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  1. Article: 10 Years of GWAS in intraocular pressure.

    Gao, Xiaoyi Raymond / Chiariglione, Marion / Choquet, Hélène / Arch, Alexander J

    Frontiers in genetics

    2023  Volume 14, Page(s) 1130106

    Abstract: Intraocular pressure (IOP) is the only modifiable risk factor for glaucoma, the leading cause of irreversible blindness worldwide. In this review, we summarize the findings of genome-wide association studies (GWASs) of IOP published in the past 10 years ... ...

    Abstract Intraocular pressure (IOP) is the only modifiable risk factor for glaucoma, the leading cause of irreversible blindness worldwide. In this review, we summarize the findings of genome-wide association studies (GWASs) of IOP published in the past 10 years and prior to December 2022. Over 190 genetic loci and candidate genes associated with IOP have been uncovered through GWASs, although most of these studies were conducted in subjects of European and Asian ancestries. We also discuss how these common variants have been used to derive polygenic risk scores for predicting IOP and glaucoma, and to infer causal relationship with other traits and conditions through Mendelian randomization. Additionally, we summarize the findings from a recent large-scale exome-wide association study (ExWAS) that identified rare variants associated with IOP in 40 novel genes, six of which are drug targets for clinical treatment or are being evaluated in clinical trials. Finally, we discuss the need for future genetic studies of IOP to include individuals from understudied populations, including Latinos and Africans, in order to fully characterize the genetic architecture of IOP.
    Language English
    Publishing date 2023-04-12
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2023.1130106
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Genome-wide Genotyping of Cerebral Cavernous Malformation Type 1 Individuals to Identify Genetic Modifiers of Disease Severity.

    Choquet, Hélène / Kim, Helen

    Methods in molecular biology (Clifton, N.J.)

    2020  Volume 2152, Page(s) 77–84

    Abstract: Familial cerebral cavernous malformation type 1 (CCM1) is an autosomal dominant disease caused by mutations in the Krev Interaction Trapped 1 (KRIT1/CCM1) gene, and characterized by brain lesions that can cause hemorrhagic strokes, seizures, and ... ...

    Abstract Familial cerebral cavernous malformation type 1 (CCM1) is an autosomal dominant disease caused by mutations in the Krev Interaction Trapped 1 (KRIT1/CCM1) gene, and characterized by brain lesions that can cause hemorrhagic strokes, seizures, and neurological deficits. Carriers of the same genetic mutation can present with variable symptoms and severity of disease, suggesting the influence of modifier factors. Genetic modifiers of CCM1 disease severity have been recently identified and included common genetic variants in inflammatory, immune response, and oxidative stress genes and pathways. Here, we describe the genotyping of CCM1 patients with the same gene mutation (Q455X) using a high-throughput genotyping array optimized for individuals of Hispanic/Latino ancestry. We then review the quality control steps following the genome-wide genotyping. Genome-wide genotyping of larger cohorts of CCM1 patients might reveal additional genetic variants contributing to the disease severity of CCM1.
    MeSH term(s) Alleles ; Genes, Modifier ; Genetic Predisposition to Disease ; Genome-Wide Association Study/methods ; Genotype ; Genotyping Techniques ; Hemangioma, Cavernous, Central Nervous System/diagnosis ; Hemangioma, Cavernous, Central Nervous System/genetics ; Humans ; Microtubule-Associated Proteins/genetics ; Mutation ; Severity of Illness Index
    Chemical Substances Microtubule-Associated Proteins
    Language English
    Publishing date 2020-06-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-0640-7_6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Multi-ancestry genome-wide meta-analysis identifies novel basal cell carcinoma loci and shared genetic effects with squamous cell carcinoma.

    Choquet, Hélène / Jiang, Chen / Yin, Jie / Kim, Yuhree / Hoffmann, Thomas J / Jorgenson, Eric / Asgari, Maryam M

    Communications biology

    2024  Volume 7, Issue 1, Page(s) 33

    Abstract: Basal cell carcinoma (BCC) is one of the most common malignancies worldwide, yet its genetic determinants are incompletely defined. We perform a European ancestry genome-wide association (GWA) meta-analysis and a Hispanic/Latino ancestry GWA meta- ... ...

    Abstract Basal cell carcinoma (BCC) is one of the most common malignancies worldwide, yet its genetic determinants are incompletely defined. We perform a European ancestry genome-wide association (GWA) meta-analysis and a Hispanic/Latino ancestry GWA meta-analysis and meta-analyze both in a multi-ancestry GWAS meta-analysis of BCC, totaling 50,531 BCC cases and 762,234 controls from four cohorts (GERA, Mass-General Brigham Biobank, UK Biobank, and 23andMe research cohort). Here we identify 122 BCC-associated loci, of which 36 were novel, and subsequently fine-mapped these associations. We also identify an association of the well-known pigment gene SLC45A2 as well as associations at RCC2 and CLPTM1L with BCC in Hispanic/Latinos. We examine these BCC loci for association with cutaneous squamous cell carcinoma (cSCC) in 16,407 SCC cases and 762,486 controls of European ancestry, and 33 SNPs show evidence of association. Our study findings provide important insights into the genetic basis of BCC and cSCC susceptibility.
    MeSH term(s) Humans ; Carcinoma, Squamous Cell/genetics ; Genome-Wide Association Study ; Skin Neoplasms/genetics ; Carcinoma, Basal Cell/genetics ; Polymorphism, Single Nucleotide
    Language English
    Publishing date 2024-01-05
    Publishing country England
    Document type Meta-Analysis ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-023-05753-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Cigarette smoking behaviors and the importance of ethnicity and genetic ancestry.

    Choquet, Hélène / Yin, Jie / Jorgenson, Eric

    Translational psychiatry

    2021  Volume 11, Issue 1, Page(s) 120

    Abstract: Cigarette smoking contributes to numerous diseases and is one of the leading causes of death in the United States. Smoking behaviors vary widely across race/ethnicity, but it is not clear why. Here, we examine the contribution of genetic ancestry to ... ...

    Abstract Cigarette smoking contributes to numerous diseases and is one of the leading causes of death in the United States. Smoking behaviors vary widely across race/ethnicity, but it is not clear why. Here, we examine the contribution of genetic ancestry to variation in two smoking-related traits in 43,485 individuals from four race/ethnicity groups (non-Hispanic white, Hispanic/Latino, East Asian, and African American) from a single U.S. healthcare plan. Smoking prevalence was the lowest among East Asians (22.7%) and the highest among non-Hispanic whites (38.5%). We observed significant associations between genetic ancestry and smoking-related traits. Within East Asians, we observed higher smoking prevalence with greater European (versus Asian) ancestry (P = 9.95 × 10
    MeSH term(s) African Americans/genetics ; Cigarette Smoking ; Ethnic Groups/genetics ; European Continental Ancestry Group/genetics ; Hispanic Americans/genetics ; Humans ; Prevalence ; United States/epidemiology
    Language English
    Publishing date 2021-02-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2609311-X
    ISSN 2158-3188 ; 2158-3188
    ISSN (online) 2158-3188
    ISSN 2158-3188
    DOI 10.1038/s41398-021-01244-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Genome-wide association study of actinic keratosis identifies new susceptibility loci implicated in pigmentation and immune regulation pathways.

    Kim, Yuhree / Yin, Jie / Huang, Hailiang / Jorgenson, Eric / Choquet, Hélène / Asgari, Maryam M

    Communications biology

    2022  Volume 5, Issue 1, Page(s) 386

    Abstract: Actinic keratosis (AK) is a common precancerous cutaneous neoplasm that arises on chronically sun-exposed skin. AK susceptibility has a moderate genetic component, and although a few susceptibility loci have been identified, including IRF4, TYR, and MC1R, ...

    Abstract Actinic keratosis (AK) is a common precancerous cutaneous neoplasm that arises on chronically sun-exposed skin. AK susceptibility has a moderate genetic component, and although a few susceptibility loci have been identified, including IRF4, TYR, and MC1R, additional loci have yet to be discovered. We conducted a genome-wide association study of AK in non-Hispanic white participants of the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort (n = 63,110, discovery cohort), with validation in the Mass-General Brigham (MGB) Biobank cohort (n = 29,130). We identified eleven loci (P < 5 × 10
    MeSH term(s) Adult ; Forkhead Transcription Factors/genetics ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Heterogeneous-Nuclear Ribonucleoprotein Group C/genetics ; Humans ; Keratosis, Actinic/genetics ; Polymorphism, Single Nucleotide ; Repressor Proteins/genetics ; Skin Neoplasms/genetics
    Chemical Substances FOXP1 protein, human ; Forkhead Transcription Factors ; Heterogeneous-Nuclear Ribonucleoprotein Group C ; RALY protein, human ; Repressor Proteins ; TRPS1 protein, human
    Language English
    Publishing date 2022-04-21
    Publishing country England
    Document type Journal Article ; Meta-Analysis ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-022-03301-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Association between lifetime smoking and cutaneous squamous cell carcinoma: A 2-sample Mendelian randomization study.

    Lee, Truelian / George, Christopher D / Jiang, Chen / Asgari, Maryam M / Nijsten, Tamar / Pardo, Luba M / Choquet, Hélène

    JAAD international

    2023  Volume 14, Page(s) 69–76

    Abstract: Background/purpose: Cutaneous squamous cell carcinoma (cSCC) is one of the most common malignancies worldwide. While several environmental risk factors for cSCC are well established, there is conflicting evidence on cigarette smoking (and its potential ... ...

    Abstract Background/purpose: Cutaneous squamous cell carcinoma (cSCC) is one of the most common malignancies worldwide. While several environmental risk factors for cSCC are well established, there is conflicting evidence on cigarette smoking (and its potential causal effect) and cSCC risk. Furthermore, it is unclear if these potential associations represent causal, modifiable risk factors for cSCC development. This study aims to assess the nature of the associations between cigarette smoking traits (smoking initiation, amount smoked, and lifetime smoking exposure) and cSCC risk using two-sample Mendelian randomization analyses.
    Methods: Genetic instruments, based on common genetic variants associated with cigarette smoking traits (
    Results: We found modest evidence that genetically determined lifetime smoking was associated with cSCC (inverse-variance weighted method: OR[95% CI] = 1.47[1.09-1.98];
    Conclusion: Study findings highlight the importance of smoking prevention and may support risk-stratified cSCC screening strategies based on carcinogen exposure and other genetic and clinical information.
    Language English
    Publishing date 2023-12-03
    Publishing country United States
    Document type Journal Article
    ISSN 2666-3287
    ISSN (online) 2666-3287
    DOI 10.1016/j.jdin.2023.11.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Transcriptome-wide association study identifies novel candidate susceptibility genes for migraine.

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

    HGG advances

    2023  Volume 4, Issue 3, Page(s) 100211

    Abstract: Genome-wide association studies (GWASs) have identified more than 130 genetic susceptibility loci for migraine; however, how most of these loci impact migraine development is unknown. To identify novel genes associated with migraine and interpret the ... ...

    Abstract Genome-wide association studies (GWASs) have identified more than 130 genetic susceptibility loci for migraine; however, how most of these loci impact migraine development is unknown. To identify novel genes associated with migraine and interpret the transcriptional products of those genes, we conducted a transcriptome-wide association study (TWAS). We performed tissue-specific and multi-tissue TWAS analyses to assess associations between imputed gene expression from 53 tissues and migraine susceptibility using FUSION software. Meta-analyzed GWAS summary statistics from 26,052 migraine cases and 487,214 controls, all of European ancestry and from two cohorts (the Kaiser Permanente GERA and the UK Biobank), were used. We evaluated the associations for genes after conditioning on variant-level effects from GWAS, and we tested for colocalization of GWAS migraine-associated loci and expression quantitative trait loci (eQTLs). Across tissue-specific and multi-tissue analyses, we identified 53 genes for which genetically predicted gene expression was associated with migraine after correcting for multiple testing. Of these 53 genes, 10 (
    MeSH term(s) Humans ; Transcriptome/genetics ; Genetic Predisposition to Disease/genetics ; Genome-Wide Association Study ; Quantitative Trait Loci/genetics ; Migraine Disorders/genetics ; Membrane Proteins/genetics ; DNA Glycosylases/genetics ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; DNA Repair Enzymes/genetics
    Chemical Substances KTN1 protein, human ; Membrane Proteins ; NEIL1 protein, human (EC 3.2.2.-) ; DNA Glycosylases (EC 3.2.2.-) ; PNKP protein, human (EC 2.7.1.-) ; Phosphotransferases (Alcohol Group Acceptor) (EC 2.7.1.-) ; DNA Repair Enzymes (EC 6.5.1.-)
    Language English
    Publishing date 2023-06-09
    Publishing country United States
    Document type Journal Article
    ISSN 2666-2477
    ISSN (online) 2666-2477
    DOI 10.1016/j.xhgg.2023.100211
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Genome-wide association study of actinic keratosis identifies new susceptibility loci implicated in pigmentation and immune regulation pathways

    Yuhree Kim / Jie Yin / Hailiang Huang / Eric Jorgenson / Hélène Choquet / Maryam M. Asgari

    Communications Biology, Vol 5, Iss 1, Pp 1-

    2022  Volume 9

    Abstract: A study on actinic keratosis identifies multiple loci showing genome-wide significant association with implicated genes within biological pathways for pigmentation, immune regulation, and extracellular matrix homeostasis. ...

    Abstract A study on actinic keratosis identifies multiple loci showing genome-wide significant association with implicated genes within biological pathways for pigmentation, immune regulation, and extracellular matrix homeostasis.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Clinical implications of recent advances in primary open-angle glaucoma genetics.

    Choquet, Hélène / Wiggs, Janey L / Khawaja, Anthony P

    Eye (London, England)

    2019  Volume 34, Issue 1, Page(s) 29–39

    Abstract: Over the last decade, genetic studies, including genome-wide association studies (GWAS), have accelerated the discovery of genes and genomic regions contributing to primary open-angle glaucoma (POAG), a leading cause of irreversible vision loss. Here, we ...

    Abstract Over the last decade, genetic studies, including genome-wide association studies (GWAS), have accelerated the discovery of genes and genomic regions contributing to primary open-angle glaucoma (POAG), a leading cause of irreversible vision loss. Here, we review the findings of genetic studies of POAG published in English prior to September 2019. In total, 74 genomic regions have been associated at a genome-wide level of significance with POAG susceptibility. Recent POAG GWAS provide not only insight into global and ethnic-specific genetic risk factors for POAG susceptibility across populations of diverse ancestry, but also important functional insights underlying biological mechanisms of glaucoma pathogenesis. In this review, we also summarize the genetic overlap between POAG, glaucoma endophenotypes, such as intraocular pressure and vertical cup-disc ratio (VCDR), and other eye disorders. We also discuss approaches recently developed to increase power for POAG locus discovery and to predict POAG risk. Finally, we discuss the recent development of POAG gene-based therapies and future strategies to treat glaucoma effectively. Understanding the genetic architecture of POAG is essential for an earlier diagnosis of this common eye disorder, predictive testing of at-risk patients, and design of gene-based targeted medical therapies none of which are currently available.
    MeSH term(s) Genome-Wide Association Study ; Glaucoma ; Glaucoma, Open-Angle/diagnosis ; Glaucoma, Open-Angle/genetics ; Humans ; Intraocular Pressure ; Tonometry, Ocular
    Language English
    Publishing date 2019-10-23
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 91001-6
    ISSN 1476-5454 ; 0950-222X
    ISSN (online) 1476-5454
    ISSN 0950-222X
    DOI 10.1038/s41433-019-0632-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Multi-ancestry genome-wide meta-analysis identifies novel basal cell carcinoma loci and shared genetic effects with squamous cell carcinoma

    Hélène Choquet / Chen Jiang / Jie Yin / Yuhree Kim / Thomas J. Hoffmann / 23andMe Research Team / Eric Jorgenson / Maryam M. Asgari

    Communications Biology, Vol 7, Iss 1, Pp 1-

    2024  Volume 10

    Abstract: Abstract Basal cell carcinoma (BCC) is one of the most common malignancies worldwide, yet its genetic determinants are incompletely defined. We perform a European ancestry genome-wide association (GWA) meta-analysis and a Hispanic/Latino ancestry GWA ... ...

    Abstract Abstract Basal cell carcinoma (BCC) is one of the most common malignancies worldwide, yet its genetic determinants are incompletely defined. We perform a European ancestry genome-wide association (GWA) meta-analysis and a Hispanic/Latino ancestry GWA meta-analysis and meta-analyze both in a multi-ancestry GWAS meta-analysis of BCC, totaling 50,531 BCC cases and 762,234 controls from four cohorts (GERA, Mass-General Brigham Biobank, UK Biobank, and 23andMe research cohort). Here we identify 122 BCC-associated loci, of which 36 were novel, and subsequently fine-mapped these associations. We also identify an association of the well-known pigment gene SLC45A2 as well as associations at RCC2 and CLPTM1L with BCC in Hispanic/Latinos. We examine these BCC loci for association with cutaneous squamous cell carcinoma (cSCC) in 16,407 SCC cases and 762,486 controls of European ancestry, and 33 SNPs show evidence of association. Our study findings provide important insights into the genetic basis of BCC and cSCC susceptibility.
    Keywords Biology (General) ; QH301-705.5
    Subject code 616
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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