1
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Yu M, Shang Y, Han L, Yu X. Bowel Habits, Obesity, Intestinal Microbiota and Their Influence on Hemorrhoidal Disease: a Mendelian Randomization Study. Clin Exp Gastroenterol 2024; 17:157-164. [PMID: 38745764 PMCID: PMC11093121 DOI: 10.2147/ceg.s450807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/12/2024] [Indexed: 05/16/2024] Open
Abstract
Purpose Hemorrhoids (HEM) are the most common perianal disease, but current observational studies have yielded inconsistent results in investigating the risk factors. Our further exploration of the risk factors will help prevent the disease. Patients and Methods We conducted a two-sample bidirectional Mendelian randomization (MR) analysis using publicly available genome-wide association studies (GWAS) statistics from multiple consortia. The inverse-variance weighted (IVW) method was used for the primary analysis. We applied four complementary methods, including weighted median, weighted mode, MR-Egger regression, and Cochrane's Q value, to detect and correct the effects of horizontal pleiotropy. Results Genetically determined constipation (OR = 0.97, 95% CI: 0.91-1.03, P = 0.28) and diarrhea (OR = 1.00, 95% CI: 0.99-1.01, P = 0.90) did not have a causal effect on HEM but stool frequency (OR = 1.28, 95% CI: 1.05-1.55, P = 0.01), waist-to-hip ratio adjusted for BMI (OR = 1.11, 95% CI: 1.06-1.64, P = 1.59×10-5), and order Burkholderiales (OR = 1.09, 95% CI = 1.04-1.14, p = 1.63×10-4) had a causal effect on. Furthermore, we found a significant causal effect of constipation on HEM in the reverse MR analysis (OR = 1.21, 95% CI: 1.13-1.28, P = 3.72×10-9). The results of MR-Egger regression, Weighted Median, and Weighted Mode methods were consistent with those of the IVW method. Horizontal pleiotropy was unlikely to distort the causal estimates, as indicated by the sensitivity analysis. Conclusion Our MR analysis reveals a causal association between stool frequency and waist-to-hip ratio with HEM, despite variations in results reported by observational studies. Unexpectedly, we found a relationship between the order Burkholderiales in the gut flora and HEM, although the mechanism is unclear.
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Affiliation(s)
- Miaozhi Yu
- Department of General Surgery, Xinhua Hospital Affiliated to Dalian University, Dalian, 116011, People’s Republic of China
| | - Yuan Shang
- Department of General Surgery, Xinhua Hospital Affiliated to Dalian University, Dalian, 116011, People’s Republic of China
| | - Lingling Han
- Department of General Surgery, Xinhua Hospital Affiliated to Dalian University, Dalian, 116011, People’s Republic of China
| | - Xi Yu
- Department of General Surgery, Xinhua Hospital Affiliated to Dalian University, Dalian, 116011, People’s Republic of China
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2
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Randolph HE, Aracena KA, Lin YL, Mu Z, Barreiro LB. Shaping immunity: The influence of natural selection on population immune diversity. Immunol Rev 2024; 323:227-240. [PMID: 38577999 DOI: 10.1111/imr.13329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Humans exhibit considerable variability in their immune responses to the same immune challenges. Such variation is widespread and affects individual and population-level susceptibility to infectious diseases and immune disorders. Although the factors influencing immune response diversity are partially understood, what mechanisms lead to the wide range of immune traits in healthy individuals remain largely unexplained. Here, we discuss the role that natural selection has played in driving phenotypic differences in immune responses across populations and present-day susceptibility to immune-related disorders. Further, we touch on future directions in the field of immunogenomics, highlighting the value of expanding this work to human populations globally, the utility of modeling the immune response as a dynamic process, and the importance of considering the potential polygenic nature of natural selection. Identifying loci acted upon by evolution may further pinpoint variants critically involved in disease etiology, and designing studies to capture these effects will enrich our understanding of the genetic contributions to immunity and immune dysregulation.
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Affiliation(s)
- Haley E Randolph
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Yen-Lung Lin
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Zepeng Mu
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Luis B Barreiro
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
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3
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Momin MM, Zhou X, Hyppönen E, Benyamin B, Lee SH. Cross-ancestry genetic architecture and prediction for cholesterol traits. Hum Genet 2024; 143:635-648. [PMID: 38536467 DOI: 10.1007/s00439-024-02660-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/13/2024] [Indexed: 05/18/2024]
Abstract
While cholesterol is essential, a high level of cholesterol is associated with the risk of cardiovascular diseases. Genome-wide association studies (GWASs) have proven successful in identifying genetic variants that are linked to cholesterol levels, predominantly in white European populations. However, the extent to which genetic effects on cholesterol vary across different ancestries remains largely unexplored. Here, we estimate cross-ancestry genetic correlation to address questions on how genetic effects are shared across ancestries. We find significant genetic heterogeneity between ancestries for cholesterol traits. Furthermore, we demonstrate that single nucleotide polymorphisms (SNPs) with concordant effects across ancestries for cholesterol are more frequently found in regulatory regions compared to other genomic regions. Indeed, the positive genetic covariance between ancestries is mostly driven by the effects of the concordant SNPs, whereas the genetic heterogeneity is attributed to the discordant SNPs. We also show that the predictive ability of the concordant SNPs is significantly higher than the discordant SNPs in the cross-ancestry polygenic prediction. The list of concordant SNPs for cholesterol is available in GWAS Catalog. These findings have relevance for the understanding of shared genetic architecture across ancestries, contributing to the development of clinical strategies for polygenic prediction of cholesterol in cross-ancestral settings.
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Affiliation(s)
- Md Moksedul Momin
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA, 5000, Australia.
- UniSA Allied Health and Human Performance, University of South Australia, Adelaide, SA, 5000, Australia.
- Department of Genetics and Animal Breeding, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University (CVASU), Khulshi, Chattogram, 4225, Bangladesh.
- South Australian Health and Medical Research Institute (SAHMRI), University of South Australia, Adelaide, SA, 5000, Australia.
| | - Xuan Zhou
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA, 5000, Australia
- UniSA Allied Health and Human Performance, University of South Australia, Adelaide, SA, 5000, Australia
- South Australian Health and Medical Research Institute (SAHMRI), University of South Australia, Adelaide, SA, 5000, Australia
| | - Elina Hyppönen
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA, 5000, Australia
- South Australian Health and Medical Research Institute (SAHMRI), University of South Australia, Adelaide, SA, 5000, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Beben Benyamin
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA, 5000, Australia
- UniSA Allied Health and Human Performance, University of South Australia, Adelaide, SA, 5000, Australia
- South Australian Health and Medical Research Institute (SAHMRI), University of South Australia, Adelaide, SA, 5000, Australia
| | - S Hong Lee
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA, 5000, Australia.
- UniSA Allied Health and Human Performance, University of South Australia, Adelaide, SA, 5000, Australia.
- South Australian Health and Medical Research Institute (SAHMRI), University of South Australia, Adelaide, SA, 5000, Australia.
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4
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Pan H, Feng C, Zhou Z, Huang J, Deng J, Zhou Y, Wang Y, Mu X, Wang Q, Wang K, Lu Z. The causal association between artificial sweeteners and the risk of cancer: a Mendelian randomization study. Food Funct 2024; 15:4527-4537. [PMID: 38576413 DOI: 10.1039/d3fo05756a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Artificial sweeteners (ASs) have been widely added to food and beverages because of their properties of low calories and sweet taste. However, whether the consumption of ASs is causally associated with cancer risk is not clear. Here, we utilized the two-sample Mendelian randomization (MR) method to study the potential causal association. Genetic variants like single-nucleotide polymorphisms (SNPs) associated with exposure (AS consumption) were extracted from a genome-wide association study (GWAS) database including 64 949 Europeans and the influence of confounding was removed. The outcome was from 98 GWAS data and included several types of cancers like lung cancer, colorectal cancer, stomach cancer, breast cancer, and so on. The exposure-outcome SNPs were harmonized and then MR analysis was performed. The inverse-variance weighted (IVW) with random effects was used as the main analytical method accompanied by four complementary methods: MR Egger, weighted median, simple mode, and weighted mode. Sensitivity analyses consisted of heterogeneity, pleiotropy, and leave-one-out analysis. Our results demonstrated that ASs added to coffee had a positive association with high-grade and low-grade serous ovarian cancer; ASs added to tea had a positive association with oral cavity and pharyngeal cancers, but a negative association with malignant neoplasm of the bronchus and lungs. No other cancers had a genetic causal association with AS consumption. Our MR study revealed that AS consumption had no genetic causal association with major cancers. Larger MR studies or RCTs are needed to investigate small effects and support this conclusion.
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Affiliation(s)
- Haotian Pan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Chenchen Feng
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Ziting Zhou
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jiamin Huang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jiasi Deng
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yuanyuan Zhou
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yuxuan Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xinru Mu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qian Wang
- School of International Education, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ke Wang
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Zhigang Lu
- School of Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Jiangsu Collaborative Innovation Center ofTraditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing 210023, China
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5
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Opsahl JO, Fragoso-Bargas N, Lee Y, Carlsen EØ, Lekanova N, Qvigstad E, Sletner L, Jenum AK, Lee-Ødegård S, Prasad RB, Birkeland KI, Moen GH, Sommer C. Epigenome-wide association study of DNA methylation in maternal blood leukocytes with BMI in pregnancy and gestational weight gain. Int J Obes (Lond) 2024; 48:584-593. [PMID: 38219005 PMCID: PMC10978488 DOI: 10.1038/s41366-024-01458-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 12/17/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024]
Abstract
OBJECTIVES We aimed to discover CpG sites with differential DNA methylation in peripheral blood leukocytes associated with body mass index (BMI) in pregnancy and gestational weight gain (GWG) in women of European and South Asian ancestry. Furthermore, we aimed to investigate how the identified sites were associated with methylation quantitative trait loci, gene ontology, and cardiometabolic parameters. METHODS In the Epigenetics in pregnancy (EPIPREG) sample we quantified maternal DNA methylation in peripheral blood leukocytes in gestational week 28 with Illumina's MethylationEPIC BeadChip. In women with European (n = 303) and South Asian (n = 164) ancestry, we performed an epigenome-wide association study of BMI in gestational week 28 and GWG between gestational weeks 15 and 28 using a meta-analysis approach. Replication was performed in the Norwegian Mother, Father, and Child Cohort Study, the Study of Assisted Reproductive Technologies (MoBa-START) (n = 877, mainly European/Norwegian). RESULTS We identified one CpG site significantly associated with GWG (p 5.8 × 10-8) and five CpG sites associated with BMI at gestational week 28 (p from 4.0 × 10-8 to 2.1 × 10-10). Of these, we were able to replicate three in MoBa-START; cg02786370, cg19758958 and cg10472537. Two sites are located in genes previously associated with blood pressure and BMI. DNA methylation at the three replicated CpG sites were associated with levels of blood pressure, lipids and glucose in EPIPREG (p from 1.2 × 10-8 to 0.04). CONCLUSIONS We identified five CpG sites associated with BMI at gestational week 28, and one with GWG. Three of the sites were replicated in an independent cohort. Several genetic variants were associated with DNA methylation at cg02786379 and cg16733643 suggesting a genetic component influencing differential methylation. The identified CpG sites were associated with cardiometabolic traits. CLINICALTRIALS GOV REGISTRATION NO Not applicable.
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Affiliation(s)
- J O Opsahl
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - N Fragoso-Bargas
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
| | - Y Lee
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - E Ø Carlsen
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - N Lekanova
- Department of Biosciences, The Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - E Qvigstad
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
| | - L Sletner
- Department of Pediatric and Adolescents Medicine, Akershus University Hospital, Lørenskog, Norway
| | - A K Jenum
- General Practice Research Unit, Department of General Practice, Institute of Health and Society, University of Oslo, Oslo, Norway
| | - S Lee-Ødegård
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - R B Prasad
- Lund University Diabetes Centre, Malmö, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - K I Birkeland
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - G-H Moen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Institute of Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - C Sommer
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway.
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6
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Chappell E, Arbour L, Laksman Z. The Inclusion of Underrepresented Populations in Cardiovascular Genetics and Epidemiology. J Cardiovasc Dev Dis 2024; 11:56. [PMID: 38392270 PMCID: PMC10888590 DOI: 10.3390/jcdd11020056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/25/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024] Open
Abstract
Novel genetic risk markers have helped us to advance the field of cardiovascular epidemiology and refine our current understanding and risk stratification paradigms. The discovery and analysis of variants can help us to tailor prognostication and management. However, populations underrepresented in cardiovascular epidemiology and cardiogenetics research may experience inequities in care if prediction tools are not applicable to them clinically. Therefore, the purpose of this article is to outline the barriers that underrepresented populations can face in participating in genetics research, to describe the current efforts to diversify cardiogenetics research, and to outline strategies that researchers in cardiovascular epidemiology can implement to include underrepresented populations. Mistrust, a lack of diverse research teams, the improper use of sensitive biodata, and the constraints of genetic analyses are all barriers for including diverse populations in genetics studies. The current work is beginning to address the paucity of ethnically diverse genetics research and has already begun to shed light on the potential benefits of including underrepresented and diverse populations. Reducing barriers for individuals, utilizing community-driven research processes, adopting novel recruitment strategies, and pushing for organizational support for diverse genetics research are key steps that clinicians and researchers can take to develop equitable risk stratification tools and improve patient care.
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Affiliation(s)
- Elias Chappell
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Laura Arbour
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Zachary Laksman
- Department of Medicine and the School of Biomedical Engineering, Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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7
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Vasavda C, Wan G, Szeto MD, Marani M, Sutaria N, Rajeh A, Lu C, Lee KK, Nguyen NTT, Adawi W, Deng J, Parthasarathy V, Bordeaux ZA, Taylor MT, Alphonse MP, Kwatra MM, Kang S, Semenov YR, Gusev A, Kwatra SG. A Polygenic Risk Score for Predicting Racial and Genetic Susceptibility to Prurigo Nodularis. J Invest Dermatol 2023; 143:2416-2426.e1. [PMID: 37245863 PMCID: PMC11290854 DOI: 10.1016/j.jid.2023.04.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/07/2023] [Accepted: 04/17/2023] [Indexed: 05/30/2023]
Abstract
Prurigo nodularis (PN) is an understudied inflammatory skin disease characterized by pruritic, hyperkeratotic nodules. Identifying the genetic factors underlying PN could help to better understand its etiology and guide the development of therapies. In this study, we developed a polygenic risk score that predicts a diagnosis of PN (OR = 1.41, P = 1.6 × 10-5) in two independent and continentally distinct populations. We also performed GWASs, which uncovered genetic variants associated with PN, including one near PLCB4 (rs6039266: OR = 3.15, P = 4.8 × 10-8) and others near TXNRD1 (rs34217906: OR = 1.71, P = 6.4 × 10-7; rs7134193: OR = 1.57, P = 1.1 × 10-6). Finally, we discovered that Black patients have over a two-times greater genetic risk of developing PN (OR = 2.63, P = 7.8 × 10-4). Combining the polygenic risk score and self-reported race together was significantly predictive of PN (OR = 1.32, P = 4.7 × 10-3). Strikingly, this association was more significant with race than after adjusting for genetic ancestry. Because race is a sociocultural construct and not a genetically bound category, our findings suggest that genetics, environmental influence, and social determinants of health likely affect the development of PN and may contribute to clinically observed racial disparities.
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Affiliation(s)
- Chirag Vasavda
- The Solomon H. Snyder Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA; Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Guihong Wan
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Mindy D Szeto
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Melika Marani
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nishadh Sutaria
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ahmad Rajeh
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Chenyue Lu
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Kevin K Lee
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nga T T Nguyen
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Waleed Adawi
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Junwen Deng
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Varsha Parthasarathy
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zachary A Bordeaux
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matthew T Taylor
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Martin P Alphonse
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Madan M Kwatra
- Department of Anesthesiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Sewon Kang
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yevgeniy R Semenov
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Alexander Gusev
- Division of Genetics, Brigham & Women's Hospital, Boston, Massachusetts, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shawn G Kwatra
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.
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8
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Su J, Kuo SIC, Aliev F, Rabinowitz JA, Jamil B, Chan G, Edenberg HJ, Francis M, Hesselbrock V, Kamarajan C, Kinreich S, Kramer J, Lai D, McCutcheon V, Meyers J, Pandey A, Pandey G, Plawecki MH, Schuckit M, Tischfield J, Dick DM. Alcohol use polygenic risk score, social support, and alcohol use among European American and African American adults. Dev Psychopathol 2023:1-13. [PMID: 37781861 PMCID: PMC10985050 DOI: 10.1017/s0954579423001141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Alcohol use is influenced by genetic and environmental factors. We examined the interactive effects between genome-wide polygenic risk scores for alcohol use (alc-PRS) and social support in relation to alcohol use among European American (EA) and African American (AA) adults across sex and developmental stages (emerging adulthood, young adulthood, and middle adulthood). Data were drawn from 4,011 EA and 1,274 AA adults from the Collaborative Study on the Genetics of Alcoholism who were between ages 18-65 and had ever used alcohol. Participants completed the Semi-Structured Assessment for the Genetics of Alcoholism and provided saliva or blood samples for genotyping. Results indicated that social support from friends, but not family, moderated the association between alc-PRS and alcohol use among EAs and AAs (only in middle adulthood for AAs); alc-PRS was associated with higher levels of alcohol use when friend support was low, but not when friend support was high. Associations were similar across sex but differed across developmental stages. Findings support the important role of social support from friends in buffering genetic risk for alcohol use among EA and AA adults and highlight the need to consider developmental changes in the role of social support in relation to alcohol use.
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Affiliation(s)
- Jinni Su
- Department of Psychology, Arizona State University, Tempe, AZ, USA
| | - Sally I-Chun Kuo
- Department of Psychiatry, Rutgers University, New Brunswick, NJ, USA
| | - Fazil Aliev
- Department of Psychiatry, Rutgers University, New Brunswick, NJ, USA
| | - Jill A Rabinowitz
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Belal Jamil
- Department of Psychology, Arizona State University, Tempe, AZ, USA
| | - Grace Chan
- Department of Psychiatry, University of Connecticut, Farmington, CT, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, IN, USA
| | - Meredith Francis
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Victor Hesselbrock
- Department of Psychiatry, University of Connecticut, Farmington, CT, USA
| | - Chella Kamarajan
- Department of Psychiatry, State University of New York Downstate Medical Center, Brooklyn, USA
| | - Sivan Kinreich
- Department of Psychiatry, State University of New York Downstate Medical Center, Brooklyn, USA
| | - John Kramer
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Donbing Lai
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, IN, USA
| | - Vivia McCutcheon
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Jacquelyn Meyers
- Department of Psychiatry, State University of New York Downstate Medical Center, Brooklyn, USA
| | - Ashwini Pandey
- Department of Psychiatry, State University of New York Downstate Medical Center, Brooklyn, USA
| | - Gayathri Pandey
- Department of Psychiatry, State University of New York Downstate Medical Center, Brooklyn, USA
| | | | - Marc Schuckit
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Jay Tischfield
- Department of Genetics, Rutgers University, New Brunswick, NJ, USA
| | - Danielle M Dick
- Rutgers Addiction Research Center, Rutgers University, New Brunswick, NJ, USA
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9
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Úbeda F, Fyon F, Bürger R. The Recombination Hotspot Paradox: Co-evolution between PRDM9 and its target sites. Theor Popul Biol 2023; 153:69-90. [PMID: 37451508 DOI: 10.1016/j.tpb.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Recombination often concentrates in small regions called recombination hotspots where recombination is much higher than the genome's average. In many vertebrates, including humans, gene PRDM9 specifies which DNA motifs will be the target for breaks that initiate recombination, ultimately determining the location of recombination hotspots. Because the sequence that breaks (allowing recombination) is converted into the sequence that does not break (preventing recombination), the latter sequence is over-transmitted to future generations and recombination hotspots are self-destructive. Given their self-destructive nature, recombination hotspots should eventually become extinct in genomes where they are found. While empirical evidence shows that individual hotspots do become inactive over time (die), hotspots are abundant in many vertebrates: a contradiction called the Recombination Hotspot Paradox. What saves recombination hotspots from their foretold extinction? Here we formulate a co-evolutionary model of the interaction among sequence-specific gene conversion, fertility selection, and recurrent mutation. We find that allelic frequencies oscillate leading to stable limit cycles. From a biological perspective this means that when fertility selection is weaker than gene conversion, it cannot stop individual hotspots from dying but can save them from extinction by driving their re-activation (resuscitation). In our model, mutation balances death and resuscitation of hotspots, thus maintaining their number over evolutionary time. Interestingly, we find that multiple alleles result in oscillations that are chaotic and multiple targets in oscillations that are asynchronous between targets thus helping to maintain the average genomic recombination probability constant. Furthermore, we find that the level of expression of PRDM9 should control for the fraction of targets that are hotspots and the overall temperature of the genome. Therefore, our co-evolutionary model improves our understanding of how hotspots may be replaced, thus contributing to solve the Recombination Hotspot Paradox. From a more applied perspective our work provides testable predictions regarding the relation between mutation probability and fertility selection with life expectancy of hotspots.
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Affiliation(s)
- Francisco Úbeda
- Department of Biology, Royal Holloway University of London, Egham TW20 0EX, UK.
| | - Frédéric Fyon
- Department of Biology, Royal Holloway University of London, Egham TW20 0EX, UK
| | - Reinhard Bürger
- Faculty of Mathematics, University of Vienna, 1090 Vienna, Austria
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10
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Mahmood AA, Abbas RF. Assessment of NLRP3 Gene Polymorphisms with Periodontitis as Compared with Healthy Periodontium in Iraqi Arabs Patients. Eur J Dent 2023; 17:1338-1348. [PMID: 36812929 PMCID: PMC10756796 DOI: 10.1055/s-0043-1761185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
OBJECTIVES The nod-like receptor pyrin domain-containing protein 3 (NLRP3) inflammasome regulates the maturation and release of the cytokines as well as the activation of caspase in response to danger signals derived from pathogenic infection, tissue damage, andmetabolic changes that have a role in the pathogenesis of different diseases as periodontitis. Yet, the susceptibility to this illness could be determined by population-based genetic differences. The aim of this study was to determine whether periodontitis in Arab populations from Iraq is correlated with NLRP3 gene polymorphisms and measure clinical periodontal parameters and investigate their association with genetic polymorphisms of the NLRP3. MATERIALS AND METHODS The study sample consisted of 94 participants ranging from 30 to 55 years old, both males and females who fulfilled the study's criteria. The selected participants were divided into two groups: the periodontitis group (62 subjects) and the healthy control group (32 subjects). The examination of clinical periodontal parameters of all participants was carried out, followed by a collection of venous blood for NLRP3 genetic analysis using the polymerase chain reaction-sequencing technique. RESULTS The genetic analysis of NLRP3 genotypes at four single nucleotide polymorphisms (SNPs) (rs10925024, rs4612666, rs34777555, and rs10754557), by Hardy-Weinberg equilibrium, identified nonsignificant differences in studied groups. The C-T genotype among periodontitis was significantly different from controls, while the C-C genotype among control was significantly different from periodontitis at NLRP3 rs10925024. Overall, there were 35 SNPs in the periodontitis group and 10 SNPs in the control group for rs10925024 with significant differences versus nonsignificant differences of the other SNPs between the studied groups. Clinical attachment loss and NLRP3 rs10925024 additionally demonstrated a significant positive correlation in the periodontitis subjects. CONCLUSION The findings suggested that polymorphisms of the NLRP3 gene may have a role and increasing the genetic susceptibility to periodontal disease in Arabs Iraqi patients.
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Affiliation(s)
- Athraa A. Mahmood
- Department of Oral Surgery and Periodontology, College of Dentistry, Mustansiriyah University, Baghdad, Iraq
| | - Raghad Fadhil Abbas
- Department of Periodontology, College of Dentistry, University of Baghdad, Baghdad, Iraq
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11
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Tan T, Atkinson EG. Strategies for the Genomic Analysis of Admixed Populations. Annu Rev Biomed Data Sci 2023; 6:105-127. [PMID: 37127050 PMCID: PMC10871708 DOI: 10.1146/annurev-biodatasci-020722-014310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Admixed populations constitute a large portion of global human genetic diversity, yet they are often left out of genomics analyses. This exclusion is problematic, as it leads to disparities in the understanding of the genetic structure and history of diverse cohorts and the performance of genomic medicine across populations. Admixed populations have particular statistical challenges, as they inherit genomic segments from multiple source populations-the primary reason they have historically been excluded from genetic studies. In recent years, however, an increasing number of statistical methods and software tools have been developed to account for and leverage admixture in the context of genomics analyses. Here, we provide a survey of such computational strategies for the informed consideration of admixture to allow for the well-calibrated inclusion of mixed ancestry populations in large-scale genomics studies, and we detail persisting gaps in existing tools.
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Affiliation(s)
- Taotao Tan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA;
| | - Elizabeth G Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA;
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12
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Svyatova G, Boranbayeva R, Berezina G, Manzhuova L, Murtazaliyeva A. Genes of Predisposition to Childhood Beta-Cell Acute Lymphoblastic Leukemia in the Kazakh Population. Asian Pac J Cancer Prev 2023; 24:2653-2666. [PMID: 37642051 PMCID: PMC10685230 DOI: 10.31557/apjcp.2023.24.8.2653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Today, acute lymphoblastic leukemia is one of the most common malignant diseases of the hematopoietic system. The genetic predisposition to ALL is not fully explored in various ethnic populations. OBJECTIVE The study aimed to conduct a comparative analysis of the population frequencies of alleles and genotypes of polymorphic gene variants: immune regulation GATA3 (rs3824662); transcription and differentiation of B cells: ARID5B (rs7089424, rs10740055), IKZF1 (rs4132601); differentiation of hematopoietic cells: PIP4K2A (rs7088318); apoptosis: CEBPE (rs2239633), tumor suppressors: CDKN2A (rs3731249), TP53 (rs1042522); carcinogen metabolism: CBR3 (rs1056892), CYP1A1 (rs104894, rs4646903), according to genome-wide association studies analyses associated with the risk of developing pediatric beta-cell acute lymphoblastic leukemia (B-cell ALL), in an ethnically homogeneous population of Kazakhs with studied populations. METHODS The genomic database consists of 1800 conditionally healthy persons of Kazakh nationality, genotyped using OmniChip 2.5-8 Illumina chips at the deCODE genetics as part of the InterPregGen 7 project of the European Union (EU) framework program under Grant Agreement No. 282540. RESULTS High population frequencies of single nucleotide polymorphism (SNP) minor alleles identified for immune regulation genes - GATA3 rs3824662 - 42.5%; transcription and differentiation of B-cells genes - ARID5B rs7089424 - 33.1% and rs10740055 - 48.5%, which suggests their significant genetic contribution to the risk of development and prognosis of the effectiveness of B-cell ALL therapy in the Kazakh population. The significantly lower population frequency of the minor allele G rs1056892 CBR3 gene - 38.6% in the Kazakhs suggests its significant protective effect in reducing the risk of childhood B-cell ALL and the smaller number of cardiac complications after anthracycline therapy. CONCLUSION The obtained results will serve as a basis for developing effective methods for predicting the risk of development, early diagnosis, and effectiveness of treatment of B-cell ALL in children.
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Affiliation(s)
- Gulnara Svyatova
- Republican Medical Genetic Consultation, Scientific Center of Obstetrics, Gynecology and Perinatology, 050020, 125 Dostyk Ave., Almaty, Kazakhstan.
| | - Riza Boranbayeva
- Scientific Center of Pediatrics and Pediatric Surgery, 050060, 146 Al-Farabi Ave., Almaty, Kazakhstan.
| | - Galina Berezina
- Republican Medical Genetic Consultation, Scientific Center of Obstetrics, Gynecology and Perinatology, 050020, 125 Dostyk Ave., Almaty, Kazakhstan.
| | - Lyazat Manzhuova
- Scientific Center of Pediatrics and Pediatric Surgery, 050060, 146 Al-Farabi Ave., Almaty, Kazakhstan.
| | - Alexandra Murtazaliyeva
- Republican Medical Genetic Consultation, Scientific Center of Obstetrics, Gynecology and Perinatology, 050020, 125 Dostyk Ave., Almaty, Kazakhstan.
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13
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Raben TG, Lello L, Widen E, Hsu SDH. Biobank-scale methods and projections for sparse polygenic prediction from machine learning. Sci Rep 2023; 13:11662. [PMID: 37468507 PMCID: PMC10356957 DOI: 10.1038/s41598-023-37580-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/23/2023] [Indexed: 07/21/2023] Open
Abstract
In this paper we characterize the performance of linear models trained via widely-used sparse machine learning algorithms. We build polygenic scores and examine performance as a function of training set size, genetic ancestral background, and training method. We show that predictor performance is most strongly dependent on size of training data, with smaller gains from algorithmic improvements. We find that LASSO generally performs as well as the best methods, judged by a variety of metrics. We also investigate performance characteristics of predictors trained on one genetic ancestry group when applied to another. Using LASSO, we develop a novel method for projecting AUC and correlation as a function of data size (i.e., for new biobanks) and characterize the asymptotic limit of performance. Additionally, for LASSO (compressed sensing) we show that performance metrics and predictor sparsity are in agreement with theoretical predictions from the Donoho-Tanner phase transition. Specifically, a future predictor trained in the Taiwan Precision Medicine Initiative for asthma can achieve an AUC of [Formula: see text] and for height a correlation of [Formula: see text] for a Taiwanese population. This is above the measured values of [Formula: see text] and [Formula: see text], respectively, for UK Biobank trained predictors applied to a European population.
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Affiliation(s)
- Timothy G Raben
- Department of Physics and Astronomy, Michigan State University, Michigan, USA.
| | - Louis Lello
- Department of Physics and Astronomy, Michigan State University, Michigan, USA
- Genomic Prediction, Inc., North Brunswick, NJ, USA
| | - Erik Widen
- Department of Physics and Astronomy, Michigan State University, Michigan, USA
- Genomic Prediction, Inc., North Brunswick, NJ, USA
| | - Stephen D H Hsu
- Department of Physics and Astronomy, Michigan State University, Michigan, USA
- Genomic Prediction, Inc., North Brunswick, NJ, USA
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Qiao J, Wu Y, Zhang S, Xu Y, Zhang J, Zeng P, Wang T. Evaluating significance of European-associated index SNPs in the East Asian population for 31 complex phenotypes. BMC Genomics 2023; 24:324. [PMID: 37312035 DOI: 10.1186/s12864-023-09425-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/01/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWASs) have identified many single-nucleotide polymorphisms (SNPs) associated with complex phenotypes in the European (EUR) population; however, the extent to which EUR-associated SNPs can be generalized to other populations such as East Asian (EAS) is not clear. RESULTS By leveraging summary statistics of 31 phenotypes in the EUR and EAS populations, we first evaluated the difference in heritability between the two populations and calculated the trans-ethnic genetic correlation. We observed the heritability estimates of some phenotypes varied substantially across populations and 53.3% of trans-ethnic genetic correlations were significantly smaller than one. Next, we examined whether EUR-associated SNPs of these phenotypes could be identified in EAS using the trans-ethnic false discovery rate method while accounting for winner's curse for SNP effect in EUR and difference of sample sizes in EAS. We found on average 54.5% of EUR-associated SNPs were also significant in EAS. Furthermore, we discovered non-significant SNPs had higher effect heterogeneity, and significant SNPs showed more consistent linkage disequilibrium and allele frequency patterns between the two populations. We also demonstrated non-significant SNPs were more likely to undergo natural selection. CONCLUSIONS Our study revealed the extent to which EUR-associated SNPs could be significant in the EAS population and offered deep insights into the similarity and diversity of genetic architectures underlying phenotypes in distinct ancestral groups.
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Affiliation(s)
- Jiahao Qiao
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Yuxuan Wu
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Shuo Zhang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Yue Xu
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Jinhui Zhang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Ping Zeng
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Center for Medical Statistics and Data Analysis, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Key Laboratory of Environment and Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Engineering Research Innovation Center of Biological Data Mining and Healthcare Transformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
| | - Ting Wang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
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15
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Zhang J, Zhang S, Qiao J, Wang T, Zeng P. Similarity and diversity of genetic architecture for complex traits between East Asian and European populations. BMC Genomics 2023; 24:314. [PMID: 37308816 DOI: 10.1186/s12864-023-09434-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/07/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Genome-wide association studies have detected a large number of single-nucleotide polymorphisms (SNPs) associated with complex traits in diverse ancestral groups. However, the trans-ethnic similarity and diversity of genetic architecture is not well understood currently. RESULTS By leveraging summary statistics of 37 traits from East Asian (Nmax=254,373) or European (Nmax=693,529) populations, we first evaluated the trans-ethnic genetic correlation (ρg) and found substantial evidence of shared genetic overlap underlying these traits between the two populations, with [Formula: see text] ranging from 0.53 (se = 0.11) for adult-onset asthma to 0.98 (se = 0.17) for hemoglobin A1c. However, 88.9% of the genetic correlation estimates were significantly less than one, indicating potential heterogeneity in genetic effect across populations. We next identified common associated SNPs using the conjunction conditional false discovery rate method and observed 21.7% of trait-associated SNPs can be identified simultaneously in both populations. Among these shared associated SNPs, 20.8% showed heterogeneous influence on traits between the two ancestral populations. Moreover, we demonstrated that population-common associated SNPs often exhibited more consistent linkage disequilibrium and allele frequency pattern across ancestral groups compared to population-specific or null ones. We also revealed population-specific associated SNPs were much likely to undergo natural selection compared to population-common associated SNPs. CONCLUSIONS Our study provides an in-depth understanding of similarity and diversity regarding genetic architecture for complex traits across diverse populations, and can assist in trans-ethnic association analysis, genetic risk prediction, and causal variant fine mapping.
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Affiliation(s)
- Jinhui Zhang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Shuo Zhang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Jiahao Qiao
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Ting Wang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
| | - Ping Zeng
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
- Center for Medical Statistics and Data Analysis, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
- Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
- Key Laboratory of Environment and Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
- Engineering Research Innovation Center of Biological Data Mining and Healthcare Transformation, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
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16
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Mester R, Hou K, Ding Y, Meeks G, Burch KS, Bhattacharya A, Henn BM, Pasaniuc B. Impact of cross-ancestry genetic architecture on GWASs in admixed populations. Am J Hum Genet 2023; 110:927-939. [PMID: 37224807 PMCID: PMC10257009 DOI: 10.1016/j.ajhg.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/26/2023] Open
Abstract
Genome-wide association studies (GWASs) have identified thousands of variants for disease risk. These studies have predominantly been conducted in individuals of European ancestries, which raises questions about their transferability to individuals of other ancestries. Of particular interest are admixed populations, usually defined as populations with recent ancestry from two or more continental sources. Admixed genomes contain segments of distinct ancestries that vary in composition across individuals in the population, allowing for the same allele to induce risk for disease on different ancestral backgrounds. This mosaicism raises unique challenges for GWASs in admixed populations, such as the need to correctly adjust for population stratification. In this work we quantify the impact of differences in estimated allelic effect sizes for risk variants between ancestry backgrounds on association statistics. Specifically, while the possibility of estimated allelic effect-size heterogeneity by ancestry (HetLanc) can be modeled when performing a GWAS in admixed populations, the extent of HetLanc needed to overcome the penalty from an additional degree of freedom in the association statistic has not been thoroughly quantified. Using extensive simulations of admixed genotypes and phenotypes, we find that controlling for and conditioning effect sizes on local ancestry can reduce statistical power by up to 72%. This finding is especially pronounced in the presence of allele frequency differentiation. We replicate simulation results using 4,327 African-European admixed genomes from the UK Biobank for 12 traits to find that for most significant SNPs, HetLanc is not large enough for GWASs to benefit from modeling heterogeneity in this way.
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Affiliation(s)
- Rachel Mester
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Kangcheng Hou
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Ding
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gillian Meeks
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis, CA 95616, USA
| | - Kathryn S Burch
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Brenna M Henn
- Department of Anthropology, Center for Population Biology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Bogdan Pasaniuc
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute of Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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17
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Zhao Q, Han B, Xu Q, Wang T, Fang C, Li R, Zhang L, Pei Y. Proteome and genome integration analysis of obesity. Chin Med J (Engl) 2023; 136:910-921. [PMID: 37000968 PMCID: PMC10278747 DOI: 10.1097/cm9.0000000000002644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Indexed: 04/03/2023] Open
Abstract
ABSTRACT The prevalence of obesity has increased worldwide in recent decades. Genetic factors are now known to play a substantial role in the predisposition to obesity and may contribute up to 70% of the risk for obesity. Technological advancements during the last decades have allowed the identification of many hundreds of genetic markers associated with obesity. However, the transformation of current genetic variant-obesity associations into biological knowledge has been proven challenging. Genomics and proteomics are complementary fields, as proteomics extends functional analyses. Integrating genomic and proteomic data can help to bridge a gap in knowledge regarding genetic variant-obesity associations and to identify new drug targets for the treatment of obesity. We provide an overview of the published papers on the integrated analysis of proteomic and genomic data in obesity and summarize four mainstream strategies: overlap, colocalization, Mendelian randomization, and proteome-wide association studies. The integrated analyses identified many obesity-associated proteins, such as leptin, follistatin, and adenylate cyclase 3. Despite great progress, integrative studies focusing on obesity are still limited. There is an increased demand for large prospective cohort studies to identify and validate findings, and further apply these findings to the prevention, intervention, and treatment of obesity. In addition, we also discuss several other potential integration methods.
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Affiliation(s)
- Qigang Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215123, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215213, China
| | - Baixue Han
- Department of Epidemiology and Biostatistics, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215123, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215213, China
| | - Qian Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215123, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215213, China
| | - Tao Wang
- Department of Endocrinology, The Second Affiliated Hospital, Soochow University, Suzhou, Jiangsu 215004, China
| | - Chen Fang
- Department of Endocrinology, The Second Affiliated Hospital, Soochow University, Suzhou, Jiangsu 215004, China
| | - Rui Li
- Department of Gastroenterology, The First Affiliated Hospital, Soochow University, Suzhou, Jiangsu 215006, China
| | - Lei Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215213, China
- Center for Genetic Epidemiology and Genomics, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215123, China
| | - Yufang Pei
- Department of Epidemiology and Biostatistics, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215123, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215213, China
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18
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Adam Y, Sadeeq S, Kumuthini J, Ajayi O, Wells G, Solomon R, Ogunlana O, Adetiba E, Iweala E, Brors B, Adebiyi E. Polygenic Risk Score in African populations: progress and challenges. F1000Res 2023; 11:175. [PMID: 37273966 PMCID: PMC10233318 DOI: 10.12688/f1000research.76218.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/10/2023] [Indexed: 06/06/2023] Open
Abstract
Polygenic Risk Score (PRS) analysis is a method that predicts the genetic risk of an individual towards targeted traits. Even when there are no significant markers, it gives evidence of a genetic effect beyond the results of Genome-Wide Association Studies (GWAS). Moreover, it selects single nucleotide polymorphisms (SNPs) that contribute to the disease with low effect size making it more precise at individual level risk prediction. PRS analysis addresses the shortfall of GWAS by taking into account the SNPs/alleles with low effect size but play an indispensable role to the observed phenotypic/trait variance. PRS analysis has applications that investigate the genetic basis of several traits, which includes rare diseases. However, the accuracy of PRS analysis depends on the genomic data of the underlying population. For instance, several studies show that obtaining higher prediction power of PRS analysis is challenging for non-Europeans. In this manuscript, we review the conventional PRS methods and their application to sub-Saharan African communities. We conclude that lack of sufficient GWAS data and tools is the limiting factor of applying PRS analysis to sub-Saharan populations. We recommend developing Africa-specific PRS methods and tools for estimating and analyzing African population data for clinical evaluation of PRSs of interest and predicting rare diseases.
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Affiliation(s)
- Yagoub Adam
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Suraju Sadeeq
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept Computer & Information Sciences, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Judit Kumuthini
- South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape, Cape Town, South Africa
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa
| | - Olabode Ajayi
- South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape, Cape Town, South Africa
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa
| | - Gordon Wells
- South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape, Cape Town, South Africa
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa
| | - Rotimi Solomon
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Biochemistry, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Olubanke Ogunlana
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Biochemistry, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Emmanuel Adetiba
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Electrical & Information Engineering (EIE), Covenant University, Ota, Ogun State, 112212, Nigeria
- HRA, Institute for Systems Science, Durban University of Technology, Durban, South Africa
| | - Emeka Iweala
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Biochemistry, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Benedikt Brors
- Applied Bioinformatics Division, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept Computer & Information Sciences, Covenant University, Ota, Ogun State, 112212, Nigeria
- Applied Bioinformatics Division, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
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19
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Adam Y, Sadeeq S, Kumuthini J, Ajayi O, Wells G, Solomon R, Ogunlana O, Adetiba E, Iweala E, Brors B, Adebiyi E. Polygenic Risk Score in African populations: progress and challenges. F1000Res 2023; 11:175. [PMID: 37273966 PMCID: PMC10233318 DOI: 10.12688/f1000research.76218.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/10/2023] [Indexed: 11/23/2023] Open
Abstract
Polygenic Risk Score (PRS) analysis is a method that predicts the genetic risk of an individual towards targeted traits. Even when there are no significant markers, it gives evidence of a genetic effect beyond the results of Genome-Wide Association Studies (GWAS). Moreover, it selects single nucleotide polymorphisms (SNPs) that contribute to the disease with low effect size making it more precise at individual level risk prediction. PRS analysis addresses the shortfall of GWAS by taking into account the SNPs/alleles with low effect size but play an indispensable role to the observed phenotypic/trait variance. PRS analysis has applications that investigate the genetic basis of several traits, which includes rare diseases. However, the accuracy of PRS analysis depends on the genomic data of the underlying population. For instance, several studies show that obtaining higher prediction power of PRS analysis is challenging for non-Europeans. In this manuscript, we review the conventional PRS methods and their application to sub-Saharan African communities. We conclude that lack of sufficient GWAS data and tools is the limiting factor of applying PRS analysis to sub-Saharan populations. We recommend developing Africa-specific PRS methods and tools for estimating and analyzing African population data for clinical evaluation of PRSs of interest and predicting rare diseases.
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Affiliation(s)
- Yagoub Adam
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Suraju Sadeeq
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept Computer & Information Sciences, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Judit Kumuthini
- South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape, Cape Town, South Africa
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa
| | - Olabode Ajayi
- South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape, Cape Town, South Africa
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa
| | - Gordon Wells
- South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape, Cape Town, South Africa
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa
| | - Rotimi Solomon
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Biochemistry, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Olubanke Ogunlana
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Biochemistry, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Emmanuel Adetiba
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Electrical & Information Engineering (EIE), Covenant University, Ota, Ogun State, 112212, Nigeria
- HRA, Institute for Systems Science, Durban University of Technology, Durban, South Africa
| | - Emeka Iweala
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Biochemistry, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Benedikt Brors
- Applied Bioinformatics Division, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept Computer & Information Sciences, Covenant University, Ota, Ogun State, 112212, Nigeria
- Applied Bioinformatics Division, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
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Suzuki K, Hatzikotoulas K, Southam L, Taylor HJ, Yin X, Lorenz KM, Mandla R, Huerta-Chagoya A, Rayner NW, Bocher O, Arruda ALDSV, Sonehara K, Namba S, Lee SSK, Preuss MH, Petty LE, Schroeder P, Vanderwerff B, Kals M, Bragg F, Lin K, Guo X, Zhang W, Yao J, Kim YJ, Graff M, Takeuchi F, Nano J, Lamri A, Nakatochi M, Moon S, Scott RA, Cook JP, Lee JJ, Pan I, Taliun D, Parra EJ, Chai JF, Bielak LF, Tabara Y, Hai Y, Thorleifsson G, Grarup N, Sofer T, Wuttke M, Sarnowski C, Gieger C, Nousome D, Trompet S, Kwak SH, Long J, Sun M, Tong L, Chen WM, Nongmaithem SS, Noordam R, Lim VJY, Tam CHT, Joo YY, Chen CH, Raffield LM, Prins BP, Nicolas A, Yanek LR, Chen G, Brody JA, Kabagambe E, An P, Xiang AH, Choi HS, Cade BE, Tan J, Broadaway KA, Williamson A, Kamali Z, Cui J, Adair LS, Adeyemo A, Aguilar-Salinas CA, Ahluwalia TS, Anand SS, Bertoni A, Bork-Jensen J, Brandslund I, Buchanan TA, Burant CF, Butterworth AS, Canouil M, Chan JCN, Chang LC, Chee ML, Chen J, Chen SH, Chen YT, Chen Z, Chuang LM, Cushman M, Danesh J, Das SK, de Silva HJ, Dedoussis G, Dimitrov L, Doumatey AP, Du S, Duan Q, Eckardt KU, Emery LS, Evans DS, Evans MK, Fischer K, Floyd JS, Ford I, Franco OH, Frayling TM, Freedman BI, Genter P, Gerstein HC, Giedraitis V, González-Villalpando C, González-Villalpando ME, Gordon-Larsen P, Gross M, Guare LA, Hackinger S, Han S, Hattersley AT, Herder C, Horikoshi M, Howard AG, Hsueh W, Huang M, Huang W, Hung YJ, Hwang MY, Hwu CM, Ichihara S, Ikram MA, Ingelsson M, Islam MT, Isono M, Jang HM, Jasmine F, Jiang G, Jonas JB, Jørgensen T, Kandeel FR, Kasturiratne A, Katsuya T, Kaur V, Kawaguchi T, Keaton JM, Kho AN, Khor CC, Kibriya MG, Kim DH, Kronenberg F, Kuusisto J, Läll K, Lange LA, Lee KM, Lee MS, Lee NR, Leong A, Li L, Li Y, Li-Gao R, Lithgart S, Lindgren CM, Linneberg A, Liu CT, Liu J, Locke AE, Louie T, Luan J, Luk AO, Luo X, Lv J, Lynch JA, Lyssenko V, Maeda S, Mamakou V, Mansuri SR, Matsuda K, Meitinger T, Metspalu A, Mo H, Morris AD, Nadler JL, Nalls MA, Nayak U, Ntalla I, Okada Y, Orozco L, Patel SR, Patil S, Pei P, Pereira MA, Peters A, Pirie FJ, Polikowsky HG, Porneala B, Prasad G, Rasmussen-Torvik LJ, Reiner AP, Roden M, Rohde R, Roll K, Sabanayagam C, Sandow K, Sankareswaran A, Sattar N, Schönherr S, Shahriar M, Shen B, Shi J, Shin DM, Shojima N, Smith JA, So WY, Stančáková A, Steinthorsdottir V, Stilp AM, Strauch K, Taylor KD, Thorand B, Thorsteinsdottir U, Tomlinson B, Tran TC, Tsai FJ, Tuomilehto J, Tusie-Luna T, Udler MS, Valladares-Salgado A, van Dam RM, van Klinken JB, Varma R, Wacher-Rodarte N, Wheeler E, Wickremasinghe AR, van Dijk KW, Witte DR, Yajnik CS, Yamamoto K, Yamamoto K, Yoon K, Yu C, Yuan JM, Yusuf S, Zawistowski M, Zhang L, Zheng W, Raffel LJ, Igase M, Ipp E, Redline S, Cho YS, Lind L, Province MA, Fornage M, Hanis CL, Ingelsson E, Zonderman AB, Psaty BM, Wang YX, Rotimi CN, Becker DM, Matsuda F, Liu Y, Yokota M, Kardia SLR, Peyser PA, Pankow JS, Engert JC, Bonnefond A, Froguel P, Wilson JG, Sheu WHH, Wu JY, Hayes MG, Ma RCW, Wong TY, Mook-Kanamori DO, Tuomi T, Chandak GR, Collins FS, Bharadwaj D, Paré G, Sale MM, Ahsan H, Motala AA, Shu XO, Park KS, Jukema JW, Cruz M, Chen YDI, Rich SS, McKean-Cowdin R, Grallert H, Cheng CY, Ghanbari M, Tai ES, Dupuis J, Kato N, Laakso M, Köttgen A, Koh WP, Bowden DW, Palmer CNA, Kooner JS, Kooperberg C, Liu S, North KE, Saleheen D, Hansen T, Pedersen O, Wareham NJ, Lee J, Kim BJ, Millwood IY, Walters RG, Stefansson K, Goodarzi MO, Mohlke KL, Langenberg C, Haiman CA, Loos RJF, Florez JC, Rader DJ, Ritchie MD, Zöllner S, Mägi R, Denny JC, Yamauchi T, Kadowaki T, Chambers JC, Ng MCY, Sim X, Below JE, Tsao PS, Chang KM, McCarthy MI, Meigs JB, Mahajan A, Spracklen CN, Mercader JM, Boehnke M, Rotter JI, Vujkovic M, Voight BF, Morris AP, Zeggini E. Multi-ancestry genome-wide study in >2.5 million individuals reveals heterogeneity in mechanistic pathways of type 2 diabetes and complications. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.31.23287839. [PMID: 37034649 PMCID: PMC10081410 DOI: 10.1101/2023.03.31.23287839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes. To characterise the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study (GWAS) data from 2,535,601 individuals (39.7% non-European ancestry), including 428,452 T2D cases. We identify 1,289 independent association signals at genome-wide significance (P<5×10-8) that map to 611 loci, of which 145 loci are previously unreported. We define eight non-overlapping clusters of T2D signals characterised by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial, and enteroendocrine cells. We build cluster-specific partitioned genetic risk scores (GRS) in an additional 137,559 individuals of diverse ancestry, including 10,159 T2D cases, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned GRS are more strongly associated with coronary artery disease and end-stage diabetic nephropathy than an overall T2D GRS across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings demonstrate the value of integrating multi-ancestry GWAS with single-cell epigenomics to disentangle the aetiological heterogeneity driving the development and progression of T2D, which may offer a route to optimise global access to genetically-informed diabetes care.
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Affiliation(s)
- Ken Suzuki
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Konstantinos Hatzikotoulas
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lorraine Southam
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Henry J. Taylor
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Xianyong Yin
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing City, China
| | - Kim M. Lorenz
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ravi Mandla
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alicia Huerta-Chagoya
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Nigel W. Rayner
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ozvan Bocher
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ana Luiza de S. V. Arruda
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Simon S. K. Lee
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lauren E. Petty
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip Schroeder
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brett Vanderwerff
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Mart Kals
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fiona Bragg
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hosptial, London NorthWest Healthcare NHS Trust, Middlesex, UK
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Young Jin Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, South Korea
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Jana Nano
- Institute of Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Amel Lamri
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sanghoon Moon
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, South Korea
| | - Robert A. Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - James P. Cook
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Jung-Jin Lee
- Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian Pan
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA
| | - Daniel Taliun
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Esteban J. Parra
- Department of Anthropology, University of Toronto at Mississsauga, Mississauga, ON, Canada
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Lawrence F. Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yang Hai
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tamar Sofer
- Department of Biostatistics, Harvard University, Boston, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard University, Boston, MA, USA
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Chloé Sarnowski
- Department of Epidemiology, Human Genetics, and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Darryl Nousome
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Soo-Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Meng Sun
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Lin Tong
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Wei-Min Chen
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Suraj S. Nongmaithem
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
| | - Raymond Noordam
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Victor J. Y. Lim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Claudia H. T. Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Yoonjung Yoonie Joo
- Institute of Data Science, Korea University, Seoul, South Korea
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Health and Biomedical Informatics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bram Peter Prins
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Aude Nicolas
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Lisa R. Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Edmond Kabagambe
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Academics, Ochsner Health, New Orleans, LA, USA
| | - Ping An
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Anny H. Xiang
- Department of Research and Evaluation, Division of Biostatistics Research, Kaiser Permanente of Southern California, Pasadena, CA, USA
| | - Hyeok Sun Choi
- Department of Biomedical Science, Hallym University, Chuncheon, South Korea
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jingyi Tan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - K. Alaine Broadaway
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alice Williamson
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Department of Clinical Biochemistry, University of Cambridge, Cambridge, UK
| | - Zoha Kamali
- Department of Epidemiology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jinrui Cui
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Linda S. Adair
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Carlos A. Aguilar-Salinas
- Unidad de Investigación en Enfermedades Metabólicas and Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Tarunveer S. Ahluwalia
- Steno Diabetes Center Copenhagen, Herlev, Denmark
- The Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sonia S. Anand
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Alain Bertoni
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivan Brandslund
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
- Department of Clinical Biochemistry, Vejle Hospital, Vejle, Denmark
| | - Thomas A. Buchanan
- Department of Medicine, Division of Endocrinology and Diabetes, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Charles F. Burant
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Adam S. Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Hinxton, UK
- National Institute for Health and Care Research (NIHR) Blood and Transplant Unit (BTRU) in Donor Health and Behaviour, Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Mickaël Canouil
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille University Hospital, Lille, France
- University of Lille, Lille, France
| | - Juliana C. N. Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Li-Ching Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Miao-Li Chee
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Ji Chen
- Exeter Centre of Excellence in Diabetes (ExCEeD), Exeter Medical School, University of Exeter, Exeter, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Shyh-Huei Chen
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Lee-Ming Chuang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Mary Cushman
- Department of Medicine, University of Vermont, Colchester, VT, USA
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Hinxton, UK
- National Institute for Health and Care Research (NIHR) Blood and Transplant Unit (BTRU) in Donor Health and Behaviour, Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Swapan K. Das
- Section on Endocrinology and Metabolism, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - H. Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - George Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | - Latchezar Dimitrov
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Ayo P. Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shufa Du
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qing Duan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Leslie S. Emery
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Michele K. Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Krista Fischer
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia
| | - James S. Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ian Ford
- Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK
| | - Oscar H. Franco
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Timothy M. Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Barry I. Freedman
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Pauline Genter
- Department of Medicine, Division of Endocrinology and Metabolism, Lundquist Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Hertzel C. Gerstein
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Clicerio González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Publica, Mexico City, Mexico
| | - Maria Elena González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Publica, Mexico City, Mexico
| | - Penny Gordon-Larsen
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Myron Gross
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Lindsay A. Guare
- Genomics and Computational Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sophie Hackinger
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sohee Han
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, South Korea
| | | | - Christian Herder
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Dusseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Momoko Horikoshi
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Annie-Green Howard
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Willa Hsueh
- Department of Internal Medicine, Diabetes and Metabolism Research Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Mengna Huang
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA
- Center for Global Cardiometabolic Health, Brown University, Providence, RI, USA
| | - Wei Huang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, China
| | - Yi-Jen Hung
- Division of Endocrine and Metabolism, Tri-Service General Hospital Songshan Branch, Taipei, Taiwan
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Mi Yeong Hwang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Chii-Min Hwu
- Section of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Sahoko Ichihara
- Department of Environmental and Preventive Medicine, Jichi Medical University School of Medicine, Shimotsuke, Japan
| | - Mohammad Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | | | - Masato Isono
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hye-Mi Jang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Farzana Jasmine
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Guozhi Jiang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Jost B. Jonas
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Torben Jørgensen
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Medicine, Aalborg University, Aalborg, Denmark
| | - Fouad R. Kandeel
- Department of Clinical Diabetes, Endocrinology and Metabolism, Department of Translational Research and Cellular Therapeutics, City of Hope, Duarte, CA, USA
| | | | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Geriatric and General Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Varinderpal Kaur
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Jacob M. Keaton
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Abel N. Kho
- Division of General Internal Medicine and Geriatrics, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Health Information Partnerships, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Muhammad G. Kibriya
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Kristi Läll
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Leslie A. Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Kyung Min Lee
- VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Myung-Shik Lee
- Severance Biomedical Science Institute and Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Nanette R. Lee
- USC-Office of Population Studies Foundation Inc., University of San Carlos, Cebu City, Philippines
| | - Aaron Leong
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Yun Li
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Symen Lithgart
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Cecilia M. Lindgren
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Big Data Institute, Li Ka Shing Centre For Health Information and Discovery, University of Oxford, Oxford, UK
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Adam E. Locke
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Medicine, Division of Genomics and Bioinformatics, Washington University School of Medicine, St Louis, MO, USA
- Present address: Regeneron Genetics Center, Tarrytown, NY, USA
| | - Tin Louie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jian’an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Andrea O. Luk
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Xi Luo
- Department of Biostatistics and Data Science, The University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Julie A. Lynch
- VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
- Department of Clinical Science, Center for Diabetes Research, University of Bergen, Bergen, Norway
| | - Shiro Maeda
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Vasiliki Mamakou
- Dromokaiteio Psychiatric Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Sohail Rafik Mansuri
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
| | - Koichi Matsuda
- Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technical University Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Huan Mo
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew D. Morris
- The Usher Institute to the Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Jerry L. Nadler
- Department of Medicine and Pharmacology, New York Medical College, Valhalla, NY, USA
| | - Michael A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Glen Echo, MD, USA
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Uma Nayak
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Sanjay R. Patel
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Snehal Patil
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pei Pei
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Mark A Pereira
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig Maximilians Universität München, Munich, Germany
| | - Fraser J. Pirie
- Department of Diabetes and Endocrinology, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hannah G. Polikowsky
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bianca Porneala
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Gauri Prasad
- Academy of Scientific and Innovative Research, CSIR-Human Resource Development Campus, Ghaziabad, India
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Laura J. Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Michael Roden
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Dusseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Rebecca Rohde
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katheryn Roll
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Kevin Sandow
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Alagu Sankareswaran
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Mohammad Shahriar
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Botong Shen
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Jinxiu Shi
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, China
| | - Dong Mun Shin
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Nobuhiro Shojima
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Wing Yee So
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Alena Stančáková
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | | | - Adrienne M. Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Chair of Genetic Epidemiology, Institute of Medical Information Processing, Biometry, and Epidemiology, Faculty of Medicine, Ludwig Maximilians Universität München, Munich, Germany
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Barbara Thorand
- Institute of Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Brian Tomlinson
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Tam C. Tran
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Fuu-Jen Tsai
- Department of Medical Genetics and Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Jaakko Tuomilehto
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, Finland, Finnish Institute for Health and Welfare, Helsinki, Finland
- National School of Public Health, Madrid, Spain
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Teresa Tusie-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Departamento de Medicina Genómica y Toxiología Ambiental, Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Miriam S. Udler
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Adan Valladares-Salgado
- Unidad de Investigacion Medica en Bioquimica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Rob M. van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Jan B. van Klinken
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Chemistry, Laboratory of Genetic Metabolic Disease, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Rohit Varma
- Southern California Eye Institute, CHA Hollywood Presbyterian Hospital, Los Angeles, CA, USA
| | - Niels Wacher-Rodarte
- Unidad de Investigación Médica en Epidemiologia Clinica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Eleanor Wheeler
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | | | - Ko Willems van Dijk
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniel R. Witte
- Department of Public Health, Aarhus University, Aarhus, Denmark
- Danish Diabetes Academy, Odense, Denmark
| | - Chittaranjan S. Yajnik
- Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, India
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kyungheon Yoon
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Salim Yusuf
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Matthew Zawistowski
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Liang Zhang
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | | | | | | | | | | | - Leslie J Raffel
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UCI Irvine School of Medicine, Irvine, CA, USA
| | - Michiya Igase
- Department of Anti-Aging Medicine, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Eli Ipp
- Department of Medicine, Division of Endocrinology and Metabolism, Lundquist Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, South Korea
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael A. Province
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, The University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Craig L. Hanis
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, US
| | - Erik Ingelsson
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Alan B. Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Ya-Xing Wang
- Beijing Institute of Ophthalmology, Ophthalmology and Visual Sciences Key Laboratory, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Diane M. Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Medicine, Division of Cardiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - James S. Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - James C. Engert
- Department of Medicine, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Amélie Bonnefond
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille University Hospital, Lille, France
- University of Lille, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Philippe Froguel
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille University Hospital, Lille, France
- University of Lille, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Wayne H. H. Sheu
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Division of Endocrinology and Metabolism, Department of Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - M. Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Ronald C. W. Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Dennis O. Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tiinamaija Tuomi
- Department of Endocrinology, Helsinki University Hospital, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Folkhalsan Research Center, Helsinki, Finland
- Lund University Diabetes Centre, Malmö, Sweden
| | - Giriraj R. Chandak
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
| | - Francis S. Collins
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dwaipayan Bharadwaj
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Guillaume Paré
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Michèle M. Sale
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Deceased
| | - Habibul Ahsan
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Ayesha A. Motala
- Department of Diabetes and Endocrinology, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kyong-Soo Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
| | - Miguel Cruz
- Unidad de Investigacion Medica en Bioquimica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Roberta McKean-Cowdin
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Harald Grallert
- Institute of Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Josee Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Woon-Puay Koh
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Donald W. Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Colin N. A. Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, University of Dundee, Dundee, UK
| | - Jaspal S. Kooner
- Department of Cardiology, Ealing Hosptial, London NorthWest Healthcare NHS Trust, Middlesex, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Simin Liu
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA
- Center for Global Cardiometabolic Health, Brown University, Providence, RI, USA
- Department of Medicine, Brown University Alpert School of Medicine, Providence, RI, USA
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Danish Saleheen
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Cardiology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicholas J. Wareham
- The Usher Institute to the Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Juyoung Lee
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Bong-Jo Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Iona Y. Millwood
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Robin G. Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Kari Stefansson
- deCODE Genetics, Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Mark O. Goodarzi
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité Universitätsmedizin, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Mindich Child Health and Development Institute, Ichan School of Medicine at Mount Sinai, New York, NY, USA
| | - Jose C. Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Daniel J. Rader
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Translational Medicine and Therapeutics, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marylyn D. Ritchie
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Center for Precision Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sebastian Zöllner
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Joshua C. Denny
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Toranomon Hospital, Tokyo, Japan
| | - John C. Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hosptial, London NorthWest Healthcare NHS Trust, Middlesex, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Maggie C. Y. Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Jennifer E. Below
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip S. Tsao
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Kyong-Mi Chang
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mark I. McCarthy
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hosptial, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Present address: Genentech, South San Francisco, CA, USA
| | - James B. Meigs
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Present address: Genentech, South San Francisco, CA, USA
| | - Cassandra N. Spracklen
- Department of Biostatistics and Epidemiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Josep M. Mercader
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marijana Vujkovic
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Epidemiology, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin F. Voight
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Andrew P. Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany
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21
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Osman W, Mousa M, Albreiki M, Baalfaqih Z, Daggag H, Hill C, McKnight AJ, Maxwell AP, Al Safar H. A genome-wide association study identifies a possible role for cannabinoid signalling in the pathogenesis of diabetic kidney disease. Sci Rep 2023; 13:4661. [PMID: 36949158 PMCID: PMC10033677 DOI: 10.1038/s41598-023-31701-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
Diabetic kidney disease (DKD), also known as diabetic nephropathy, is the leading cause of renal impairment and end-stage renal disease. Patients with diabetes are at risk for DKD because of poor control of their blood glucose, as well as nonmodifiable risk factors including age, ethnicity, and genetics. This genome-wide association study (GWAS) was conducted for the first time in the Emirati population to investigate possible genetic factors associated with the development and progression of DKD. We included data on 7,921,925 single nucleotide polymorphism (SNPs) in 258 cases of type 2 diabetes mellitus (T2DM) who developed DKD and 938 control subjects with T2DM who did not develop DKD. GWAS suggestive results (P < 1 × 10-5) were further replicated using summary statistics from three cohorts with T2DM-induced DKD (Bio Bank Japan data, UK Biobank, and FinnGen Project data) and T1DM-induced DKD (UK-ROI cohort data from Belfast, UK). When conducting a multiple linear regression model for gene-set analyses, the CNR2 gene demonstrated genome-wide significance at 1.46 × 10-6. SNPs in CNR2 gene, encodes cannabinoid receptor 2 or CB2, were replicated in Japanese samples with the leading SNP rs2501391 showing a Pcombined = 9.3 × 10-7, and odds ratio = 0.67 in association with DKD associated with T2DM, but not with T1DM, without any significant association with T2DM itself. The allele frequencies of our cohort and those of the replication cohorts were in most cases markedly different. In addition, we replicated the association between rs1564939 in the GLRA3 gene and DKD in T2DM (P = 0.016, odds ratio = 0.54 per allele C). Our findings suggest evidence that cannabinoid signalling may be involved in the development of DKD through CB2, which is expressed in different kidney regions and known to be involved in insulin resistance, inflammation, and the development of kidney fibrosis.
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Affiliation(s)
- Wael Osman
- Center for Biotechnology, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates
- Department of Biology, College of Arts and Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Mira Mousa
- Center for Biotechnology, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Mohammed Albreiki
- Center for Biotechnology, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Zahrah Baalfaqih
- Center for Biotechnology, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Hinda Daggag
- Imperial College of London Diabetes Centre, Abu Dhabi, United Arab Emirates
| | - Claire Hill
- Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | | | | | - Habiba Al Safar
- Center for Biotechnology, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates.
- Department of Biomedical Engineering, College of Engineering, Khalifa University, Abu Dhabi, United Arab Emirates.
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22
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Ghoussaini M, Nelson MR, Dunham I. Future prospects for human genetics and genomics in drug discovery. Curr Opin Struct Biol 2023; 80:102568. [PMID: 36963162 PMCID: PMC7614359 DOI: 10.1016/j.sbi.2023.102568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/27/2023] [Accepted: 02/13/2023] [Indexed: 03/26/2023]
Abstract
Evidence from human genetics supporting the therapeutic hypothesis increases the likelihood that a drug will succeed in clinical trials. Rare and common disease genetics yield a wide array of alleles with a range of effect sizes that can proxy for the effect of a drug in disease. Recent advances in large scale population collections and whole genome sequencing approaches have provided a rich resource of human genetic evidence to support drug target selection. As the range of phenotypes profiled increases and ever more alleles are discovered across world-wide populations, these approaches will increasingly influence multiple stages across the lifespan of a drug discovery programme.
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Affiliation(s)
- Maya Ghoussaini
- Wellcome Sanger Institute, Wellcome Genome Campus, United Kingdom; Open Targets, Wellcome Genome Campus, United Kingdom. https://twitter.com/MayaGhoussaini
| | | | - Ian Dunham
- Wellcome Sanger Institute, Wellcome Genome Campus, United Kingdom; Open Targets, Wellcome Genome Campus, United Kingdom; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, United Kingdom.
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23
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Juárez-Luis J, Canseco-Ocaña M, Cid-Soto MA, Castro-Martínez XH, Martínez-Hernández A, Orozco L, Hernández-Zavala A, Córdova EJ. Single nucleotide variants in microRNA biosynthesis genes in Mexican individuals. Front Genet 2023; 14:1022912. [PMID: 36968598 PMCID: PMC10037310 DOI: 10.3389/fgene.2023.1022912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/02/2023] [Indexed: 03/08/2023] Open
Abstract
Background: MicroRNAs (miRNAs) are important regulators in a variety of biological processes, and their dysregulation is associated with multiple human diseases. Single nucleotide variants (SNVs) in genes involved in the processing of microRNAs may alter miRNA regulation and could present high allele heterogeneity in populations from different ethnic groups. Thus, the aim of this study was to genotype 15 SNVs in eight genes involved in the miRNA processing pathway in Mexican individuals and compare their frequencies across 21 populations from five continental groups.Methods: Genomic DNA was obtained from 399 healthy Mexican individuals. SNVs in AGO2 (rs2293939 and rs4961280), DGCR8 (rs720012), DICER (rs3742330 and rs13078), DROSHA (rs10719 and rs6877842), GEMIN3 (rs197388 and rs197414), GEMIN4 (rs7813, rs2740349, and rs4968104), TNRC6B (rs9611280), and XP05 (rs11077 and rs34324334) were genotyped using TaqMan probes. The minor allele frequency of each SNV was compared to those reported in the 1,000 Genomes database using chi-squared. Sankey plot was created in the SankeyMATIC package to visualize the frequency range of each variant in the different countries analyzed.Results: In Mexican individuals, all 15 SNVs were found in Hardy-Weinberg equilibrium, with frequencies ranging from 0.04 to 0.45. The SNVs rs4961280, rs2740349, rs34324334, and rs720012 in Mexican individuals had the highest minor allele frequencies worldwide, whereas the minor allele frequencies of rs197388, rs10719, rs197414, and rs1107 were among the lowest in Mexican individuals. The variants had high allele heterogeneity among the sub-continental populations, ranging from monomorphic, as was the case for rs9611280 and rs34324334 in African groups, to >0.50, which was the case for variants rs11077 and rs10719 in most of the populations. Importantly, the variants rs197388, rs720012, and rs197414 had FST values > 0.18, indicating a directional selective process. Finally, the SNVs rs13078 and rs10719 significantly correlated with both latitude and longitude.Conclusion: These data indicate the presence of high allelic heterogeneity in the worldwide distribution of the frequency of SNVs located in components of the miRNA processing pathway, which could modify the genetic susceptibility associated with human diseases in populations with different ancestry.
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Affiliation(s)
- Jesús Juárez-Luis
- Section of Research and Postgraduate, Superior School of Medicine, National Institute Polytechnique, Mexico City, Mexico
| | - Moisés Canseco-Ocaña
- Oncogenomics Consortium Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Miguel Angel Cid-Soto
- Oncogenomics Consortium Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Xochitl H. Castro-Martínez
- Genomics of Psychiatric and Neurogenerative diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Araceli Hernández-Zavala
- Section of Research and Postgraduate, Superior School of Medicine, National Institute Polytechnique, Mexico City, Mexico
| | - Emilio J. Córdova
- Oncogenomics Consortium Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- *Correspondence: Emilio J. Córdova,
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24
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Costantini I, Sallis H, Tilling K, Major‐Smith D, Pearson RM, Kounali D. Childhood trajectories of internalising and externalising problems associated with a polygenic risk score for neuroticism in a UK birth cohort study. JCPP ADVANCES 2023; 3:e12141. [PMID: 37431323 PMCID: PMC10241477 DOI: 10.1002/jcv2.12141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/14/2022] [Indexed: 02/25/2023] Open
Abstract
Background Neuroticism represents a personality disposition towards experiencing negative emotions more frequently and intensely. Longitudinal studies suggest that neuroticism increases risk of several psychological problems. Improved understanding of how this trait manifests in early life could help inform preventative strategies in those liable to neuroticism. Methods This study explored how a polygenic risk score for neuroticism (NEU PRS) is expressed from infancy to late childhood across various psychological outcomes using multivariable linear and ordinal regression models. In addition, we employed a three-level mixed-effect model to characterise child internalising and externalising trajectories and estimate how a child PRS associated with both their overall levels and rates of change in 5279 children aged 3-11 in the Avon Longitudinal Study of Parents and Children cohort. Results We found evidence that the NEU PRS was associated with a more emotionally sensitive temperament in early infancy in addition to higher emotional and behavioural problems and a higher risk of meeting diagnostic criteria for a variety of clinical disorders, particularly anxiety disorders, in childhood. The NEU PRS was associated with overall levels of internalising and externalising trajectories, with a larger magnitude of association on the internalising trajectory. The PRS was also associated with slower rates of reduction of internalising problems across childhood. Conclusions Our findings using a large, well-characterised birth cohort study suggest that phenotypic manifestations of a PRS for adult neuroticism can be detected as early as in infancy and that this PRS associates with several mental health problems and differences in emotional trajectories across childhood.
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Affiliation(s)
- Ilaria Costantini
- Centre for Academic Mental HealthUniversity of BristolBristolUK
- Department of Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Hannah Sallis
- Centre for Academic Mental HealthUniversity of BristolBristolUK
- Department of Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- Medical Research Council (MRC) Integrative Epidemiology UnitUniversity of BristolBristolUK
- School of Psychological ScienceUniversity of BristolBristolUK
| | - Kate Tilling
- Department of Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- Medical Research Council (MRC) Integrative Epidemiology UnitUniversity of BristolBristolUK
| | - Daniel Major‐Smith
- Department of Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- Medical Research Council (MRC) Integrative Epidemiology UnitUniversity of BristolBristolUK
- Centre for Academic Child HealthBristol Medical SchoolUniversity of BristolBristolUK
| | - Rebecca M. Pearson
- Centre for Academic Mental HealthUniversity of BristolBristolUK
- Department of Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- Medical Research Council (MRC) Integrative Epidemiology UnitUniversity of BristolBristolUK
- Department of PsychologyManchester Metropolitan UniversityManchesterUK
| | - Daphne‐Zacharenia Kounali
- Centre for Academic Mental HealthUniversity of BristolBristolUK
- Department of Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
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25
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Long Y, Tang L, Zhou Y, Zhao S, Zhu H. Causal relationship between gut microbiota and cancers: a two-sample Mendelian randomisation study. BMC Med 2023; 21:66. [PMID: 36810112 PMCID: PMC9945666 DOI: 10.1186/s12916-023-02761-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 94.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Evidence from observational studies and clinical trials suggests that the gut microbiota is associated with cancer. However, the causal association between gut microbiota and cancer remains to be determined. METHODS We first identified two sets of gut microbiota based on phylum, class, order, family, and genus level information, and cancer data were obtained from the IEU Open GWAS project. We then performed two-sample Mendelian randomisation (MR) to determine whether the gut microbiota is causally associated with eight cancer types. Furthermore, we performed a bi-directional MR analysis to examine the direction of the causal relations. RESULTS We identified 11 causal relationships between genetic liability in the gut microbiome and cancer, including those involving the genus Bifidobacterium. We found 17 strong associations between genetic liability in the gut microbiome and cancer. Moreover, we found 24 associations between genetic liability in the gut microbiome and cancer using multiple datasets. CONCLUSIONS Our MR analysis revealed that the gut microbiota was causally associated with cancers and may be useful in providing new insights for further mechanistic and clinical studies of microbiota-mediated cancer.
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Affiliation(s)
- Yiwen Long
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Lanhua Tang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Yangying Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Shushan Zhao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China. .,Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
| | - Hong Zhu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
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26
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Mester R, Hou K, Ding Y, Meeks G, Burch KS, Bhattacharya A, Henn BM, Pasaniuc B. Impact of cross-ancestry genetic architecture on GWAS in admixed populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524946. [PMID: 36747759 PMCID: PMC9900755 DOI: 10.1101/2023.01.20.524946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Genome-wide association studies (GWAS) have identified thousands of variants for disease risk. These studies have predominantly been conducted in individuals of European ancestries, which raises questions about their transferability to individuals of other ancestries. Of particular interest are admixed populations, usually defined as populations with recent ancestry from two or more continental sources. Admixed genomes contain segments of distinct ancestries that vary in composition across individuals in the population, allowing for the same allele to induce risk for disease on different ancestral backgrounds. This mosaicism raises unique challenges for GWAS in admixed populations, such as the need to correctly adjust for population stratification to balance type I error with statistical power. In this work we quantify the impact of differences in estimated allelic effect sizes for risk variants between ancestry backgrounds on association statistics. Specifically, while the possibility of estimated allelic effect-size heterogeneity by ancestry (HetLanc) can be modeled when performing GWAS in admixed populations, the extent of HetLanc needed to overcome the penalty from an additional degree of freedom in the association statistic has not been thoroughly quantified. Using extensive simulations of admixed genotypes and phenotypes we find that modeling HetLanc in its absence reduces statistical power by up to 72%. This finding is especially pronounced in the presence of allele frequency differentiation. We replicate simulation results using 4,327 African-European admixed genomes from the UK Biobank for 12 traits to find that for most significant SNPs HetLanc is not large enough for GWAS to benefit from modeling heterogeneity.
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Affiliation(s)
- Rachel Mester
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095 USA
| | - Kangcheng Hou
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095 USA
| | - Yi Ding
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095 USA
| | - Gillian Meeks
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis, CA, 95616 USA
| | - Kathryn S. Burch
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095 USA
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095 USA
| | - Brenna M. Henn
- Department of Anthropology, Center for Population Biology and the Genome Center, University of California, Davis, Davis, CA, 95616 USA
| | - Bogdan Pasaniuc
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095 USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095 USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095 USA
- Institute of Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095 USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095 USA
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27
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Mann FD, Clouston SA, Cuevas A, Waszczuk MA, Kuan PF, Carr MA, Docherty AR, Shabalin AA, Gandy SE, Luft BJ. Genetic Liability, Exposure Severity, and Post-Traumatic Stress Disorder Predict Cognitive Impairment in World Trade Center Responders. J Alzheimers Dis 2023; 92:701-712. [PMID: 36776056 PMCID: PMC10648279 DOI: 10.3233/jad-220892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
BACKGROUND There is a high incidence of cognitive impairment among World Trade Center (WTC) responders, comorbid with post-traumatic stress disorder (PTSD). Yet, it remains unknown whether genetic liability for Alzheimer's disease, PTSD, educational attainment, or for a combination of these phenotypes, is associated with cognitive impairment in this high-risk population. Similarly, whether the effects of genetic liability are comparable to PTSD and indicators of exposure severity remains unknown. OBJECTIVE In a study of 3,997 WTC responders, polygenic scores for Alzheimer's disease, PTSD, and educational attainment were used to test whether genome-wide risk for one or more of these phenotypes is associated with cognitive impairment, controlling for population stratification, while simultaneously estimating the effects of demographic factors and indicators of 9/11 exposure severity, including symptoms of PTSD. RESULTS Polygenic scores for Alzheimer's disease and educational attainment were significantly associated with an increase and decrease, respectively, in the hazard rate of mild cognitive impairment. The polygenic score for Alzheimer's disease was marginally associated with an increase in the hazard rate of severe cognitive impairment, but only age, exposure severity, and symptoms of PTSD were statistically significant predictors. CONCLUSION These results add to the emerging evidence that many WTC responders are suffering from mild cognitive impairments that resemble symptoms of Alzheimer's disease, as genetic liability for Alzheimer's disease predicted incidence of mild cognitive impairment. However, compared to polygenic scores, effect sizes were larger for PTSD and the type of work that responders completed during rescue and recovery efforts.
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Affiliation(s)
- Frank D. Mann
- Program in Public Health and Department of Family, Population, and Preventive Medicine, Renaissance School of Medicine at Stony Brook University
| | - Sean A.P. Clouston
- Program in Public Health and Department of Family, Population, and Preventive Medicine, Renaissance School of Medicine at Stony Brook University
| | | | - Monika A. Waszczuk
- Department of Psychology, Rosalind Franklin University of Medicine and Science
| | - Pei-Fen Kuan
- Department of Applied Mathematics and Statistics, Stony Brook University
| | - Melissa A. Carr
- World Trade Center Program Clinical Center of Excellence, Renaissance School of Medicine at Stony Brook University
| | | | | | | | - Benjamin J. Luft
- World Trade Center Program Clinical Center of Excellence, Renaissance School of Medicine at Stony Brook University
- Department of Medicine, Renaissance School of Medicine at Stony Brook University
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28
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Kulm S, Langhans MT, Shen TS, Kolin DA, Elemento O, Rodeo SA. Genome-Wide Association Study of Adhesive Capsulitis Suggests Significant Genetic Risk Factors. J Bone Joint Surg Am 2022; 104:1869-1876. [PMID: 36223477 DOI: 10.2106/jbjs.21.01407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Adhesive capsulitis of the shoulder involves loss of passive range of motion with associated pain and can develop spontaneously, with no obvious injury or inciting event. The pathomechanism of this disorder remains to be elucidated, but known risk factors for adhesive capsulitis include diabetes, female sex, and thyroid dysfunction. Additionally, transcriptional profiling and pedigree analyses have suggested a role for genetics. Identification of elements of genetic risk for adhesive capsulitis using population-based techniques can provide the basis for guiding both the personalized treatment of patients based on their genetic profiles and the development of new treatments by identification of the pathomechanism. METHODS A genome-wide association study (GWAS) was conducted using the U.K. Biobank (a collection of approximately 500,000 patients with genetic data and associated ICD-10 [International Classification of Diseases, 10th Revision] codes), comparing 2,142 patients with the ICD-10 code for adhesive capsulitis (M750) to those without. Separate GWASs were conducted controlling for 2 of the known risk factors of adhesive capsulitis-hypothyroidism and diabetes. Logistic regression analysis was conducted controlling for factors including sex, thyroid dysfunction, diabetes, shoulder dislocation, smoking, and genetics. RESULTS Three loci of significance were identified: rs34315830 (in WNT7B; odds ratio [OR] = 1.28; 95% confidence interval [CI], 1.22 to 1.39), rs2965196 (in MAU2; OR = 1.67; 95% CI, 1.39 to 2.00), and rs1912256 (in POU1F1; OR = 1.22; 95% CI, 1.14 to 1.31). These loci retained significance when controlling for thyroid dysfunction and diabetes. The OR for total genetic risk was 5.81 (95% CI, 4.08 to 8.31), compared with 1.70 (95% CI, 1.18 to 2.36) for hypothyroidism and 4.23 (95% CI, 2.32 to 7.05) for diabetes. CONCLUSIONS The total genetic risk associated with adhesive capsulitis was significant and similar to the risks associated with hypothyroidism and diabetes. Identification of WNT7B, POU1F1, and MAU2 implicates the Wnt pathway and cell proliferation response in the pathomechanism of adhesive capsulitis. LEVEL OF EVIDENCE Prognostic Level III . See Instructions for Authors for a complete description of levels of evidence.
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29
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Gao Y, Jiang G, Yang W, Jin W, Gong J, Xu X, Niu X. Animal-SNPAtlas: a comprehensive SNP database for multiple animals. Nucleic Acids Res 2022; 51:D816-D826. [PMID: 36300636 PMCID: PMC9825464 DOI: 10.1093/nar/gkac954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/06/2022] [Accepted: 10/26/2022] [Indexed: 01/30/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) as the most important type of genetic variation are widely used in describing population characteristics and play vital roles in animal genetics and breeding. Large amounts of population genetic variation resources and tools have been developed in human, which provided solid support for human genetic studies. However, compared with human, the development of animal genetic variation databases was relatively slow, which limits the genetic researches in these animals. To fill this gap, we systematically identified ∼ 499 million high-quality SNPs from 4784 samples of 20 types of animals. On that basis, we annotated the functions of SNPs, constructed high-density reference panels and calculated genome-wide linkage disequilibrium (LD) matrixes. We further developed Animal-SNPAtlas, a user-friendly database (http://gong_lab.hzau.edu.cn/Animal_SNPAtlas/) which includes high-quality SNP datasets and several support tools for multiple animals. In Animal-SNPAtlas, users can search the functional annotation of SNPs, perform online genotype imputation, explore and visualize LD information, browse variant information using the genome browser and download SNP datasets for each species. With the massive SNP datasets and useful tools, Animal-SNPAtlas will be an important fundamental resource for the animal genomics, genetics and breeding community.
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Affiliation(s)
| | | | - Wenqian Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Weiwei Jin
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Jing Gong
- To whom correspondence should be addressed. Tel: +86 27 87285085; Fax: +86 27 87285085;
| | - Xuewen Xu
- Correspondence may also be addressed to Xuewen Xu. Tel: +86 27 87285085; Fax: +86 27 87285085;
| | - Xiaohui Niu
- Correspondence may also be addressed to Xiaohui Niu. Tel: +86 27 87285085; Fax: +86 27 87285085;
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30
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Kulm S, Kolin DA, Langhans MT, Kaidi AC, Elemento O, Bostrom MP, Shen TS. Characterization of Genetic Risk of End-Stage Knee Osteoarthritis Treated with Total Knee Arthroplasty: A Genome-Wide Association Study. J Bone Joint Surg Am 2022; 104:1814-1820. [PMID: 36000784 DOI: 10.2106/jbjs.22.00364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND End-stage knee osteoarthritis (OA) is a highly debilitating disease for which total knee arthroplasty (TKA) serves as an effective treatment option. Although a genetic component to OA in general has been described, evaluation of the genetic contribution to end-stage OA of the knee is limited. To this end, we present a genome-wide association study involving patients undergoing TKA for primary knee OA to characterize the genetic features of severe disease on a population level. METHODS Individuals with the diagnosis of knee OA who underwent primary TKA were identified in the U.K. Biobank using administrative codes. The U.K. Biobank is a data repository containing prospectively collected clinical and genomic data for >500,000 patients. A genome-wide association analysis was performed using the REGENIE software package. Logistic regression was also used to compare the total genetic risk between subgroups stratified by age and body mass index (BMI). RESULTS A total of 16,032 patients with end-stage knee OA who underwent primary TKA were identified. Seven genetic loci were found to be significantly associated with end-stage knee OA. The odds ratio (OR) for developing end-stage knee OA attributable to genetics was 1.12 (95% confidence interval [CI], 1.10 to 1.14), which was lower than the OR associated with BMI (OR = 1.81; 95% CI, 1.78 to 1.83) and age (OR = 2.38; 95% CI, 2.32 to 2.45). The magnitude of the OR for developing end-stage knee OA attributable to genetics was greater in patients <60 years old than in patients ≥60 years old (p = 0.002). CONCLUSIONS This population-level genome-wide association study of end-stage knee OA treated with primary TKA was notable for identifying multiple significant genetic variants. These loci involve genes responsible for cartilage development, cartilage homeostasis, cell signaling, and metabolism. Age and BMI appear to have a greater impact on the risk of developing end-stage disease compared with genetic factors. The genetic contribution to the development of severe disease is greater in younger patients. LEVEL OF EVIDENCE Prognostic Level III . See Instructions for Authors for a complete description of levels of evidence.
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Affiliation(s)
- Scott Kulm
- Weill Cornell Medicine, Cornell University, New York, NY.,Englander Institute for Precision Medicine, Weill Cornell Medicine, Cornell University, New York, NY
| | - David A Kolin
- Weill Cornell Medicine, Cornell University, New York, NY
| | | | | | - Olivier Elemento
- Weill Cornell Medicine, Cornell University, New York, NY.,Englander Institute for Precision Medicine, Weill Cornell Medicine, Cornell University, New York, NY
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31
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Coronavirus Host Genomics Study: South Africa (COVIGen-SA). GLOBAL HEALTH 2022; 2022:7405349. [PMID: 36263375 PMCID: PMC9560830 DOI: 10.1155/2022/7405349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/04/2022] [Accepted: 07/08/2022] [Indexed: 11/17/2022]
Abstract
Host genetic factors are known to modify the susceptibility, severity, and outcomes of COVID-19 and vary across populations. However, continental Africans are yet to be adequately represented in such studies despite the importance of genetic factors in understanding Africa's response to the pandemic. We describe the development of a research resource for coronavirus host genomics studies in South Africa known as COVIGen-SA-a multicollaborator strategic partnership designed to provide harmonised demographic, clinical, and genetic information specific to Black South Africans with COVID-19. Over 2,000 participants have been recruited to date. Preliminary results on 1,354 SARS-CoV-2 positive participants from four participating studies showed that 64.7% were female, 333 had severe disease, and 329 were people living with HIV. Through this resource, we aim to provide insights into host genetic factors relevant to African-ancestry populations, using both genome-wide association testing and targeted sequencing of important genomic loci. This project will promote and enhance partnerships, build skills, and develop resources needed to address the COVID-19 burden and associated risk factors in South African communities.
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32
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Promoting Inclusive Recruitment: a Qualitative Study of Black Adults' Decision to Participate in Genetic Research. J Urban Health 2022; 99:803-812. [PMID: 35879487 PMCID: PMC9312310 DOI: 10.1007/s11524-022-00664-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/02/2022] [Indexed: 11/05/2022]
Abstract
Underrepresentation of Black individuals in genetic research is a longstanding issue. There are well-documented strategies to improve the enrollment of Black participants; however, few studies explore these strategies-as well as the barriers and facilitators for participation-by sampling Black people who have previously participated in genetic research. This study explores the decision-making process of Black adults who have participated in genetic research to identify best practices in the recruitment of Black subjects in genetic research. We conducted 18 semi-structured interviews with Black adults with prior research participation in genetic studies housed at an urban academic medical center in the United States of America (USA). An online survey was conducted with the participants to gather demographic data and information on prior research participation. Trust in research was ascertained with the Corbie-Smith Distrust in Clinical Research Index. Two participants scored high levels of distrust using the validated index. Using thematic content analysis, 4 themes emerged from the interviews: (1) Participants are active players in health system, (2) information is power, and transparency is key, (3) therapeutic alliances and study characteristics facilitate participation, and (4) race pervades the research process. The decision to participate in genetic research for the participants in our study was prompted by participants' internal motivations and facilitated by trust in their doctor, trust in the institution, and ease of participation. Most participants viewed their enrollment in genetic research in the context of their own racial identity and the history of medical racism in the USA.
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33
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Caliebe A, Tekola‐Ayele F, Darst BF, Wang X, Song YE, Gui J, Sebro RA, Balding DJ, Saad M, Dubé M. Including diverse and admixed populations in genetic epidemiology research. Genet Epidemiol 2022; 46:347-371. [PMID: 35842778 PMCID: PMC9452464 DOI: 10.1002/gepi.22492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022]
Abstract
The inclusion of ancestrally diverse participants in genetic studies can lead to new discoveries and is important to ensure equitable health care benefit from research advances. Here, members of the Ethical, Legal, Social, Implications (ELSI) committee of the International Genetic Epidemiology Society (IGES) offer perspectives on methods and analysis tools for the conduct of inclusive genetic epidemiology research, with a focus on admixed and ancestrally diverse populations in support of reproducible research practices. We emphasize the importance of distinguishing socially defined population categorizations from genetic ancestry in the design, analysis, reporting, and interpretation of genetic epidemiology research findings. Finally, we discuss the current state of genomic resources used in genetic association studies, functional interpretation, and clinical and public health translation of genomic findings with respect to diverse populations.
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Affiliation(s)
- Amke Caliebe
- Institute of Medical Informatics and StatisticsKiel University and University Hospital Schleswig‐HolsteinKielGermany
| | - Fasil Tekola‐Ayele
- Epidemiology Branch, Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaMarylandUSA
| | - Burcu F. Darst
- Center for Genetic EpidemiologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Public Health Sciences DivisionFred Hutchinson Cancer Research CenterSeattleWashingtonUSA
| | - Xuexia Wang
- Department of MathematicsUniversity of North TexasDentonTexasUSA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Jiang Gui
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth CollegeOne Medical Center Dr.LebanonNew HampshireUSA
| | | | - David J. Balding
- Melbourne Integrative Genomics, Schools of BioSciences and of Mathematics & StatisticsUniversity of MelbourneMelbourneAustralia
| | - Mohamad Saad
- Qatar Computing Research InstituteHamad Bin Khalifa UniversityDohaQatar
- Neuroscience Research Center, Faculty of Medical SciencesLebanese UniversityBeirutLebanon
| | - Marie‐Pierre Dubé
- Department of Medicine, and Social and Preventive MedicineUniversité de MontréalMontréalQuébecCanada
- Beaulieu‐Saucier Pharmacogenomcis CentreMontreal Heart InstituteMontrealCanada
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Oliveira MLG, Castelli EC, Veiga‐Castelli LC, Pereira ALE, Marcorin L, Carratto TMT, Souza AS, Andrade HS, Simões AL, Donadi EA, Courtin D, Sabbagh A, Giuliatti S, Mendes‐Junior CT. Genetic diversity of the
LILRB1
and
LILRB2
coding regions in an admixed Brazilian population sample. HLA 2022; 100:325-348. [DOI: 10.1111/tan.14725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/02/2022] [Accepted: 06/24/2022] [Indexed: 11/27/2022]
Affiliation(s)
| | - Erick C. Castelli
- Pathology Department, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Luciana C. Veiga‐Castelli
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Alison Luis E. Pereira
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Letícia Marcorin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Thássia M. T. Carratto
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Andreia S. Souza
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Heloisa S. Andrade
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Aguinaldo L. Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Eduardo A. Donadi
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | | | | | - Silvana Giuliatti
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Celso Teixeira Mendes‐Junior
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
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35
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Qiao J, Shao Z, Wu Y, Zeng P, Wang T. Detecting associated genes for complex traits shared across East Asian and European populations under the framework of composite null hypothesis testing. Lab Invest 2022; 20:424. [PMID: 36138484 PMCID: PMC9503281 DOI: 10.1186/s12967-022-03637-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/12/2022] [Indexed: 11/21/2022]
Abstract
Background Detecting trans-ethnic common associated genetic loci can offer important insights into shared genetic components underlying complex diseases/traits across diverse continental populations. However, effective statistical methods for such a goal are currently lacking. Methods By leveraging summary statistics available from global-scale genome-wide association studies, we herein proposed a novel genetic overlap detection method called CONTO (COmposite Null hypothesis test for Trans-ethnic genetic Overlap) from the perspective of high-dimensional composite null hypothesis testing. Unlike previous studies which generally analyzed individual genetic variants, CONTO is a gene-centric method which focuses on a set of genetic variants located within a gene simultaneously and assesses their joint significance with the trait of interest. By borrowing the similar principle of joint significance test (JST), CONTO takes the maximum P value of multiple associations as the significance measurement. Results Compared to JST which is often overly conservative, CONTO is improved in two aspects, including the construction of three-component mixture null distribution and the adjustment of trans-ethnic genetic correlation. Consequently, CONTO corrects the conservativeness of JST with well-calibrated P values and is much more powerful validated by extensive simulation studies. We applied CONTO to discover common associated genes for 31 complex diseases/traits between the East Asian and European populations, and identified many shared trait-associated genes that had otherwise been missed by JST. We further revealed that population-common genes were generally more evolutionarily conserved than population-specific or null ones. Conclusion Overall, CONTO represents a powerful method for detecting common associated genes across diverse ancestral groups; our results provide important implications on the transferability of GWAS discoveries in one population to others. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03637-8.
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Affiliation(s)
- Jiahao Qiao
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Zhonghe Shao
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Yuxuan Wu
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Ping Zeng
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China. .,Center for Medical Statistics and Data Analysis, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China. .,Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China. .,Key Laboratory of Environment and Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China. .,Engineering Research Innovation Center of Biological Data Mining and Healthcare Transformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
| | - Ting Wang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
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36
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No person left behind: Mapping the health policy landscape for genomics research in the Caribbean. LANCET REGIONAL HEALTH. AMERICAS 2022; 15:100367. [PMID: 36778076 PMCID: PMC9904062 DOI: 10.1016/j.lana.2022.100367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Caribbean has long been an under-represented geographical region in the field of genomics research. Such under-representation may result in Caribbean people being underserved by precision medicine and other public health benefits of genomics. A collaboration among regional and international researchers aims to address this issue through the H3ECaribbean project (Human Heredity, Environment, and Health in the Caribbean), which builds on the lessons and success of H3Africa. The Caribbean project aims to target issues of social justice by encouraging the inclusion of diverse Caribbean communities in genomics research. This paper explores a framework for the ethical and socially acceptable conduct of genomics research in the Caribbean, taking account of the cultural peculiarities of the region. This is done in part by exploring research ethics issues identified in indigenous communities in North America, Small Island Developing States, and similar endeavours from the African continent. The framework provides guidance for interacting with local community leaders, as well as detailing steps for obtaining informed consent of all participants. Specifically, the authors outline the methods to ensure effective interaction and enforce full transparency with study participants to combat historical neglect when working with under-represented communities in the Caribbean.
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O'Sullivan JW, Raghavan S, Marquez-Luna C, Luzum JA, Damrauer SM, Ashley EA, O'Donnell CJ, Willer CJ, Natarajan P. Polygenic Risk Scores for Cardiovascular Disease: A Scientific Statement From the American Heart Association. Circulation 2022; 146:e93-e118. [PMID: 35862132 PMCID: PMC9847481 DOI: 10.1161/cir.0000000000001077] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Cardiovascular disease is the leading contributor to years lost due to disability or premature death among adults. Current efforts focus on risk prediction and risk factor mitigation' which have been recognized for the past half-century. However, despite advances, risk prediction remains imprecise with persistently high rates of incident cardiovascular disease. Genetic characterization has been proposed as an approach to enable earlier and potentially tailored prevention. Rare mendelian pathogenic variants predisposing to cardiometabolic conditions have long been known to contribute to disease risk in some families. However, twin and familial aggregation studies imply that diverse cardiovascular conditions are heritable in the general population. Significant technological and methodological advances since the Human Genome Project are facilitating population-based comprehensive genetic profiling at decreasing costs. Genome-wide association studies from such endeavors continue to elucidate causal mechanisms for cardiovascular diseases. Systematic cataloging for cardiovascular risk alleles also enabled the development of polygenic risk scores. Genetic profiling is becoming widespread in large-scale research, including in health care-associated biobanks, randomized controlled trials, and direct-to-consumer profiling in tens of millions of people. Thus, individuals and their physicians are increasingly presented with polygenic risk scores for cardiovascular conditions in clinical encounters. In this scientific statement, we review the contemporary science, clinical considerations, and future challenges for polygenic risk scores for cardiovascular diseases. We selected 5 cardiometabolic diseases (coronary artery disease, hypercholesterolemia, type 2 diabetes, atrial fibrillation, and venous thromboembolic disease) and response to drug therapy and offer provisional guidance to health care professionals, researchers, policymakers, and patients.
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Wang QS, Edahiro R, Namkoong H, Hasegawa T, Shirai Y, Sonehara K, Tanaka H, Lee H, Saiki R, Hyugaji T, Shimizu E, Katayama K, Kanai M, Naito T, Sasa N, Yamamoto K, Kato Y, Morita T, Takahashi K, Harada N, Naito T, Hiki M, Matsushita Y, Takagi H, Ichikawa M, Nakamura A, Harada S, Sandhu Y, Kabata H, Masaki K, Kamata H, Ikemura S, Chubachi S, Okamori S, Terai H, Morita A, Asakura T, Sasaki J, Morisaki H, Uwamino Y, Nanki K, Uchida S, Uno S, Nishimura T, Ishiguro T, Isono T, Shibata S, Matsui Y, Hosoda C, Takano K, Nishida T, Kobayashi Y, Takaku Y, Takayanagi N, Ueda S, Tada A, Miyawaki M, Yamamoto M, Yoshida E, Hayashi R, Nagasaka T, Arai S, Kaneko Y, Sasaki K, Tagaya E, Kawana M, Arimura K, Takahashi K, Anzai T, Ito S, Endo A, Uchimura Y, Miyazaki Y, Honda T, Tateishi T, Tohda S, Ichimura N, Sonobe K, Sassa CT, Nakajima J, Nakano Y, Nakajima Y, Anan R, Arai R, Kurihara Y, Harada Y, Nishio K, Ueda T, Azuma M, Saito R, Sado T, Miyazaki Y, Sato R, Haruta Y, Nagasaki T, Yasui Y, Hasegawa Y, Mutoh Y, Kimura T, Sato T, Takei R, Hagimoto S, Noguchi Y, Yamano Y, Sasano H, Ota S, Nakamori Y, Yoshiya K, Saito F, Yoshihara T, Wada D, Iwamura H, Kanayama S, Maruyama S, Yoshiyama T, Ohta K, Kokuto H, Ogata H, Tanaka Y, Arakawa K, Shimoda M, Osawa T, Tateno H, Hase I, Yoshida S, Suzuki S, Kawada M, Horinouchi H, Saito F, Mitamura K, Hagihara M, Ochi J, Uchida T, Baba R, Arai D, Ogura T, Takahashi H, Hagiwara S, Nagao G, Konishi S, Nakachi I, Murakami K, Yamada M, Sugiura H, Sano H, Matsumoto S, Kimura N, Ono Y, Baba H, Suzuki Y, Nakayama S, Masuzawa K, Namba S, Shiroyama T, Noda Y, Niitsu T, Adachi Y, Enomoto T, Amiya S, Hara R, Yamaguchi Y, Murakami T, Kuge T, Matsumoto K, Yamamoto Y, Yamamoto M, Yoneda M, Tomono K, Kato K, Hirata H, Takeda Y, Koh H, Manabe T, Funatsu Y, Ito F, Fukui T, Shinozuka K, Kohashi S, Miyazaki M, Shoko T, Kojima M, Adachi T, Ishikawa M, Takahashi K, Inoue T, Hirano T, Kobayashi K, Takaoka H, Watanabe K, Miyazawa N, Kimura Y, Sado R, Sugimoto H, Kamiya A, Kuwahara N, Fujiwara A, Matsunaga T, Sato Y, Okada T, Hirai Y, Kawashima H, Narita A, Niwa K, Sekikawa Y, Nishi K, Nishitsuji M, Tani M, Suzuki J, Nakatsumi H, Ogura T, Kitamura H, Hagiwara E, Murohashi K, Okabayashi H, Mochimaru T, Nukaga S, Satomi R, Oyamada Y, Mori N, Baba T, Fukui Y, Odate M, Mashimo S, Makino Y, Yagi K, Hashiguchi M, Kagyo J, Shiomi T, Fuke S, Saito H, Tsuchida T, Fujitani S, Takita M, Morikawa D, Yoshida T, Izumo T, Inomata M, Kuse N, Awano N, Tone M, Ito A, Nakamura Y, Hoshino K, Maruyama J, Ishikura H, Takata T, Odani T, Amishima M, Hattori T, Shichinohe Y, Kagaya T, Kita T, Ohta K, Sakagami S, Koshida K, Hayashi K, Shimizu T, Kozu Y, Hiranuma H, Gon Y, Izumi N, Nagata K, Ueda K, Taki R, Hanada S, Kawamura K, Ichikado K, Nishiyama K, Muranaka H, Nakamura K, Hashimoto N, Wakahara K, Koji S, Omote N, Ando A, Kodama N, Kaneyama Y, Maeda S, Kuraki T, Matsumoto T, Yokote K, Nakada TA, Abe R, Oshima T, Shimada T, Harada M, Takahashi T, Ono H, Sakurai T, Shibusawa T, Kimizuka Y, Kawana A, Sano T, Watanabe C, Suematsu R, Sageshima H, Yoshifuji A, Ito K, Takahashi S, Ishioka K, Nakamura M, Masuda M, Wakabayashi A, Watanabe H, Ueda S, Nishikawa M, Chihara Y, Takeuchi M, Onoi K, Shinozuka J, Sueyoshi A, Nagasaki Y, Okamoto M, Ishihara S, Shimo M, Tokunaga Y, Kusaka Y, Ohba T, Isogai S, Ogawa A, Inoue T, Fukuyama S, Eriguchi Y, Yonekawa A, Kan-o K, Matsumoto K, Kanaoka K, Ihara S, Komuta K, Inoue Y, Chiba S, Yamagata K, Hiramatsu Y, Kai H, Asano K, Oguma T, Ito Y, Hashimoto S, Yamasaki M, Kasamatsu Y, Komase Y, Hida N, Tsuburai T, Oyama B, Takada M, Kanda H, Kitagawa Y, Fukuta T, Miyake T, Yoshida S, Ogura S, Abe S, Kono Y, Togashi Y, Takoi H, Kikuchi R, Ogawa S, Ogata T, Ishihara S, Kanehiro A, Ozaki S, Fuchimoto Y, Wada S, Fujimoto N, Nishiyama K, Terashima M, Beppu S, Yoshida K, Narumoto O, Nagai H, Ooshima N, Motegi M, Umeda A, Miyagawa K, Shimada H, Endo M, Ohira Y, Watanabe M, Inoue S, Igarashi A, Sato M, Sagara H, Tanaka A, Ohta S, Kimura T, Shibata Y, Tanino Y, Nikaido T, Minemura H, Sato Y, Yamada Y, Hashino T, Shinoki M, Iwagoe H, Takahashi H, Fujii K, Kishi H, Kanai M, Imamura T, Yamashita T, Yatomi M, Maeno T, Hayashi S, Takahashi M, Kuramochi M, Kamimaki I, Tominaga Y, Ishii T, Utsugi M, Ono A, Tanaka T, Kashiwada T, Fujita K, Saito Y, Seike M, Watanabe H, Matsuse H, Kodaka N, Nakano C, Oshio T, Hirouchi T, Makino S, Egi M, Omae Y, Nannya Y, Ueno T, Takano T, Katayama K, Ai M, Kumanogoh A, Sato T, Hasegawa N, Tokunaga K, Ishii M, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K, Okada Y. The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force. Nat Commun 2022; 13:4830. [PMID: 35995775 PMCID: PMC9395416 DOI: 10.1038/s41467-022-32276-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/25/2022] [Indexed: 11/12/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection. Genetic mechanisms influencing COVID-19 susceptibility are not well understood. Here, the authors analyzed whole blood RNA-seq data of 465 Japanese individuals with COVID-19, highlighting thousands of fine-mapped variants affecting expression and splicing of genes, as well as the presence of COVID-19 severity-interaction eQTLs.
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Willcox MC, Burgueño JA, Jeffers D, Rodriguez-Chanona E, Guadarrama-Espinoza A, Kehel Z, Chepetla D, Shrestha R, Swarts K, Buckler ES, Hearne S, Chen C. Mining alleles for tar spot complex resistance from CIMMYT's maize Germplasm Bank. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.937200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The tar spot complex (TSC) is a devastating disease of maize (Zea mays L.), occurring in 17 countries throughout Central, South, and North America and the Caribbean, and can cause grain yield losses of up to 80%. As yield losses from the disease continue to intensify in Central America, Phyllachora maydis, one of the causal pathogens of TSC, was first detected in the United States in 2015, and in 2020 in Ontario, Canada. Both the distribution and yield losses due to TSC are increasing, and there is a critical need to identify the genetic resources for TSC resistance. The Seeds of Discovery Initiative at CIMMYT has sought to combine next-generation sequencing technologies and phenotypic characterization to identify valuable alleles held in the CIMMYT Germplasm Bank for use in germplasm improvement programs. Individual landrace accessions of the “Breeders' Core Collection” were crossed to CIMMYT hybrids to form 918 unique accessions topcrosses (F1 families) which were evaluated during 2011 and 2012 for TSC disease reaction. A total of 16 associated SNP variants were identified for TSC foliar leaf damage resistance and increased grain yield. These variants were confirmed by evaluating the TSC reaction of previously untested selections of the larger F1 testcross population (4,471 accessions) based on the presence of identified favorable SNPs. We demonstrated the usefulness of mining for donor alleles in Germplasm Bank accessions for newly emerging diseases using genomic variation in landraces.
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Byun J, Han Y, Li Y, Xia J, Long E, Choi J, Xiao X, Zhu M, Zhou W, Sun R, Bossé Y, Song Z, Schwartz A, Lusk C, Rafnar T, Stefansson K, Zhang T, Zhao W, Pettit RW, Liu Y, Li X, Zhou H, Walsh KM, Gorlov I, Gorlova O, Zhu D, Rosenberg SM, Pinney S, Bailey-Wilson JE, Mandal D, de Andrade M, Gaba C, Willey JC, You M, Anderson M, Wiencke JK, Albanes D, Lam S, Tardon A, Chen C, Goodman G, Bojeson S, Brenner H, Landi MT, Chanock SJ, Johansson M, Muley T, Risch A, Wichmann HE, Bickeböller H, Christiani DC, Rennert G, Arnold S, Field JK, Shete S, Le Marchand L, Melander O, Brunnstrom H, Liu G, Andrew AS, Kiemeney LA, Shen H, Zienolddiny S, Grankvist K, Johansson M, Caporaso N, Cox A, Hong YC, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Patel A, Lan Q, Rothman N, Taylor F, Kachuri L, Witte JS, Sakoda LC, Spitz M, Brennan P, Lin X, McKay J, Hung RJ, Amos CI. Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer. Nat Genet 2022; 54:1167-1177. [PMID: 35915169 PMCID: PMC9373844 DOI: 10.1038/s41588-022-01115-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 05/27/2022] [Indexed: 02/03/2023]
Abstract
To identify new susceptibility loci to lung cancer among diverse populations, we performed cross-ancestry genome-wide association studies in European, East Asian and African populations and discovered five loci that have not been previously reported. We replicated 26 signals and identified 10 new lead associations from previously reported loci. Rare-variant associations tended to be specific to populations, but even common-variant associations influencing smoking behavior, such as those with CHRNA5 and CYP2A6, showed population specificity. Fine-mapping and expression quantitative trait locus colocalization nominated several candidate variants and susceptibility genes such as IRF4 and FUBP1. DNA damage assays of prioritized genes in lung fibroblasts indicated that a subset of these genes, including the pleiotropic gene IRF4, potentially exert effects by promoting endogenous DNA damage.
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Affiliation(s)
- Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Yafang Li
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jun Xia
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Erping Long
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiangjun Xiao
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, P. R. China
| | - Wen Zhou
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, University of Texas, M.D. Anderson Cancer Center, Houston, TX, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Zhuoyi Song
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ann Schwartz
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Karmanos Cancer Institute, Detroit, MI, USA
| | - Christine Lusk
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Karmanos Cancer Institute, Detroit, MI, USA
| | | | | | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rowland W Pettit
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Yanhong Liu
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Xihao Li
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Hufeng Zhou
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Kyle M Walsh
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Ivan Gorlov
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Olga Gorlova
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Dakai Zhu
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Susan M Rosenberg
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Susan Pinney
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Diptasri Mandal
- Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | | | - Colette Gaba
- The University of Toledo College of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA
| | - James C Willey
- The University of Toledo College of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA
| | - Ming You
- Center for Cancer Prevention, Houston Methodist Research Institute, Houston, TX, USA
| | | | - John K Wiencke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephan Lam
- Department of Integrative Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Adonina Tardon
- Public Health Department, University of Oviedo, ISPA and CIBERESP, Asturias, Spain
| | - Chu Chen
- Program in Epidemiology, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Stig Bojeson
- Department of Clinical Biochemistry, Herlev Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mattias Johansson
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Thomas Muley
- Division of Cancer Epigenomics, DKFZ - German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Angela Risch
- Division of Cancer Epigenomics, DKFZ - German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Biosciences and Medical Biology, Allergy-Cancer-BioNano Research Centre, University of Salzburg, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | | | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - David C Christiani
- Department of Epidemiology, Harvard T.H.Chan School of Public Health, Boston, MA, USA
| | - Gad Rennert
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Susanne Arnold
- University of Kentucky, Markey Cancer Center, Lexington, KY, USA
| | - John K Field
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Sanjay Shete
- Department of Biostatistics, University of Texas, M.D. Anderson Cancer Center, Houston, TX, USA
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | | | - Geoffrey Liu
- University Health Network- The Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Angeline S Andrew
- Departments of Epidemiology and Community and Family Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, P. R. China
| | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Mikael Johansson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Angela Cox
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jian-Min Yuan
- UPMC Hillman Cancer Center and Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, WA, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Melinda C Aldrich
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alpa Patel
- American Cancer Society, Atlanta, GA, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Fiona Taylor
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Margaret Spitz
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Paul Brennan
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Xihong Lin
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - James McKay
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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Thanh Nguyen D, Hoang Nguyen Q, Thuy Duong N, Vo NS. LmTag: functional-enrichment and imputation-aware tag SNP selection for population-specific genotyping arrays. Brief Bioinform 2022; 23:6627269. [PMID: 35780383 DOI: 10.1093/bib/bbac252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/02/2022] [Accepted: 05/31/2022] [Indexed: 12/16/2022] Open
Abstract
Despite the rapid development of sequencing technology, single-nucleotide polymorphism (SNP) arrays are still the most cost-effective genotyping solutions for large-scale genomic research and applications. Recent years have witnessed the rapid development of numerous genotyping platforms of different sizes and designs, but population-specific platforms are still lacking, especially for those in developing countries. SNP arrays designed for these countries should be cost-effective (small size), yet incorporate key information needed to associate genotypes with traits. A key design principle for most current platforms is to improve genome-wide imputation so that more SNPs not included in the array (imputed SNPs) can be predicted. However, current tag SNP selection methods mostly focus on imputation accuracy and coverage, but not the functional content of the array. It is those functional SNPs that are most likely associated with traits. Here, we propose LmTag, a novel method for tag SNP selection that not only improves imputation performance but also prioritizes highly functional SNP markers. We apply LmTag on a wide range of populations using both public and in-house whole-genome sequencing databases. Our results show that LmTag improved both functional marker prioritization and genome-wide imputation accuracy compared to existing methods. This novel approach could contribute to the next generation genotyping arrays that provide excellent imputation capability as well as facilitate array-based functional genetic studies. Such arrays are particularly suitable for under-represented populations in developing countries or non-model species, where little genomics data are available while investment in genome sequencing or high-density SNP arrays is limited. $\textrm{LmTag}$ is available at: https://github.com/datngu/LmTag.
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Affiliation(s)
- Dat Thanh Nguyen
- Center for Biomedical Informatics, Vingroup Big Data Institute, 458 Minh Khai, 10000, Hanoi, Vietnam
| | - Quan Hoang Nguyen
- Institute for Molecular Bioscience, University of Queensland, st Lucia, QLD 4067, Brisbane, Australia
| | - Nguyen Thuy Duong
- Center for Biomedical Informatics, Vingroup Big Data Institute, 458 Minh Khai, 10000, Hanoi, Vietnam.,Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, 10000, Hanoi, Vietnam
| | - Nam S Vo
- Center for Biomedical Informatics, Vingroup Big Data Institute, 458 Minh Khai, 10000, Hanoi, Vietnam.,College of Engineering and Computer Science, VinUniversity, Vinhomes Ocean Park, 10000, Hanoi, Vietnam
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Abstract
PURPOSE OF REVIEW This article discusses the spectrum of genetic risk in familial and sporadic forms of early- and late-onset Alzheimer disease (AD). Recent work illuminating the complex genetic architecture of AD is discussed in the context of high and low risk and what is known in different populations. RECENT FINDINGS A small proportion of AD is autosomal dominant familial AD caused by variants in PSEN1, PSEN2, or APP, although more recently described rare genetic changes can also increase risk substantially over the general population, with odds ratios estimated at 2 to 4. APOE remains the strongest genetic risk factor for late-onset AD, and understanding the biology of APOE has yielded mechanistic insights and leads for therapeutic interventions. Genome-wide studies enabled by rapidly developing technologic advances in sequencing have identified numerous risk factors that have a low impact on risk but are widely shared throughout the population and involve a repertoire of cell pathways, again shining light on potential paths to intervention. Population studies aimed at defining and stratifying genetic AD risk have been informative, although they are not yet widely applicable clinically because the studies were not performed in people with diverse ancestry and ethnicity and thus population-wide data are lacking. SUMMARY The value of genetic information to practitioners in the clinic is distinct from information sought by researchers looking to identify novel therapeutic targets. It is possible to envision a future in which genetic stratification joins other biomarkers to facilitate therapeutic choices and inform prognosis. Genetics already has transformed our understanding of AD pathogenesis and will, no doubt, continue to reveal the complexity of brain biology in health and disease.
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Zimmermann MT. Molecular Modeling is an Enabling Approach to Complement and Enhance Channelopathy Research. Compr Physiol 2022; 12:3141-3166. [PMID: 35578963 DOI: 10.1002/cphy.c190047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hundreds of human membrane proteins form channels that transport necessary ions and compounds, including drugs and metabolites, yet details of their normal function or how function is altered by genetic variants to cause diseases are often unknown. Without this knowledge, researchers are less equipped to develop approaches to diagnose and treat channelopathies. High-resolution computational approaches such as molecular modeling enable researchers to investigate channelopathy protein function, facilitate detailed hypothesis generation, and produce data that is difficult to gather experimentally. Molecular modeling can be tailored to each physiologic context that a protein may act within, some of which may currently be difficult or impossible to assay experimentally. Because many genomic variants are observed in channelopathy proteins from high-throughput sequencing studies, methods with mechanistic value are needed to interpret their effects. The eminent field of structural bioinformatics integrates techniques from multiple disciplines including molecular modeling, computational chemistry, biophysics, and biochemistry, to develop mechanistic hypotheses and enhance the information available for understanding function. Molecular modeling and simulation access 3D and time-dependent information, not currently predictable from sequence. Thus, molecular modeling is valuable for increasing the resolution with which the natural function of protein channels can be investigated, and for interpreting how genomic variants alter them to produce physiologic changes that manifest as channelopathies. © 2022 American Physiological Society. Compr Physiol 12:3141-3166, 2022.
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Affiliation(s)
- Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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Khan SU, Zheng Y, Chachar Z, Zhang X, Zhou G, Zong N, Leng P, Zhao J. Dissection of Maize Drought Tolerance at the Flowering Stage Using Genome-Wide Association Studies. Genes (Basel) 2022; 13:genes13040564. [PMID: 35456369 PMCID: PMC9031386 DOI: 10.3390/genes13040564] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 01/01/2023] Open
Abstract
Drought is one of the most critical environmental factors constraining maize production. When it occurs at the flowering stage, serious yield losses are caused, and often, the damage is irretrievable. In this study, anthesis to silk interval (ASI), plant height (PH), and ear biomass at the silking date (EBM) of 279 inbred lines were studied under both water-stress (WS) and well-water (WW) field conditions, for three consecutive years. Averagely, ASI was extended by 25.96%, EBM was decreased by 17.54%, and the PH was reduced by 12.47% under drought stress. Genome-wide association studies were carried out using phenotypic values under WS, WW, and drought-tolerance index (WS-WW or WS/WW) and applying a mixed linear model that controls both population structure and relative kinship. In total, 71, 159, and 21 SNPs, located in 32, 59, and 12 genes, were significantly (P < 10−5) associated with ASI, EBM, and PH, respectively. Only a few overlapped candidate genes were found to be associated with the same drought-related traits under different environments, for example, ARABIDILLO 1, glycoprotein, Tic22-like, and zinc-finger family protein for ASI; 26S proteasome non-ATPase and pyridoxal phosphate transferase for EBM; 11-ß-hydroxysteroid dehydrogenase, uncharacterised, Leu-rich repeat protein kinase, and SF16 protein for PH. Furthermore, most candidate genes were revealed to be drought-responsive in an association panel. Meanwhile, the favourable alleles/key variations were identified with a haplotype analysis. These candidate genes and their key variations provide insight into the genetic basis of drought tolerance, especially for the female inflorescence, and will facilitate drought-tolerant maize breeding.
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Affiliation(s)
- Siffat Ullah Khan
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
| | - Yanxiao Zheng
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
| | - Zaid Chachar
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
| | - Xuhuan Zhang
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
| | - Guyi Zhou
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
| | - Na Zong
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
| | - Pengfei Leng
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
- Correspondence: (P.L.); (J.Z.)
| | - Jun Zhao
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.U.K.); (Y.Z.); (Z.C.); (X.Z.); (G.Z.); (N.Z.)
- Correspondence: (P.L.); (J.Z.)
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VEGF-A, VEGFR1 and VEGFR2 single nucleotide polymorphisms and outcomes from the AGITG MAX trial of capecitabine, bevacizumab and mitomycin C in metastatic colorectal cancer. Sci Rep 2022; 12:1238. [PMID: 35075138 PMCID: PMC8786898 DOI: 10.1038/s41598-021-03952-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/24/2021] [Indexed: 02/08/2023] Open
Abstract
The phase III MAX clinical trial randomised patients with metastatic colorectal cancer (mCRC) to receive first-line capecitabine chemotherapy alone or in combination with the anti-VEGF-A antibody bevacizumab (± mitomycin C). We utilised this cohort to examine whether single nucleotide polymorphisms (SNPs) in VEGF-A, VEGFR1, and VEGFR2 are predictive of efficacy outcomes with bevacizumab or the development of hypertension. Genomic DNA extracted from archival FFPE tissue for 325 patients (69% of the MAX trial population) was used to genotype 16 candidate SNPs in VEGF-A, VEGFR1, and VEGFR2, which were analysed for associations with efficacy outcomes and hypertension. The VEGF-A rs25648 ‘CC’ genotype was prognostic for improved PFS (HR 0.65, 95% CI 0.49 to 0.85; P = 0.002) and OS (HR 0.70, 95% CI 0.52 to 0.94; P = 0.019). The VEGF-A rs699947 ‘AA’ genotype was prognostic for shorter PFS (HR 1.32, 95% CI 1.002 to 1.74; P = 0.048). None of the analysed SNPs were predictive of bevacizumab efficacy outcomes. VEGFR2 rs11133360 ‘TT’ was associated with a lower risk of grade ≥ 3 hypertension (P = 0.028). SNPs in VEGF-A, VEGFR1 and VEGFR2 did not predict bevacizumab benefit. However, VEGF-A rs25648 and rs699947 were identified as novel prognostic biomarkers and VEGFR2 rs11133360 was associated with less grade ≥ 3 hypertension.
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Aftab F, Ahmed S, Ali SM, Ame SM, Bahl R, Baqui AH, Chowdhury NH, Deb S, Dhingra U, Dutta A, Hasan T, Hotwani A, Ilyas M, Javaid M, Jehan F, Juma MH, Khalid F, Khanam R, Manu AA, Mehmood U, Minckas N, Mitra DK, Nisar I, Polašek O, Rahman S, Rudan I, Sajid M, Sazawal S, Yoshida S. Cohort Profile: The Alliance for Maternal and Newborn Health Improvement (AMANHI) biobanking study. Int J Epidemiol 2022; 50:1780-1781i. [PMID: 34999881 PMCID: PMC8743110 DOI: 10.1093/ije/dyab124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 11/20/2022] Open
Affiliation(s)
- Fahad Aftab
- Center for Public Health Kinetics, Global Zanzibar, Tanzania
| | | | | | | | - Rajiv Bahl
- Department for Maternal, Newborn, Child, and Adolescent Health, and Ageing, World Health Organization, Geneva, Switzerland
| | - Abdullah H Baqui
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Saikat Deb
- Public Health Laboratory-IdC, Pemba, Zanzibar, Tanzania
- Center for Public Health Kinetics, New Delhi, India
| | - Usha Dhingra
- Center for Public Health Kinetics, New Delhi, India
| | - Arup Dutta
- Center for Public Health Kinetics, New Delhi, India
| | | | - Aneeta Hotwani
- The Department of Paediatrics and Child Health, Aga Khan University, Karachi, Sind Pakistan
| | - Muhammad Ilyas
- The Department of Paediatrics and Child Health, Aga Khan University, Karachi, Sind Pakistan
| | - Mohammad Javaid
- The Department of Paediatrics and Child Health, Aga Khan University, Karachi, Sind Pakistan
| | - Fyezah Jehan
- The Department of Paediatrics and Child Health, Aga Khan University, Karachi, Sind Pakistan
| | | | - Farah Khalid
- The Department of Paediatrics and Child Health, Aga Khan University, Karachi, Sind Pakistan
| | - Rasheda Khanam
- International Center for Maternal and Newborn Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Alexander Ansah Manu
- Department of Epidemiology and Disease Control, University of Ghana School of Public Health, Legon, Accra, Ghana
| | - Usma Mehmood
- The Department of Paediatrics and Child Health, Aga Khan University, Karachi, Sind Pakistan
| | - Nicole Minckas
- Department for Maternal, Newborn, Child, and Adolescent Health, and Ageing, World Health Organization, Geneva, Switzerland
| | | | - Imran Nisar
- The Department of Paediatrics and Child Health, Aga Khan University, Karachi, Sind Pakistan
| | - Ozren Polašek
- University of Split School of Medicine, Split, Croatia
- Gen–info Ltd, Zagreb, Croatia
| | | | - Igor Rudan
- Centre for Global Health, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Muhammad Sajid
- The Department of Paediatrics and Child Health, Aga Khan University, Karachi, Sind Pakistan
| | - Sunil Sazawal
- Center for Public Health Kinetics, Global Zanzibar, Tanzania
- Center for Public Health Kinetics, New Delhi, India
| | - Sachiyo Yoshida
- Department for Maternal, Newborn, Child, and Adolescent Health, and Ageing, World Health Organization, Geneva, Switzerland
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Wang T, Huang YY, Liu XL, Molassiotis A, Yao LQ, Zheng SL, Tan JY(B, Huang HQ. Prevalence and correlates of joint pain among Chinese breast cancer survivors receiving aromatase inhibitor treatment. Support Care Cancer 2022; 30:9279-9288. [PMID: 36065027 PMCID: PMC9633515 DOI: 10.1007/s00520-022-07345-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/24/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND Aromatase inhibitor (AI)-induced joint pain is a common toxicity of AI treatment. Although many studies have been conducted to examine the occurrence and severity of AI-induced joint pain in breast cancer survivors, none of the studies focused on the Chinese population with breast cancer. Given that the differences in cultural background and the genetic structure between Asians and Caucasians may contribute to different phenotypes of joint pain, this cross-sectional study was therefore conducted to examine the prevalence of AI-induced joint pain among Chinese breast cancer survivors receiving AI treatment and the correlates of pain. METHODS This cross-sectional study was conducted in a tertiary hospital in China. Breast cancer survivors undergoing AI treatment were recruited to complete the following questionnaires: a self-designed baseline data form, the Nordic Musculoskeletal Questionnaire (NMQ), the Brief Pain Inventory (BPI), the 36-Item Short Form Health Survey (SF-36), and the Functional Assessment of Cancer Therapy-Breast (FACT-B). Based on the assessment results of NMQ (if the participant indicated pain in specific body parts), participants were then invited to complete other questionnaires to specifically assess the joint symptoms, including the Oxford Knee Score (OKS), the Oxford Hip Score (OHS), the Michigan Hand Outcomes Questionnaire (MHQ), and the Manchester Foot Pain Disability Questionnaire (MFPDQ). Descriptive analysis was used to analyse participants' baseline data and the prevalence of pain. Stepwise multiple regression was used to identify the correlates of pain. RESULTS Four hundred and ten participants were analysed. According to the NMQ, 71.7% of the participants experienced joint symptoms in at least one joint, and the most frequently mentioned joint was knee (39.0%). The diagram in BPI indicated that 28.0% of the participants had the worst pain around knees. In patients with knee pain, the mean OKS score was 40.46 ± 6.19. The sub-scores of BPI for pain intensity and pain interference were 1.30 ± 1.63 and 1.24 ± 1.79, respectively. Patients' poorer physical well-being/functioning, previous use of AI treatment, presence of osteoarthritis, and receiving of physiotherapy were identified as four common correlates of greater severity of pain and pain interference (p < 0.05). CONCLUSIONS Chinese breast cancer survivors can experience joint pain at various locations, particularly knees. In addition to increasing the use of interventions for pain alleviation, a comprehensive assessment of survivors' conditions such as physical functioning, history of AI treatment, and presence of osteoarthritis should be emphasized to identify survivors who need more attention and tailored interventions.
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Affiliation(s)
- Tao Wang
- College of Nursing and Midwifery, Charles Darwin University, 410 Ann Street, Brisbane, QLD 4000 Australia
| | - Yu-Yan Huang
- School of Nursing, Southwest Medical University, 319 Zhongshan Rd 3rd Section, Luzhou, 646000 Sichuan China
| | - Xian-Liang Liu
- College of Nursing and Midwifery, Charles Darwin University, 410 Ann Street, Brisbane, QLD 4000 Australia
| | - Alex Molassiotis
- School of Nursing, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR
| | - Li-Qun Yao
- College of Nursing and Midwifery, Charles Darwin University, 410 Ann Street, Brisbane, QLD 4000 Australia
| | - Si-Lin Zheng
- The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, 646000 Sichuan China
| | - Jing-Yu (Benjamin) Tan
- College of Nursing and Midwifery, Charles Darwin University, 410 Ann Street, Brisbane, QLD 4000 Australia
| | - Hou-Qiang Huang
- The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, 646000 Sichuan China
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Zenebe-Gete S, Salowe R, O'Brien JM. Benefits of Cohort Studies in a Consortia-Dominated Landscape. Front Genet 2021; 12:801653. [PMID: 34950194 PMCID: PMC8688987 DOI: 10.3389/fgene.2021.801653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Selam Zenebe-Gete
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Rebecca Salowe
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Joan M O'Brien
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, United States
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A missense variant in SHARPIN mediates Alzheimer's disease-specific brain damages. Transl Psychiatry 2021; 11:590. [PMID: 34785643 PMCID: PMC8595886 DOI: 10.1038/s41398-021-01680-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 08/04/2021] [Accepted: 08/27/2021] [Indexed: 01/23/2023] Open
Abstract
Established genetic risk factors for Alzheimer's disease (AD) account for only a portion of AD heritability. The aim of this study was to identify novel associations between genetic variants and AD-specific brain atrophy. We conducted genome-wide association studies for brain magnetic resonance imaging measures of hippocampal volume and entorhinal cortical thickness in 2643 Koreans meeting the clinical criteria for AD (n = 209), mild cognitive impairment (n = 1449) or normal cognition (n = 985). A missense variant, rs77359862 (R274W), in the SHANK-associated RH Domain Interactor (SHARPIN) gene was associated with entorhinal cortical thickness (p = 5.0 × 10-9) and hippocampal volume (p = 5.1 × 10-12). It revealed an increased risk of developing AD in the mediation analyses. This variant was also associated with amyloid-β accumulation (p = 0.03) and measures of memory (p = 1.0 × 10-4) and executive function (p = 0.04). We also found significant association of other SHARPIN variants with hippocampal volume in the Alzheimer's Disease Neuroimaging Initiative (rs3417062, p = 4.1 × 10-6) and AddNeuroMed (rs138412600, p = 5.9 × 10-5) cohorts. Further, molecular dynamics simulations and co-immunoprecipitation indicated that the variant significantly reduced the binding of linear ubiquitination assembly complex proteins, SHPARIN and HOIL-1 Interacting Protein (HOIP), altering the downstream NF-κB signaling pathway. These findings suggest that SHARPIN plays an important role in the pathogenesis of AD.
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50
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Osteopontin Gene Polymorphisms Are Associated with Cardiovascular Risk Factors in Patients with Premature Coronary Artery Disease. Biomedicines 2021; 9:biomedicines9111600. [PMID: 34829826 PMCID: PMC8615378 DOI: 10.3390/biomedicines9111600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/30/2021] [Accepted: 10/31/2021] [Indexed: 11/20/2022] Open
Abstract
Osteopontin (OPN) is considered a clinical predictor of cardiovascular disease. We aimed to evaluate the association of the OPN gene polymorphisms rs2728127 and rs11730582 with the development of premature coronary artery disease (pCAD), cardiovascular risk factors, and cardiometabolic parameters. We evaluated 1142 patients with pCAD and 1073 controls. Both polymorphisms were determined by Taqman assays. Similar allele and genotype frequencies were observed in both groups; additionally, an association of these polymorphisms with CAD and cardiometabolic parameters was observed in both groups. In patients with pCAD, the rs11730582 was associated with a high risk of hypoadiponectinemia (OR = 1.300, P additive = 0.003), low risk of hypertension (OR = 0.709, P codominant 1 = 0.030), and low risk of having high non-HDL cholesterol (OR = 0.637, P additive = 0.038). In the control group, the rs2728127 was associated with a low risk of fatty liver (OR = 0.766, P additive = 0.038); while the rs11730582 was associated with a low risk of hypoadiponectinemia (OR = 0.728, P dominant = 0.022), and risk of having elevated apolipoprotein B (OR = 1.400, P dominant = 0.031). Our results suggest that in Mexican individuals, the rs11730582 and rs2728127 OPN gene polymorphisms are associated with some abnormal metabolic variables in patients with pCAD and controls.
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