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Hélène Choquet, PhD

Hélène  Choquet, PhD

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 Positions

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

Section Affiliations

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 Websites


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


Transcriptome-wide association study identifies novel candidate susceptibility genes for migraine

Authors: Meyers, Travis J;Yin, Jie;Herrera, Victor A;Pressman, Alice R;Hoffmann, Thomas J;Schaefer, Catherine;Avins, Andrew L;Choquet, Hélène

HGG Adv. 2023 Jul 13;4(3):100211. Epub 2023-06-09.

PubMed abstract

Association of Behavioral and Clinical Risk Factors With Cataract: A Two-Sample Mendelian Randomization Study

Authors: Jiang, Chen;Melles, Ronald B;Sangani, Poorab;Hoffmann, Thomas J;Hysi, Pirro G;Glymour, M Maria;Jorgenson, Eric;Lachke, Salil A;Choquet, Hélène

Invest Ophthalmol Vis Sci. 2023 Jul 03;64(10):19.

PubMed abstract

Large-scale multitrait genome-wide association analyses identify hundreds of glaucoma risk loci

Authors: Han, Xikun;Jorgenson, Eric;MacGregor, Stuart;et al.

Nat Genet. 2023 Jul;55(7):1116-1125. Epub 2023-06-29.

PubMed abstract

Multi-ancestry GWAS of Fuchs corneal dystrophy highlights roles of laminins, collagen, and endothelial cell regulation

Authors: Peachey, Neal;Hysi, Pirro;Iyengar, Sudha;et al.

Res Sq. 2023 May 03.

PubMed abstract

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

Authors: Clark, Rosie;Williams, Cathy;UK Biobank Eye and Vision Consortium,;et al.

EBioMedicine. 2023 May;91:104551. Epub 2023-04-11.

PubMed abstract

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

Authors: Kim, Yuhree; Yin, Jie; Le Breton, Stephen; Jorgenson, Eric; Huang, Hailiang; Choquet, Hélène; Asgari, Maryam M

J Invest Dermatol. 2023 Apr;143(4):664-667. Epub 2022-11-05.

PubMed abstract

A multiethnic genome-wide analysis of 19,420 individuals identifies novel loci associated with axial length and shared genetic influences with refractive error and myopia

Authors: Jiang, Chen;Jorgenson, Eric;Choquet, Hélène;et al.

Front Genet. 2023;14:1113058. Epub 2023-06-07.

PubMed abstract

10 Years of GWAS in intraocular pressure

Authors: Gao, Xiaoyi Raymond;Chiariglione, Marion;Choquet, Hélène;Arch, Alexander J

Front Genet. 2023;14:1130106. Epub 2023-04-12.

PubMed abstract

Genetic diversity fuels gene discovery for tobacco and alcohol use

Authors: Saunders, Gretchen R B; Choquet, Hélène; Vrieze, Scott; et al.

Nature. 2022 Dec;612(7941):720-724. Epub 2022-12-07.

PubMed abstract

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

Authors: Choquet, Hélène; Khawaja, Anthony P; Jiang, Chen; Yin, Jie; Melles, Ronald B; Glymour, M Maria; Hysi, Pirro G; Jorgenson, Eric

JAMA Ophthalmol. 2022 Sep 01;140(9):864-871.

PubMed abstract

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

Authors: Choquet, Hélène; Li, Weiyu; Yin, Jie; Bradley, Rachael; Hoffmann, Thomas J; Nandakumar, Priyanka; 23andMe Research Team,; Mostaedi, Rouzbeh; Tian, Chao; Ahituv, Nadav; Jorgenson, Eric

Hum Mol Genet. 2022 07 07;31(13):2279-2293.

PubMed abstract

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

Authors: Simcoe, Mark J; Choquet, Hélène; Hammond, Christopher J; et al.

Ophthalmology. 2022 06;129(6):626-636. Epub 2022-01-11.

PubMed abstract

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

Authors: Kim, Yuhree; Yin, Jie; Huang, Hailiang; Jorgenson, Eric; Choquet, Hélène; Asgari, Maryam M

Commun Biol. 2022 Apr 21;5(1):386. Epub 2022-04-21.

PubMed abstract

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

Authors: Little, Amarise; Correa, Adolfo; Raffield, Laura M; et al.

Hum Mol Genet. 2022 02 03;31(3):347-361.

PubMed abstract

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

Authors: Tapia, Amanda L; Choquet, Hélène; Raffield, Laura M; et al.

Genet Epidemiol. 2022 02;46(1):3-16. Epub 2021-11-15.

PubMed abstract

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

Authors: Mikhaylova, Anna V; Choquet, Hélène; Auer, Paul L; et al.

Am J Hum Genet. 2021 10 07;108(10):1836-1851. Epub 2021-09-27.

PubMed abstract

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

Authors: Nair, K Saidas; Choquet, H�l�ne; Jetten, Anton M; et al.

Nat Commun. 2021 08 12;12(1):4877. Epub 2021-08-12.

PubMed abstract

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

Authors: Choquet, Hélène; Yin, Jie; Jacobson, Alice S; Horton, Brandon H; Hoffmann, Thomas J; Jorgenson, Eric; Avins, Andrew L; Pressman, Alice R

Commun Biol. 2021 07 22;4(1):864. Epub 2021-07-22.

PubMed abstract

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

Authors: Wen, Jia; Fornage, Myriam; Li, Yun; et al.

Genes (Basel). 2021 07 08;12(7). Epub 2021-07-08.

PubMed abstract

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

Authors: Choquet, Hélène; Jorgenson, Eric; et al.

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

PubMed abstract

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

Authors: Hu, Yao; Choquet, Hélène; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium,; et al.

Am J Hum Genet. 2021 05 06;108(5):874-893. Epub 2021-04-21.

PubMed abstract

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

Authors: Currant, Hannah; Choquet, Hélène; Khawaja, Anthony P; et al.

PLoS Genet. 2021 05;17(5):e1009497. Epub 2021-05-12.

PubMed abstract

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

Authors: Hardcastle, Alison J; Choquet, Hélène; Hysi, Pirro G; et al.

Commun Biol. 2021 03 01;4(1):266. Epub 2021-03-01.

PubMed abstract

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

Authors: Gharahkhani, Puya; Qassim, Ayub; Wiggs, Janey L; et al.

Nat Commun. 2021 02 24;12(1):1258. Epub 2021-02-24.

PubMed abstract

Cigarette smoking behaviors and the importance of ethnicity and genetic ancestry

Authors: Choquet, Hélène; Yin, Jie; Jorgenson, Eric

Transl Psychiatry. 2021 02 11;11(1):120. Epub 2021-02-11.

PubMed abstract

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

Authors: Jorgenson, Eric; Choquet, Hélène; Yin, Jie; Hoffmann, Thomas J; Banda, Yambazi; Kvale, Mark N; Risch, Neil; Schaefer, Catherine; Asgari, Maryam M

Commun Biol. 2020 12 14;3(1):765. Epub 2020-12-14.

PubMed abstract

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

Authors: Chen, Ming-Huei; Choquet, Hélène; Lettre, Guillaume; et al.

Cell. 2020 09 03;182(5):1198-1213.e14.

PubMed abstract

The Polygenic and Monogenic Basis of Blood Traits and Diseases

Authors: Vuckovic, Dragana; Danesh, John; Soranzo, Nicole; et al.

Cell. 2020 09 03;182(5):1214-1231.e11.

PubMed abstract

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

Authors: Choquet H; Thai KK; Jiang C; Ranatunga DK; Hoffmann TJ; Go AS; Lindsay AC; Ehm MG; Waterworth DM; Risch N; Schaefer C

Circ Genom Precis Med. 2020 08;13(4):e002804. Epub 2020-06-30.

PubMed abstract

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

Authors: Choquet H; Schaefer C; Risch N; Jorgenson E; et al.

Commun Biol. 2020 06 11;3(1):301. Epub 2020-06-11.

PubMed abstract

Genetic and environmental factors underlying keratinocyte carcinoma risk

Authors: Choquet H; Ashrafzadeh S; Kim Y; Asgari MM; Jorgenson E

JCI Insight. 2020 05 21;5(10). Epub 2020-05-21.

PubMed abstract

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

Authors: Hysi PG; Khawaja AP; Hammond CJ; et al.

Nat Genet. 2020 04;52(4):401-407. Epub 2020-03-30.

PubMed abstract

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

Authors: Thompson A; Cook J; Choquet H; Jorgenson E; Yin J; Kinnunen T; Barclay J; Morris AP; Pirmohamed M

Sci Adv. 2020 Jan;6(3):eaay5034. Epub 2020-01-15.

PubMed abstract

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

Authors: Choquet H; Kim H

Methods Mol Biol. 2020;2152:77-84.

PubMed abstract

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

Authors: Choquet H; Wiggs JL; Khawaja AP

Eye (Lond). 2020 01;34(1):29-39. Epub 2019-10-23.

PubMed abstract

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

Authors: Kowalski MH; Choquet H; Li Y; et al.

PLoS Genet. 2019 12;15(12):e1008500. Epub 2019-12-23.

PubMed abstract

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

Authors: Meyre D; Choquet H; Linton KJ; et al.

Sci Rep. 2019 11 20;9(1):17123. Epub 2019-11-20.

PubMed abstract

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

Authors: Liu M; Choquet H; Weisner C; Vrieze S; et al.

Nat Genet. 2019 02;51(2):237-244. Epub 2019-01-14.

PubMed abstract

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

Authors: Hoffmann TJ; Choquet H; Yin J; Banda Y; Kvale MN; Glymour M; Schaefer C; Risch N; Jorgenson E

Genetics. 2018 10;210(2):499-515. Epub 2018-08-14.

PubMed abstract

Common mitochondrial haplogroups and cutaneous squamous cell carcinoma risk

Authors: Jorgenson E; Choquet H; Yin J; Asgari MM

Cancer Epidemiol Biomarkers Prev. 2018 07;27(7):838-841. Epub 2018-04-25.

PubMed abstract

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

Authors: Choquet H; Schaefer C; Risch N; Jorgenson E; et al.

Nat Commun. 2018 06 11;9(1):2278. Epub 2018-06-11.

PubMed abstract

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

Authors: Choquet H; Thai KK; Yin J; Hoffmann TJ; Kvale MN; Banda Y; Schaefer C; Risch N; Nair KS; Melles R; Jorgenson E

Nat Commun. 2017 Dec 13;8(1):2108. Epub 2017-12-13.

PubMed abstract

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

Authors: Jorgenson E; Thai KK; Hoffmann TJ; Sakoda LC; Kvale MN; Banda Y; Schaefer C; Risch N; Mertens J; Weisner C; Choquet H

Mol Psychiatry. 2017 Sep;22(9):1359-1367. Epub 2017-05-09.

PubMed abstract

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

Authors: Choquet H; Trapani E; Goitre L; Trabalzini L; Akers A; Fontanella M; Hart BL; Morrison LA; Pawlikowska L; Kim H; Retta SF

Free Radic Biol Med. 2016 Mar;92:100-9. doi: 10.1016/j.freeradbiomed.2016.01.008. Epub 2016 Jan 19.

PubMed abstract

Genetics of cerebral cavernous malformations: current status and future prospects

Authors: Choquet H; Pawlikowska L; Lawton MT; Kim H.

J Neurosurg Sci. 2015 Sep;59(3):211-20. Epub 2015 Apr 22.

PubMed abstract

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

Authors: Choquet H; Pawlikowska L; Nelson J; McCulloch CE; Akers A; Baca B; Khan Y; Hart B; Morrison L; Kim H; Brain Vascular Malformation Consortium (BVMC) Study

Cerebrovasc Dis. 2014;38(6):433-40. doi: 10.1159/000369200. Epub 2014 Dec 3.

PubMed abstract

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

Authors: Choquet H; Nelson J; Pawlikowska L; McCulloch CE; Akers A; Baca B; Khan Y; Hart B; Morrison L; Kim H.

Cerebrovasc Dis. 2014;37(1):57-63. doi: 10.1159/000356839. Epub 2013 Dec 21.

PubMed abstract

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

Authors: Choquet H; Joslyn G; Lee A; Kasberger J; Robertson M; Brush G; Schuckit MA; White R; Jorgenson E

Alcohol Clin Exp Res. 2013 Aug;37(8):1311-6. doi: 10.1111/acer.12099. Epub 2013 Mar 4.

PubMed abstract

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

Authors: Hamidovic A; Goodloe RJ; Young TR; Styn MA; Mukamal KJ; Choquet H; Kasberger JL; Buxbaum SG; Papanicolaou GJ; White W; Volcik K; Spring B; Hitsman B; Levy D; Jorgenson E.;

​J Clin Psychopharmacol. 2013 Apr;33(2):206-10. doi: 10.1097/JCP.0b013e318287009a.

PubMed abstract

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

Authors: Choquet H; Kasberger J; Hamidovic A; Jorgenson E

PLoS One. 2013;8(2):e57857. doi: 10.1371/journal.pone.0057857. Epub 2013 Feb 25.

PubMed abstract

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

Authors: Hamidovic A; Goodloe RJ; Bergen AW; Benowitz NL; Styn MA; Kasberger JL; Choquet H; Young TR; Meng Y; Palmer C; Pletcher M; Kertesz S; Hitsman B; Spring B; Jorgenson E

Neuropsychopharmacology. 2012 Mar;37(4):968-74. doi: 10.1038/npp.2011.280. Epub 2011 Nov 16.

PubMed abstract

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

Authors: Ichimura A; Hirasawa A; Poulain-Godefroy O; Bonnefond A; Hara T; Yengo L; Kimura I; Leloire A; Liu N; Iida K; Choquet H; Besnard P; Lecoeur C; Vivequin S; Ayukawa K; Takeuchi M; Ozawa K; Tauber M; Maffeis C; Morandi A; Buzzetti R; Elliott P; Pouta A; Jarvelin MR; Körner A; Kiess W; Pigeyre M; Caiazzo R; Van Hul W; Van Gaal L; Horber F; Balkau B; Lévy-Marchal C; Rouskas K; Kouvatsi A; Hebebrand J; Hinney A; Scherag A; Pattou F; Meyre D; Koshimizu TA; Wolowczuk I; Tsujimoto G; Froguel P

Nature. 2012 Feb 19;483(7389):350-4. doi: 10.1038/nature10798.

PubMed abstract

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

Authors: Creemers JW; Choquet H; Stijnen P; Vatin V; Pigeyre M; Beckers S; Meulemans S; Than ME; Yengo L; Tauber M; Balkau B; Elliott P; Jarvelin MR; Van Hul W; Van Gaal L; Horber F; Pattou F; Froguel P; Meyre D

Diabetes. 2012 Feb;61(2):383-90. doi: 10.2337/db11-0305. Epub 2011 Dec 30.

PubMed abstract

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