to direct effects or shared etiology, or both, by conducting a series of genetic analyses of the two conditions; and 2) Determine the contribution of refractive error (myopia) and relevant biological pathways in the development of glaucomatous neurodegeneration.
Investigator: Choquet, Helene
Funder: National Eye Institute

Highlighted Publications

A large multiethnic GWAS meta-analysis of cataract identifies new risk loci and sex-specific effects

Author(s): Choquet, Hélène; Jorgenson, Eric; et al.

Nat Commun. 2021 06 14;12(1):3595. Epub 2021-06-14.

Current Position(s):

Section Affiliations:

Primary Research Interests:

Related Website(s):

Studies

Prioritizing diversity in polygenic risk prediction of primary open-angle glaucoma

The Role of Genetic and Non-Genetic Factors and Causal Mechanisms Underlying Cataract Susceptibility For Risk Prediction

Genetic and non-genetic factors affecting weight loss variability after bariatric surgery

Identification of genetic loci and pathways underlying hidradenitis suppurativa risk

The Role of Genetic Risk Factors in Keratinocyte Carcinoma Susceptibility

Genetic Etiology of Abdominal Hernia Susceptibility

The Role of Refractive Error in the Etiology of Glaucoma

Highlighted Publications

A large multiethnic GWAS meta-analysis of cataract identifies new risk loci and sex-specific effects

Meta-analysis of 542,934 subjects of European ancestry identifies new genes and mechanisms predisposing to refractive error and myopia

A multiethnic genome-wide association study of primary open-angle glaucoma identifies novel risk loci

A large multi-ethnic genome-wide association study identifies novel genetic loci for intraocular pressure

Publications

A new polygenic score for refractive error improves detection of children at risk of high myopia but not the prediction of those at risk of myopic macular degeneration

Genetically Predicted Serum Vitamin C Levels and Cutaneous Squamous Cell Carcinoma Risk

Genetic diversity fuels gene discovery for tobacco and alcohol use

Association Between Myopic Refractive Error and Primary Open-Angle Glaucoma: A 2-Sample Mendelian Randomization Study

Ancestry- and sex-specific effects underlying inguinal hernia susceptibility identified in a multiethnic genome-wide association study meta-analysis

GWAS identifies two common loci associated with pigment dispersion syndrome/pigmentary glaucoma and implicate myopia in its development

Genome-wide association study of actinic keratosis identifies new susceptibility loci implicated in pigmentation and immune regulation pathways

Whole genome sequence analysis of platelet traits in the NHLBI trans-omics for precision medicine initiative

Full title: A large-scale transcriptome-wide association study (TWAS) of 10 blood cell phenotypes reveals complexities of TWAS fine-mapping

Whole-genome sequencing in diverse subjects identifies genetic correlates of leukocyte traits: The NHLBI TOPMed program

GLIS1 regulates trabecular meshwork function and intraocular pressure and is associated with glaucoma in humans

New and sex-specific migraine susceptibility loci identified from a multiethnic genome-wide meta-analysis

Transcriptome-Wide Association Study of Blood Cell Traits in African Ancestry and Hispanic/Latino Populations

A large multiethnic GWAS meta-analysis of cataract identifies new risk loci and sex-specific effects

Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program

Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images

A multi-ethnic genome-wide association study implicates collagen matrix integrity and cell differentiation pathways in keratoconus

Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries

Cigarette smoking behaviors and the importance of ethnicity and genetic ancestry

Genetic ancestry, skin pigmentation, and the risk of cutaneous squamous cell carcinoma in Hispanic/Latino and non-Hispanic white populations

The Polygenic and Monogenic Basis of Blood Traits and Diseases

Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations

Meta-analysis of 26,638 Individuals Identifies Two Genetic Loci Associated with Left Ventricular Ejection Fraction

A multiethnic genome-wide analysis of 44,039 individuals identifies 41 new loci associated with central corneal thickness

Genetic and environmental factors underlying keratinocyte carcinoma risk

Meta-analysis of 542,934 subjects of European ancestry identifies new genes and mechanisms predisposing to refractive error and myopia

Functional validity, role, and implications of heavy alcohol consumption genetic loci

Clinical implications of recent advances in primary open-angle glaucoma genetics

Genome-wide Genotyping of Cerebral Cavernous Malformation Type 1 Individuals to Identify Genetic Modifiers of Disease Severity

Use of >100,000 NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium whole genome sequences improves imputation quality and detection of rare variant associations in admixed African and Hispanic/Latino populations

Contribution of rare coding mutations in CD36 to type 2 diabetes and cardio-metabolic complications

Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use

A Large Multi-ethnic Genome-Wide Association Study of Adult Body Mass Index Identifies Novel Loci

Common mitochondrial haplogroups and cutaneous squamous cell carcinoma risk

A multiethnic genome-wide association study of primary open-angle glaucoma identifies novel risk loci

A large multi-ethnic genome-wide association study identifies novel genetic loci for intraocular pressure

Genetic contributors to variation in alcohol consumption vary by race/ethnicity in a large multi-ethnic genome-wide association study

Cytochrome P450 and matrix metalloproteinase genetic modifiers of disease severity in Cerebral Cavernous Malformation type 1

Genetics of cerebral cavernous malformations: current status and future prospects

Association of cardiovascular risk factors with disease severity in cerebral cavernous malformation type 1 subjects with the common Hispanic mutation

Polymorphisms in inflammatory and immune response genes associated with cerebral cavernous malformation type 1 severity

Examination of rare missense variants in the CHRNA5-A3-B4 gene cluster to level of response to alcohol in the San Diego Sibling Pair study

​Genetic analysis of a population heavy drinking phenotype identifies risk variants in whites

Contribution of common PCSK1 genetic variants to obesity in 8,359 subjects from multi-ethnic American population

Gene-centric analysis of serum cotinine levels in African and European American populations

Dysfunction of lipid sensor GPR120 leads to obesity in both mouse and human

Heterozygous mutations causing partial prohormone convertase 1 deficiency contribute to human obesity

Genetic analysis of a population heavy drinking phenotype identifies risk variants in whites