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Betschart RO, Riccio C, Aguilera-Garcia D, Blankenberg S, Guo L, Moch H, Seidl D, Solleder H, Thalén F, Thiéry A, Twerenbold R, Zeller T, Zoche M, Ziegler A. Biostatistical Aspects of Whole Genome Sequencing Studies: Preprocessing and Quality Control. Biom J 2024; 66:e202300278. [PMID: 38988195 DOI: 10.1002/bimj.202300278] [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: 10/09/2023] [Revised: 03/21/2024] [Accepted: 05/14/2024] [Indexed: 07/12/2024]
Abstract
Rapid advances in high-throughput DNA sequencing technologies have enabled large-scale whole genome sequencing (WGS) studies. Before performing association analysis between phenotypes and genotypes, preprocessing and quality control (QC) of the raw sequence data need to be performed. Because many biostatisticians have not been working with WGS data so far, we first sketch Illumina's short-read sequencing technology. Second, we explain the general preprocessing pipeline for WGS studies. Third, we provide an overview of important QC metrics, which are applied to WGS data: on the raw data, after mapping and alignment, after variant calling, and after multisample variant calling. Fourth, we illustrate the QC with the data from the GENEtic SequencIng Study Hamburg-Davos (GENESIS-HD), a study involving more than 9000 human whole genomes. All samples were sequenced on an Illumina NovaSeq 6000 with an average coverage of 35× using a PCR-free protocol. For QC, one genome in a bottle (GIAB) trio was sequenced in four replicates, and one GIAB sample was successfully sequenced 70 times in different runs. Fifth, we provide empirical data on the compression of raw data using the DRAGEN original read archive (ORA). The most important quality metrics in the application were genetic similarity, sample cross-contamination, deviations from the expected Het/Hom ratio, relatedness, and coverage. The compression ratio of the raw files using DRAGEN ORA was 5.6:1, and compression time was linear by genome coverage. In summary, the preprocessing, joint calling, and QC of large WGS studies are feasible within a reasonable time, and efficient QC procedures are readily available.
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Affiliation(s)
| | | | - Domingo Aguilera-Garcia
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Stefan Blankenberg
- Cardio-CARE, Medizincampus Davos, Davos, Switzerland
- Department of Cardiology, University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Population Health Innovation (POINT), University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Linlin Guo
- Department of Cardiology, University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Holger Moch
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Dagmar Seidl
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Hugo Solleder
- Cardio-CARE, Medizincampus Davos, Davos, Switzerland
| | - Felix Thalén
- Cardio-CARE, Medizincampus Davos, Davos, Switzerland
| | | | - Raphael Twerenbold
- Department of Cardiology, University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Population Health Innovation (POINT), University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Tanja Zeller
- Department of Cardiology, University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Population Health Innovation (POINT), University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Martin Zoche
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Andreas Ziegler
- Cardio-CARE, Medizincampus Davos, Davos, Switzerland
- Department of Cardiology, University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Population Health Innovation (POINT), University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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Unnikrishnan P, Grzesik S, Trojańska M, Klimek B, Plesnar-Bielak A. 6Pgdh polymorphism in wild bulb mite populations: prevalence, environmental correlates and life history trade-offs. EXPERIMENTAL & APPLIED ACAROLOGY 2024; 93:115-132. [PMID: 38597987 PMCID: PMC11182828 DOI: 10.1007/s10493-024-00909-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
Genetic polymorphism in key metabolic genes plays a pivotal role in shaping phenotypes and adapting to varying environments. Polymorphism in the metabolic gene 6-phosphogluconate dehydrogenase (6Pgdh) in bulb mites, Rhizoglyphus robini is characterized by two alleles, S and F, that differ by a single amino acid substitution and correlate with male reproductive fitness. The S-bearing males demonstrate a reproductive advantage. Although the S allele rapidly fixes in laboratory settings, the persistence of polymorphic populations in the wild is noteworthy. This study examines the prevalence and stability of 6Pgdh polymorphism in natural populations across Poland, investigating potential environmental influences and seasonal variations. We found widespread 6Pgdh polymorphism in natural populations, with allele frequencies varying across locations and sampling dates but without clear geographical or seasonal clines. This widespread polymorphism and spatio-temporal variability may be attributed to population demography and gene flow between local populations. We found some correlation between soil properties, particularly cation content (Na, K, Ca, and Mg) and 6Pgdh allele frequencies, showcasing the connection between mite physiology and soil characteristics and highlighting the presence of environment-dependent balancing selection. We conducted experimental fitness assays to determine whether the allele providing the advantage in male-male competition has antagonistic effects on life-history traits and if these effects are temperature-dependent. We found that temperature does not differentially influence development time or juvenile survival in different 6Pgdh genotypes. This study reveals the relationship between genetic variation, environmental factors, and reproductive fitness in natural bulb mite populations, shedding light on the dynamic mechanisms governing 6Pgdh polymorphism.
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Affiliation(s)
- Pranav Unnikrishnan
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland.
| | - Szymon Grzesik
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Magdalena Trojańska
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
- Department of Pathobiology, Institute of Microbiology, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Beata Klimek
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Agata Plesnar-Bielak
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
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3
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Bellavance J, Wang L, Gagliano Taliun SA. Eight quick tips for including chromosome X in genome-wide association studies. PLoS Comput Biol 2024; 20:e1012160. [PMID: 38843110 PMCID: PMC11156303 DOI: 10.1371/journal.pcbi.1012160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024] Open
Affiliation(s)
- Justin Bellavance
- Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
- Research Centre, Montréal Heart Institute, Montréal, Québec, Canada
| | - Linda Wang
- Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
- Research Centre, Montréal Heart Institute, Montréal, Québec, Canada
| | - Sarah A. Gagliano Taliun
- Research Centre, Montréal Heart Institute, Montréal, Québec, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
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Chávez-Vélez E, Álvarez-Nava F, Torres-Vinueza A, Balarezo-Díaz T, Pilataxi K, Acosta-López C, Peña IZ, Narváez K. Single nucleotide variants in the CCL2, OAS1 and DPP9 genes and their association with the severity of COVID-19 in an Ecuadorian population. Front Cell Infect Microbiol 2024; 14:1322882. [PMID: 38694517 PMCID: PMC11061356 DOI: 10.3389/fcimb.2024.1322882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/15/2024] [Indexed: 05/04/2024] Open
Abstract
COVID-19 has a broad clinical spectrum, ranging from asymptomatic-mild form to severe phenotype. The severity of COVID-19 is a complex trait influenced by various genetic and environmental factors. Ethnic differences have been observed in relation to COVID-19 severity during the pandemic. It is currently unknown whether genetic variations may contribute to the increased risk of severity observed in Latin-American individuals The aim of this study is to investigate the potential correlation between gene variants at CCL2, OAS1, and DPP9 genes and the severity of COVID-19 in a population from Quito, Ecuador. This observational case-control study was conducted at the Carrera de Biologia from the Universidad Central del Ecuador and the Hospital Quito Sur of the Instituto Ecuatoriano de Seguridad Social (Quito-SUR-IESS), Quito, Ecuador. Genotyping for gene variants at rs1024611 (A>G), rs10774671 (A>G), and rs10406145 (G>C) of CCL2, OAS1, and DPP9 genes was performed on 100 COVID-19 patients (43 with severe form and 57 asymptomatic-mild) using RFLP-PCR. The genotype distribution of all SNVs throughout the entire sample of 100 individuals showed Hardy Weinberg equilibrium (P=0.53, 0.35, and 0.4 for CCL2, OAS1, and DPP9, respectively). The HWE test did not find any statistically significant difference in genotype distribution between the study and control groups for any of the three SNVs. The multivariable logistic regression analysis showed that individuals with the GG of the CCL2 rs1024611 gene variant had an increased association with the severe COVID-19 phenotype in a recessive model (P = 0.0003, OR = 6.43, 95% CI 2.19-18.89) and for the OAS1 rs10774671 gene variant, the log-additive model showed a significant association with the severe phenotype of COVID-19 (P=0.0084, OR=3.85, 95% CI 1.33-11.12). Analysis of haplotype frequencies revealed that the coexistence of GAG at CCL2, OAS1, and DPP9 variants, respectively, in the same individual increased the presence of the severe COVID-19 phenotype (OR=2.273, 95% CI: 1.271-4.068, P=0.005305). The findings of the current study suggests that the ethnic background affects the allele and genotype frequencies of genes associated with the severity of COVID-19. The experience with COVID-19 has provided an opportunity to identify an ethnicity-based approach to recognize genetically high-risk individuals in different populations for emerging diseases.
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Affiliation(s)
- Erik Chávez-Vélez
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Francisco Álvarez-Nava
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Alisson Torres-Vinueza
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Thalía Balarezo-Díaz
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Kathya Pilataxi
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Camila Acosta-López
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Ivonne Z. Peña
- Unidad de Cuidados Críticos de Adultos, Hospital Quito Sur del Instituto Ecuatoriano de Securidad Social, Quito, Ecuador
| | - Katherin Narváez
- Unidad de Cuidados Críticos de Adultos, Hospital Quito Sur del Instituto Ecuatoriano de Securidad Social, Quito, Ecuador
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Li W, Liu W, Wang X, Dou R, Zhu Z. SLCO1B1 Polymorphisms are Associated with the Susceptibility to Pulmonary Tuberculosis in Chinese Females. Biochem Genet 2024; 62:385-394. [PMID: 37355503 DOI: 10.1007/s10528-023-10392-y] [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: 02/04/2023] [Accepted: 05/01/2023] [Indexed: 06/26/2023]
Abstract
This study aimed to evaluate the role of SLCO1B1 polymorphisms in pulmonary tuberculosis (PTB) risk among Chinese patients. This study comprised 600 PTB patients (mean age: 37.43 ± 12.73 years) and 600 healthy controls (mean age: 37.39 ± 12.57 years) from a Chinese population. The SLCO1B1 rs2306283 and rs4149056 polymorphisms were detected using TaqMan genotyping assay. Chi-square (χ2) test was applied to calculate the Hardy-Weinberg Equilibrium (HWE) among controls. Logistic regression analysis was used to examine the odds ratio (OR) and 95% confidence interval (CI). After adjustment for age and gender, the frequency of rs4149056-C was significantly higher in PTB group (P = 0.017, OR = 1.375, 95% CI 1.058-1.786); meanwhile, rs4149056 was associated with increased PTB risk in dominant model (P = 0.015, OR = 1.424, 95% CI 1.072-1.892). The frequency and genotype of rs2306283 showed no significant difference between the two groups. In stratified analysis, rs2306283-GG showed notable susceptibility to PTB (P = 0.027, OR = 1.563, 95% CI 1.051-2.323 in recessive model) in females; rs4149056-C was also significantly higher in female PTB group (P = 0.039, OR = 1.741, 95% CI 1.028-2.948). Neither of rs2306283 and rs4149056 polymorphisms was associated with PTB risk in males. A haplotype analysis showed that patients carrying at least one SLCO1B1*15 haplotype had higher PTB risk (P = 0.004, OR = 1.527, 95% CI 1.145-2.034). SLCO1B1 polymorphisms are associated with the susceptibility to pulmonary tuberculosis in Chinese females.
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Affiliation(s)
- Wei Li
- Institute of Hematology, Henan Key Laboratory of Stem Cell Differentiation and Modification, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Liu
- Department of Public Health, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiong Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Dou
- Institute of Hematology, Henan Key Laboratory of Stem Cell Differentiation and Modification, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China.
| | - Zunmin Zhu
- Institute of Hematology, Henan Key Laboratory of Stem Cell Differentiation and Modification, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China.
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Wang KW, Yuan YX, Zhu B, Zhang Y, Wei YF, Meng FS, Zhang S, Wang JX, Zhou JY. X chromosome-wide association study of quantitative biomarkers from the Alzheimer's Disease Neuroimaging Initiative study. Front Aging Neurosci 2023; 15:1277731. [PMID: 38035272 PMCID: PMC10682795 DOI: 10.3389/fnagi.2023.1277731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/20/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Alzheimer's disease (AD) is a complex neurodegenerative disease with high heritability. Compared to autosomes, a higher proportion of disorder-associated genes on X chromosome are expressed in the brain. However, only a few studies focused on the identification of the susceptibility loci for AD on X chromosome. Methods Using the data from the Alzheimer's Disease Neuroimaging Initiative Study, we conducted an X chromosome-wide association study between 16 AD quantitative biomarkers and 19,692 single nucleotide polymorphisms (SNPs) based on both the cross-sectional and longitudinal studies. Results We identified 15 SNPs statistically significantly associated with different quantitative biomarkers of the AD. For the cross-sectional study, six SNPs (rs5927116, rs4596772, rs5929538, rs2213488, rs5920524, and rs5945306) are located in or near to six genes DMD, TBX22, LOC101928437, TENM1, SPANXN1, and ZFP92, which have been reported to be associated with schizophrenia or neuropsychiatric diseases in literature. For the longitudinal study, four SNPs (rs4829868, rs5931111, rs6540385, and rs763320) are included in or near to two genes RAC1P4 and AFF2, which have been demonstrated to be associated with brain development or intellectual disability in literature, while the functional annotations of other five novel SNPs (rs12157031, rs428303, rs5953487, rs10284107, and rs5955016) have not been found. Discussion 15 SNPs were found statistically significantly associated with the quantitative biomarkers of the AD. Follow-up study in molecular genetics is needed to verify whether they are indeed related to AD. The findings in this article expand our understanding of the role of the X chromosome in exploring disease susceptibility, introduce new insights into the molecular genetics behind the AD, and may provide a mechanistic clue to further AD-related studies.
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Affiliation(s)
- Kai-Wen Wang
- State Key Laboratory of Organ Failure Research, Ministry of Education, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Yu-Xin Yuan
- State Key Laboratory of Organ Failure Research, Ministry of Education, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Bin Zhu
- State Key Laboratory of Organ Failure Research, Ministry of Education, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Yi Zhang
- State Key Laboratory of Organ Failure Research, Ministry of Education, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Yi-Fang Wei
- State Key Laboratory of Organ Failure Research, Ministry of Education, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Fan-Shuo Meng
- State Key Laboratory of Organ Failure Research, Ministry of Education, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Shun Zhang
- State Key Laboratory of Organ Failure Research, Ministry of Education, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jing-Xuan Wang
- State Key Laboratory of Organ Failure Research, Ministry of Education, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China
| | - Ji-Yuan Zhou
- State Key Laboratory of Organ Failure Research, Ministry of Education, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
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Shin C, Baek IC, Cho WK, Kim TG, Suh BK. Comprehensive analysis of chemokine gene polymorphisms in Korean children with autoimmune thyroid disease. Sci Rep 2023; 13:15642. [PMID: 37730733 PMCID: PMC10511635 DOI: 10.1038/s41598-023-42021-4] [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: 02/06/2023] [Accepted: 09/04/2023] [Indexed: 09/22/2023] Open
Abstract
Chemokines are chemotactic cytokines that can cause directed migration of leukocytes. The aim of this study was to examine differences in single nucleotide polymorphisms (SNP) of chemokine in AITD patients compared to normal controls. A total of 86 Korean pediatric patients were included in the patient group and 183 adults were included in the normal control group. To compare influences of several chemokine gene polymorphisms, 25 SNPs in 16 chemokine genes were analyzed. Genotype frequencies of CCL11(rs3744508)AA(OR = 6.9) and CCR2(rs1799864)AA(OR = 3.8) were higher in the AITD patients than in the controls, whereas CCL17(rs223828)CC was lower in the AITD patients than in the controls(OR = 0.4). In comparison between Graves' disease (GD) patients and controls, genotype frequency of CCL17(rs223828)CC(OR = 0.4) was lower in the GD group, whereas those of CCR2(rs1799864)AA(OR = 4.8) were higher in the GD group. The genotype frequency of CCL11(rs3744508)AA(OR = 11.3) was higher in Hashimoto's thyroiditis (HT) patients, whereas that of CXCL8(rs2227306)CC(OR = 0.4) was lower in HT patients. Polymorphisms of CCL11(rs3744508), CCL17(rs223828), and CCR2(rs1799864) might be associated with AITD, with CCL17(rs223828), CCR2(rs1799864) and CXCR2(rs2230054, rs1126579) affecting GD and CCL11(rs3744508) and CXCL8(rs2227306) affecting HT in Korean children.
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Affiliation(s)
- Chungwoo Shin
- Department of Pediatrics, College of Medicine, St. Vincent's Hospital, The Catholic University of Korea, Seoul, 065941, Korea
| | - In-Cheol Baek
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, 065941, Korea.
| | - Won Kyoung Cho
- Department of Pediatrics, College of Medicine, St. Vincent's Hospital, The Catholic University of Korea, Seoul, 065941, Korea.
| | - Tai-Gyu Kim
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, 065941, Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 065941, Korea
| | - Byung-Kyu Suh
- Department of Pediatrics, College of Medicine, St. Vincent's Hospital, The Catholic University of Korea, Seoul, 065941, Korea
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Gerard D. Double reduction estimation and equilibrium tests in natural autopolyploid populations. Biometrics 2023; 79:2143-2156. [PMID: 35848417 DOI: 10.1111/biom.13722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 07/11/2022] [Indexed: 11/27/2022]
Abstract
Many bioinformatics pipelines include tests for equilibrium. Tests for diploids are well studied and widely available, but extending these approaches to autopolyploids is hampered by the presence of double reduction, the comigration of sister chromatid segments into the same gamete during meiosis. Though a hindrance for equilibrium tests, double reduction rates are quantities of interest in their own right, as they provide insights about the meiotic behavior of autopolyploid organisms. Here, we develop procedures to (i) test for equilibrium while accounting for double reduction, and (ii) estimate the double reduction rate given equilibrium. To do so, we take two approaches: a likelihood approach, and a novel U-statistic minimization approach that we show generalizes the classical equilibrium χ2 test in diploids. For small sample sizes and uncertain genotypes, we further develop a bootstrap procedure based on our U-statistic to test for equilibrium. We validate our methods on both simulated and real data.
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Affiliation(s)
- David Gerard
- Department of Mathematics and Statistics, American University, Washington, District of Columbia, USA
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9
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Ariff A, Song Y, Aguilar R, Nhabomba A, Manaca MN, Khoo SK, Wiertsema S, Bassat Q, Barbosa A, Quintó L, Laing IA, Guinovart C, Alonso PL, Dobaño C, Le Souëf P, Zhang G. Genetic variants of TLR4, including the novel variant, rs5030719, and related genes are associated with susceptibility to clinical malaria in African children. Malar J 2023; 22:177. [PMID: 37287037 DOI: 10.1186/s12936-023-04549-8] [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: 09/26/2022] [Accepted: 03/31/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND Malaria is a deadly disease caused by Plasmodium spp. Several blood phenotypes have been associated with malarial resistance, which suggests a genetic component to immune protection. METHODS One hundred and eighty-seven single nucleotide polymorphisms (SNPs) in 37 candidate genes were genotyped and investigated for associations with clinical malaria in a longitudinal cohort of 349 infants from Manhiça, Mozambique, in a randomized controlled clinical trial (RCT) (AgeMal, NCT00231452). Malaria candidate genes were selected according to involvement in known malarial haemoglobinopathies, immune, and pathogenesis pathways. RESULTS Statistically significant evidence was found for the association of TLR4 and related genes with the incidence of clinical malaria (p = 0.0005). These additional genes include ABO, CAT, CD14, CD36, CR1, G6PD, GCLM, HP, IFNG, IFNGR1, IL13, IL1A, IL1B, IL4R, IL4, IL6, IL13, MBL, MNSOD, and TLR2. Of specific interest, the previously identified TLR4 SNP rs4986790 and the novel finding of TRL4 SNP rs5030719 were associated with primary cases of clinical malaria. CONCLUSIONS These findings highlight a potential central role of TLR4 in clinical malarial pathogenesis. This supports the current literature and suggests that further research into the role of TLR4, as well as associated genes, in clinical malaria may provide insight into treatment and drug development.
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Affiliation(s)
- Amir Ariff
- Centre for Genetic Origins of Health and Disease, The University of Western Australia and Curtin University, Perth, WA, 6009, Australia
- School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | - Yong Song
- Centre for Genetic Origins of Health and Disease, The University of Western Australia and Curtin University, Perth, WA, 6009, Australia
- School of Public Health, Curtin University, Perth, WA, 6102, Australia
| | - Ruth Aguilar
- ISGlobal, Hospital Clínic of Barcelona, Universitat de Barcelona, 08036, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
| | - Augusto Nhabomba
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
| | - Maria Nelia Manaca
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
| | - Siew-Kim Khoo
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6008, Australia
| | - Selma Wiertsema
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6008, Australia
| | - Quique Bassat
- ISGlobal, Hospital Clínic of Barcelona, Universitat de Barcelona, 08036, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues, Barcelona, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Arnoldo Barbosa
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
| | - Llorenç Quintó
- ISGlobal, Hospital Clínic of Barcelona, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Ingrid A Laing
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6008, Australia
- School of Medicine, The University of Western Australia, Perth, WA, 6008, Australia
| | - Caterina Guinovart
- ISGlobal, Hospital Clínic of Barcelona, Universitat de Barcelona, 08036, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
| | - Pedro L Alonso
- ISGlobal, Hospital Clínic of Barcelona, Universitat de Barcelona, 08036, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
| | - Carlota Dobaño
- ISGlobal, Hospital Clínic of Barcelona, Universitat de Barcelona, 08036, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), 1929, Maputo, Mozambique
| | - Peter Le Souëf
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, WA, 6009, Australia.
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6008, Australia.
- School of Medicine, The University of Western Australia, Perth, WA, 6008, Australia.
| | - Guicheng Zhang
- Centre for Genetic Origins of Health and Disease, The University of Western Australia and Curtin University, Perth, WA, 6009, Australia.
- School of Public Health, Curtin University, Perth, WA, 6102, Australia.
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6008, Australia.
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, 6102, Australia.
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10
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Sun L, Wang Z, Lu T, Manolio TA, Paterson AD. eXclusionarY: 10 years later, where are the sex chromosomes in GWASs? Am J Hum Genet 2023; 110:903-912. [PMID: 37267899 DOI: 10.1016/j.ajhg.2023.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
10 years ago, a detailed analysis showed that only 33% of genome-wide association study (GWAS) results included the X chromosome. Multiple recommendations were made to combat such exclusion. Here, we re-surveyed the research landscape to determine whether these earlier recommendations had been translated. Unfortunately, among the genome-wide summary statistics reported in 2021 in the NHGRI-EBI GWAS Catalog, only 25% provided results for the X chromosome and 3% for the Y chromosome, suggesting that the exclusion phenomenon not only persists but has also expanded into an exclusionary problem. Normalizing by physical length of the chromosome, the average number of studies published through November 2022 with genome-wide-significant findings on the X chromosome is ∼1 study/Mb. By contrast, it ranges from ∼6 to ∼16 studies/Mb for chromosomes 4 and 19, respectively. Compared with the autosomal growth rate of ∼0.086 studies/Mb/year over the last decade, studies of the X chromosome grew at less than one-seventh that rate, only ∼0.012 studies/Mb/year. Among the studies that reported significant associations on the X chromosome, we noted extreme heterogeneities in data analysis and reporting of results, suggesting the need for clear guidelines. Unsurprisingly, among the 430 scores sampled from the PolyGenic Score Catalog, 0% contained weights for sex chromosomal SNPs. To overcome the dearth of sex chromosome analyses, we provide five sets of recommendations and future directions. Finally, until the sex chromosomes are included in a whole-genome study, instead of GWASs, we propose such studies would more properly be referred to as "AWASs," meaning "autosome-wide scans."
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Affiliation(s)
- Lei Sun
- Department of Statistical Sciences, Faculty of Arts and Science, University of Toronto, Toronto, ON, Canada; Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
| | - Zhong Wang
- Department of Statistics and Data Science, Faculty of Science, National University of Singapore, Singapore
| | - Tianyuan Lu
- Department of Statistical Sciences, Faculty of Arts and Science, University of Toronto, Toronto, ON, Canada; Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Andrew D Paterson
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada; Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada; Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
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11
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Khramtsova EA, Wilson MA, Martin J, Winham SJ, He KY, Davis LK, Stranger BE. Quality control and analytic best practices for testing genetic models of sex differences in large populations. Cell 2023; 186:2044-2061. [PMID: 37172561 PMCID: PMC10266536 DOI: 10.1016/j.cell.2023.04.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 01/31/2023] [Accepted: 04/07/2023] [Indexed: 05/15/2023]
Abstract
Phenotypic sex-based differences exist for many complex traits. In other cases, phenotypes may be similar, but underlying biology may vary. Thus, sex-aware genetic analyses are becoming increasingly important for understanding the mechanisms driving these differences. To this end, we provide a guide outlining the current best practices for testing various models of sex-dependent genetic effects in complex traits and disease conditions, noting that this is an evolving field. Insights from sex-aware analyses will not only teach us about the biology of complex traits but also aid in achieving the goals of precision medicine and health equity for all.
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Affiliation(s)
- Ekaterina A Khramtsova
- Population Analytics and Insights, Data Science Analytics & Insights, Janssen R&D, Lower Gwynedd Township, PA, USA.
| | - Melissa A Wilson
- School of Life Sciences, Center for Evolution and Medicine, Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85282, USA
| | - Joanna Martin
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Stacey J Winham
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Karen Y He
- Population Analytics and Insights, Data Science Analytics & Insights, Janssen R&D, Lower Gwynedd Township, PA, USA
| | - Lea K Davis
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Barbara E Stranger
- Center for Genetic Medicine, Department of Pharmacology, Northwestern University, Chicago, IL, USA.
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12
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Cho WK, Baek I, Kim SE, Kim M, Kim T, Suh B. Association of ITM2A rs1751094 polymorphism on X chromosome in Korean pediatric patients with autoimmune thyroid disease. Immun Inflamm Dis 2023; 11:e800. [PMID: 36988246 PMCID: PMC10013136 DOI: 10.1002/iid3.800] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/08/2023] [Accepted: 02/21/2023] [Indexed: 03/17/2023] Open
Abstract
Background Autoimmune thyroid disease (AITD) manifests with a female predominance, and much attention has been directed towards the integral membrane protein 2 A (ITM2A) gene located on the X chromosome. Methods In a study of 166 pediatric patients with autoimmune thyroid disease (AITD), the ITM2A rs1751094 single‐nucleotide polymorphism (SNP) was genotyped. The sample comprised 143 females and 23 males, with 67 patients diagnosed with Hashimoto chronic thyroiditis (HD) and 99 with Graves' disease (GD). In the 99 GD patients, 49 (49.5%) exhibited thyroid‐associated ophthalmopathy (TAO). Among the 85 GD patients, 70.6% (60/85) were considered intractable GD. The results were compared to those from 198 healthy Korean individuals, including 97 females and 101 males. Results The frequency of the rs1751094 C allele and CC/AC genotype were higher in AITD, GD and HD patients compared to controls, while the frequency of the A allele and AA genotype were lower. The results were more pronounced in female AITD and GD patients compared to male patients. The association was also found in intractable GD and TAO patients. Target SNP fits Hardy–Weinberg equilibrium. Conclusions These findings indicate that the ITM2A gene polymorphism on the X chromosome may contribute to the immunological basis of female‐predominant AITD in Korean children.
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Affiliation(s)
- Won K. Cho
- Department of Pediatrics, College of Medicine, St. Vincent's HospitalThe Catholic University of KoreaSeoulKorea
| | - In‐Cheol Baek
- Catholic Hematopoietic Stem Cell Bank, College of MedicineThe Catholic University of KoreaSeoulKorea
| | - Sung E. Kim
- Department of Pediatrics, Incheon St. Mary's Hospital, College of MedicineThe Catholic University of KoreaSeoulKorea
| | - Mirae Kim
- Catholic Hematopoietic Stem Cell Bank, College of MedicineThe Catholic University of KoreaSeoulKorea
| | - Tai‐Gyu Kim
- Catholic Hematopoietic Stem Cell Bank, College of MedicineThe Catholic University of KoreaSeoulKorea,Department of Microbiology, College of MedicineThe Catholic University of KoreaSeoulKorea
| | - Byung‐Kyu Suh
- Department of Pediatrics, College of Medicine, Seoul St. Mary's HospitalThe Catholic University of KoreaSeoulKorea
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13
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Why does the X chromosome lag behind autosomes in GWAS findings? PLoS Genet 2023; 19:e1010472. [PMID: 36848382 PMCID: PMC9997976 DOI: 10.1371/journal.pgen.1010472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/09/2023] [Accepted: 02/15/2023] [Indexed: 03/01/2023] Open
Abstract
The X-chromosome is among the largest human chromosomes. It differs from autosomes by a number of important features including hemizygosity in males, an almost complete inactivation of one copy in females, and unique patterns of recombination. We used data from the Catalog of Published Genome Wide Association Studies to compare densities of the GWAS-detected SNPs on the X-chromosome and autosomes. The density of GWAS-detected SNPs on the X-chromosome is 6-fold lower compared to the density of the GWAS-detected SNPs on autosomes. Differences between the X-chromosome and autosomes cannot be explained by differences in the overall SNP density, lower X-chromosome coverage by genotyping platforms or low call rate of X-chromosomal SNPs. Similar differences in the density of GWAS-detected SNPs were found in female-only GWASs (e.g. ovarian cancer GWASs). We hypothesized that the lower density of GWAS-detected SNPs on the X-chromosome compared to autosomes is not a result of a methodological bias, e.g. differences in coverage or call rates, but has a real underlying biological reason-a lower density of functional SNPs on the X-chromosome versus autosomes. This hypothesis is supported by the observation that (i) the overall SNP density of X-chromosome is lower compared to the SNP density on autosomes and that (ii) the density of genic SNPs on the X-chromosome is lower compared to autosomes while densities of intergenic SNPs are similar.
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14
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Martinez-Chapoy D, Cruz-Arroyo FJ, Ancer-Leal FD, Rodriguez-Leal RA, Camacho-Zamora BD, Guzman-Sanchez DA, Espinoza-Gonzalez NA, Martinez-Jacobo L, Marino-Martinez IA. Pilot study: genetic distribution of AR, FGF5, SULT1A1 and CYP3A5 polymorphisms in male Mexican population with androgenetic alopecia. INTERNATIONAL JOURNAL OF MOLECULAR EPIDEMIOLOGY AND GENETICS 2022; 13:32-41. [PMID: 36660495 PMCID: PMC9845865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/17/2022] [Indexed: 01/21/2023]
Abstract
Genetics is responsible for 80% of androgenetic alopecia (AGA) predisposition. Several single nucleotide polymorphisms (SNPs) have been linked to AGA risk and the metabolism of its first-line therapies. Genotypic and allelic frequencies have not been described in Mexican individuals; therefore, the aim of this study was to describe the genetic distribution of SNPs associated with AGA predisposition and drug metabolism. Using Real Time-PCR, we genotyped SNPs rs4827528 (AR), rs7680591 (FGF5), rs1042028, rs1042157, rs788068 and rs6839 (SULT1A1) and rs776746 (CYP3A5) in 125 (controls = 60, cases = 65) male volunteers from Northern and Western Mexico. The SULT1A1 SNPs rs1042028 (C/T) and rs788068 (T/A/C) resulted in a 100% distribution of the ancestral allele C and mutated allele A, respectively; rs1042028 diverges from the previously reported frequency, while the rs788068 ancestral allele was found to be more predominant than the reported frequency. Rs1042028, rs788068 and rs4827528, were not in Hardy-Weinberg (HW) equilibrium; conversely, rs1042157 and rs6839, rs776746, and rs7680591 followed HW principles. A statistically significant difference (P<0.05) was obtained for the rs1042157 allelic frequency between cases and controls in Western Mexico. We reported the genotypic and allelic frequencies of seven polymorphisms in Mexican individuals from Northern and Western Mexico.
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15
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Shriyan B, Mehta P, Patil A, Jadhav S, Kumar S, Puri AS, Govalkar R, Krishnamurthy MN, Punatar S, Gokarn A, Khattry N, Gota V. Role of ADME gene polymorphisms on imatinib disposition: results from a population pharmacokinetic study in chronic myeloid leukaemia. Eur J Clin Pharmacol 2022; 78:1321-1330. [PMID: 35652931 DOI: 10.1007/s00228-022-03345-8] [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: 01/27/2022] [Accepted: 05/24/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE Imatinib is a substrate of CYP3A4, ABCB1 and ABCG2, and is known to have wide variability in pharmacokinetics (PK). At the same time, a clear relationship between drug levels and response also exists for imatinib in chronic myeloid leukaemia (CML). Therefore, pharmacogenetic-based dosing of imatinib is an attractive proposition. This study aims to characterize the population pharmacokinetics of imatinib in order to identify significant covariates including pharmacogenetic variants. METHODS Forty-nine patients with CML were enrolled in the study after being on imatinib for at least 4 consecutive weeks. Steady-state pharmacokinetic sampling was performed either in a sparse (4 samples each, n = 44) or intensive manner (9 samples each, n = 5). An additional pharmacogenetic sample was also collected from all patients. Plasma imatinib levels were estimated using a validated HPLC method. Pharmacogenetic variants were identified using the PharmacoScan array platform. Population pharmacokinetic analysis was carried out using NONMEM v7.2. Seven SNPs within CYP3A4, ABCB1 and ABCG2 genes were evaluated for covariate effect on the clearance of imatinib. RESULTS Imatinib PK was well characterized using a one-compartment model with zero-order absorption. The clearance and volume of distribution were found to be 10.2 L/h and 389 L respectively. Only SNP rs1128503 of the ABCB1 gene had a small but insignificant effect on imatinib clearance, with a 25% reduction in clearance observed in patients carrying the polymorphism. Twenty-three out of forty-nine patients (47%) carried the polymorphic allele, of whom 17 were heterozygous and six were homozygous. CONCLUSION Our study conclusively proves that genetic polymorphisms in the CYP3A4 and ABC family of transporters do not have any role in the personalized dosing of imatinib in CML.
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Affiliation(s)
- Bharati Shriyan
- Department of Clinical Pharmacology, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
| | - Parsshava Mehta
- Department of Clinical Pharmacology, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
| | - Anand Patil
- Department of Clinical Pharmacology, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
| | - Shraddha Jadhav
- Department of Clinical Pharmacology, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
| | - Sharath Kumar
- Department of Clinical Pharmacology, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
| | - Apeksha S Puri
- Department of Clinical Pharmacology, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
| | - Ravina Govalkar
- Department of Clinical Pharmacology, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India.,Gahlot Institute of Pharmacy, Koparkhairane, Navi Mumbai, 400709, India
| | - Manjunath Nookala Krishnamurthy
- Department of Clinical Pharmacology, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India.,Homi Bhabha National Institute, Mumbai, 400094, India
| | - Sachin Punatar
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, 400012, India.,Homi Bhabha National Institute, Mumbai, 400094, India
| | - Anant Gokarn
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, 400012, India.,Homi Bhabha National Institute, Mumbai, 400094, India
| | - Navin Khattry
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, 400012, India.,Homi Bhabha National Institute, Mumbai, 400094, India
| | - Vikram Gota
- Department of Clinical Pharmacology, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India. .,Homi Bhabha National Institute, Mumbai, 400094, India.
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16
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Wright JW, Stevens KA, Hodgskiss P, Langley CH. SNPs in a Large Genomic Scaffold Are Strongly Associated with Cr1R, Major Gene for Resistance to White Pine Blister Rust in Range-Wide Samples of Sugar Pine ( Pinus lambertiana). PLANT DISEASE 2022; 106:1639-1644. [PMID: 35512301 DOI: 10.1094/pdis-08-21-1608-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Sugar pine, Pinus lambertiana Douglas, is a keystone species of montane forests from Baja California to southern Oregon. Like other North American white pines, populations of sugar pine have been greatly reduced by the disease white pine blister rust (WPBR) caused by a fungal pathogen, Cronartium ribicola, that was introduced into North America early in the twentieth century. Major gene resistance to WPBR segregating in natural populations has been documented in sugar pine. Indeed, the dominant resistance gene in this species, Cr1, was genetically mapped, although not precisely. Genomic single nucleotide polymorphisms (SNPs) placed in a large scaffold were reported to be associated with the allele for this major gene resistance (Cr1R). Forest restoration efforts often include sugar pine seed derived from the rare resistant individuals (typically Cr1R/Cr1r) identified through an expensive 2-year phenotypic testing program. To validate and geographically characterize the variation in this association and investigate its potential to expedite genetic improvement in forest restoration, we developed a simple PCR-based, diploid genotyping of DNA from needle tissue. By applying this to range-wide samples of susceptible and resistant (Cr1R) trees, we show that the SNPs exhibit a strong, though not complete, association with Cr1R. Paralleling earlier studies of the geographic distribution of Cr1R and the inferred demographic history of sugar pine, the resistance-associated SNPs are marginally more common in southern populations, as is the frequency of Cr1R. Although the strength of the association of the SNPs with Cr1R and thus, their predictive value, also varies with geography, the potential value of this new tool in quickly and efficiently identifying candidate WPBR-resistant seed trees is clear.
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Affiliation(s)
- Jessica W Wright
- U.S. Department of Agriculture Forest Service, Pacific Southwest Research Station, Davis, CA 95618
| | - Kristian A Stevens
- Departments of Computer Science and Evolution and Ecology, University of California Davis, Davis, CA 95616
| | - Paul Hodgskiss
- U.S. Department of Agriculture Forest Service, Pacific Southwest Research Station, Davis, CA 95618
| | - Charles H Langley
- Department of Evolution and Ecology, University of California Davis, Davis, CA 95616
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17
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Wang Z, Sun L, Paterson AD. Major sex differences in allele frequencies for X chromosomal variants in both the 1000 Genomes Project and gnomAD. PLoS Genet 2022; 18:e1010231. [PMID: 35639794 PMCID: PMC9187127 DOI: 10.1371/journal.pgen.1010231] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 06/10/2022] [Accepted: 05/03/2022] [Indexed: 12/19/2022] Open
Abstract
An unexpectedly high proportion of SNPs on the X chromosome in the 1000 Genomes Project phase 3 data were identified with significant sex differences in minor allele frequencies (sdMAF). sdMAF persisted for many of these SNPs in the recently released high coverage whole genome sequence of the 1000 Genomes Project that was aligned to GRCh38, and it was consistent between the five super-populations. Among the 245,825 common (MAF>5%) biallelic X-chromosomal SNPs in the phase 3 data presumed to be of high quality, 2,039 have genome-wide significant sdMAF (p-value <5e-8). sdMAF varied by location: non-pseudo-autosomal region (NPR) = 0.83%, pseudo-autosomal regions (PAR1) = 0.29%, PAR2 = 13.1%, and X-transposed region (XTR)/PAR3 = 0.85% of SNPs had sdMAF, and they were clustered at the NPR-PAR boundaries, among others. sdMAF at the NPR-PAR boundaries are biologically expected due to sex-linkage, but have generally been ignored in association studies. For comparison, similar analyses found only 6, 1 and 0 SNPs with significant sdMAF on chromosomes 1, 7 and 22, respectively. Similar sdMAF results for the X chromosome were obtained from the high coverage whole genome sequence data from gnomAD V 3.1.2 for both the non-Finnish European and African/African American samples. Future X chromosome analyses need to take sdMAF into account.
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Affiliation(s)
- Zhong Wang
- Department of Statistics and Data Science, Faculty of Science, National University of Singapore, Singapore
| | - Lei Sun
- Department of Statistic Sciences, Faculty of Arts and Science, University of Toronto, Ontario, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
| | - Andrew D. Paterson
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
- Genetics and Genome Biology, The Hospital for Sick Children, Ontario, Canada
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
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18
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Graffelman J, Weir BS. The transitivity of the Hardy-Weinberg law. Forensic Sci Int Genet 2022; 58:102680. [PMID: 35313226 PMCID: PMC10693928 DOI: 10.1016/j.fsigen.2022.102680] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/12/2022] [Accepted: 02/20/2022] [Indexed: 11/27/2022]
Abstract
The Hardy-Weinberg law is shown to be transitive in the sense that a multi-allelic polymorphism that is in equilibrium will retain its equilibrium status if any allele together with its corresponding genotypes is deleted from the population. Similarly, the transitivity principle also applies if alleles are joined, which leads to the summation of allele frequencies and their corresponding genotype frequencies. These basic polymorphism properties are intuitive, but they have apparently not been formalized or investigated. This article provides a straightforward proof of the transitivity principle, and its usefulness in genetic data analysis is explored, using high-quality autosomal microsatellite databases from the US National Institute of Standards and Technology. We address the reduction of multi-allelic polymorphisms to variants with fewer alleles, two in the limit. Equilibrium test results obtained with the original and reduced polymorphisms are generally observed to be coherent, in particular when results obtained with length-based and sequence-based microsatellites are compared. We exploit the transitivity principle in order to identify disequilibrium-related alleles, and show its usefulness for detecting population substructure and genotyping problems that relate to null alleles and allele imbalance.
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Affiliation(s)
- Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Carrer Jordi Girona, 1-3, 08034, Barcelona, Spain; Department of Biostatistics, University of Washington, University Tower, 15th Floor, 4333 Brooklyn Avenue, Seattle, WA 98105-9461, United States of America.
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, University Tower, 15th Floor, 4333 Brooklyn Avenue, Seattle, WA 98105-9461, United States of America
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19
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Homann J, Osburg T, Ohlei O, Dobricic V, Deecke L, Bos I, Vandenberghe R, Gabel S, Scheltens P, Teunissen CE, Engelborghs S, Frisoni G, Blin O, Richardson JC, Bordet R, Lleó A, Alcolea D, Popp J, Clark C, Peyratout G, Martinez-Lage P, Tainta M, Dobson RJB, Legido-Quigley C, Sleegers K, Van Broeckhoven C, Wittig M, Franke A, Lill CM, Blennow K, Zetterberg H, Lovestone S, Streffer J, ten Kate M, Vos SJB, Barkhof F, Visser PJ, Bertram L. Genome-Wide Association Study of Alzheimer's Disease Brain Imaging Biomarkers and Neuropsychological Phenotypes in the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery Dataset. Front Aging Neurosci 2022; 14:840651. [PMID: 35386118 PMCID: PMC8979334 DOI: 10.3389/fnagi.2022.840651] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/15/2022] [Indexed: 12/24/2022] Open
Abstract
Alzheimer's disease (AD) is the most frequent neurodegenerative disease with an increasing prevalence in industrialized, aging populations. AD susceptibility has an established genetic basis which has been the focus of a large number of genome-wide association studies (GWAS) published over the last decade. Most of these GWAS used dichotomized clinical diagnostic status, i.e., case vs. control classification, as outcome phenotypes, without the use of biomarkers. An alternative and potentially more powerful study design is afforded by using quantitative AD-related phenotypes as GWAS outcome traits, an analysis paradigm that we followed in this work. Specifically, we utilized genotype and phenotype data from n = 931 individuals collected under the auspices of the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery (EMIF-AD MBD) study to perform a total of 19 separate GWAS analyses. As outcomes we used five magnetic resonance imaging (MRI) traits and seven cognitive performance traits. For the latter, longitudinal data from at least two timepoints were available in addition to cross-sectional assessments at baseline. Our GWAS analyses revealed several genome-wide significant associations for the neuropsychological performance measures, in particular those assayed longitudinally. Among the most noteworthy signals were associations in or near EHBP1 (EH domain binding protein 1; on chromosome 2p15) and CEP112 (centrosomal protein 112; 17q24.1) with delayed recall as well as SMOC2 (SPARC related modular calcium binding 2; 6p27) with immediate recall in a memory performance test. On the X chromosome, which is often excluded in other GWAS, we identified a genome-wide significant signal near IL1RAPL1 (interleukin 1 receptor accessory protein like 1; Xp21.3). While polygenic score (PGS) analyses showed the expected strong associations with SNPs highlighted in relevant previous GWAS on hippocampal volume and cognitive function, they did not show noteworthy associations with recent AD risk GWAS findings. In summary, our study highlights the power of using quantitative endophenotypes as outcome traits in AD-related GWAS analyses and nominates several new loci not previously implicated in cognitive decline.
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Affiliation(s)
- Jan Homann
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Tim Osburg
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Olena Ohlei
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Laura Deecke
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Isabelle Bos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, Netherlands
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Rik Vandenberghe
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
- Neurology Service, University Hospital Leuven, Leuven, Belgium
| | - Silvy Gabel
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Philip Scheltens
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Charlotte E. Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, Netherlands
| | - Sebastiaan Engelborghs
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Center for Neurosciences, Universitair Ziekenhuis Brussel and Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Giovanni Frisoni
- Department of Psychiatry, University of Geneva, Geneva, Switzerland
- IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Olivier Blin
- Institut Neurosciences Timone, AIX Marseille University, Marseille, France
| | - Jill C. Richardson
- Neurosciences Therapeutic Area, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Regis Bordet
- Lille Neuroscience and Cognition, University of Lille, Inserm, CHU Lille, Lille, France
| | - Alberto Lleó
- Memory Unit, Neurology Department, Hospital de Sant Pau, Barcelona and Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Daniel Alcolea
- Memory Unit, Neurology Department, Hospital de Sant Pau, Barcelona and Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Julius Popp
- Department of Geriatric Psychiatry, University Hospital of Psychiatry Zurich, Zurich, Switzerland
- Old Age Psychiatry, Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
| | - Christopher Clark
- Department of Geriatric Psychiatry, University Hospital of Psychiatry Zurich, Zurich, Switzerland
| | - Gwendoline Peyratout
- Old Age Psychiatry, Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
| | - Pablo Martinez-Lage
- Department of Neurology, Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, Donostia-San Sebastian, Spain
| | - Mikel Tainta
- Department of Neurology, Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, Donostia-San Sebastian, Spain
| | - Richard J. B. Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College London, London, United Kingdom
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom
- Health Data Research UK London, University College London, London, United Kingdom
- Institute of Health Informatics, University College London, London, United Kingdom
- NIHR Biomedical Research Centre at University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Cristina Legido-Quigley
- Steno Diabetes Center, Copenhagen, Denmark
- King’s College London, Institute of Pharmaceutical Sciences, London, United Kingdom
| | - Kristel Sleegers
- Complex Genetics of Alzheimer’s Disease Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Christina M. Lill
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
- Ageing Epidemiology Research Unit, School of Public Health, Imperial College London, London, United Kingdom
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, University College London, Queen Square Institute of Neurology, Queen Square, London, United Kingdom
- UK Dementia Research Institute at University College London, London, United Kingdom
| | - Simon Lovestone
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Johannes Streffer
- Reference Center for Biological Markers of Dementia (BIODEM), Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Janssen R&D, LLC. Beerse, Belgium
| | - Mara ten Kate
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Centers, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Stephanie J. B. Vos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, Netherlands
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Centers, Amsterdam Neuroscience, Amsterdam, Netherlands
- Institutes of Neurology and Healthcare Engineering, University College London, London, United Kingdom
| | - Pieter Jelle Visser
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, Netherlands
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
- Department of Psychology, University of Oslo, Oslo, Norway
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A measure of evidence based on the likelihood-ratio statistics. Stat Pap (Berl) 2022. [DOI: 10.1007/s00362-022-01301-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Tariq S, Tariq S, Khaliq S, Lone KP. Serum Resistin Levels and Related Genetic Variants Are Associated With Bone Mineral Density in Postmenopausal Women. Front Endocrinol (Lausanne) 2022; 13:868120. [PMID: 35992125 PMCID: PMC9389046 DOI: 10.3389/fendo.2022.868120] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Osteoporosis is a multifactorial disorder and a number of genetic variants or loci responsible for bone mineral density (BMD) have been identified. Resistin, a novel adipokine has diverse role in human body including its function in bone remodeling. The objective of this study was to see the association of serum resistin levels and related genetic variants (rs3931020, rs13144478) with BMD in postmenopausal females. METHODS This comparative analytical study was conducted on postmenopausal osteoporotic (n=101), osteopenic (n=77) and non-osteoporotic (n=74) females. For comparison and correlational analysis, Kruskal-Wallis test and Spearman's rho correlation were used respectively. Hardy-Weinberg equilibrium (HWE) was calculated by using Chi-square test (χ2). RESULTS There was significant difference in the serum levels of resistin (p <0.001), among the three groups. Significant negative correlation of resistin was observed with BMD at various sites. Serum resistin levels were significantly low in the rs3931020 AA homozygous genotype (p = 0.010), and significantly high in the rs13144478 AT heterozygous genotype (p = 0.020), BMD at all sites except left femoral neck was significantly high in rs3931020 AA genotype, while BMD at lumbar spine, left hip and total BMD were significantly low in the rs13144478 TT homozygotes. CONCLUSION High serum resistin levels are associated with low BMD and single nucleotide variation in rs3931020 and rs13144478 may lead to high serum resistin levels and low bone mineral density. Resistin can serve as a new genetic marker, potential therapeutic target and predictor of osteoporosis.
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Affiliation(s)
- Sundus Tariq
- Physiology, University Medical & Dental College, The University of Faisalabad, Faisalabad, Pakistan
- Physiology and Cell Biology, University of Health Sciences, Lahore, Pakistan
- *Correspondence: Saba Tariq, ; Sundus Tariq,
| | - Saba Tariq
- Pharmacology and Therapeutics, University Medical & Dental College, The University of Faisalabad, Faisalabad, Pakistan
- Pharmacology and Therapeutics, University of Health Sciences, Lahore, Pakistan
- *Correspondence: Saba Tariq, ; Sundus Tariq,
| | - Saba Khaliq
- Physiology and Cell Biology, University of Health Sciences, Lahore, Pakistan
| | - Khalid Parvez Lone
- Physiology/Metabolic Disorders, Government College University, Lahore, Pakistan
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22
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Recursive Test of Hardy-Weinberg Equilibrium in Tetraploids. Trends Genet 2021; 37:504-513. [DOI: 10.1016/j.tig.2020.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 02/08/2023]
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Graffelman J, Ortoleva L. A network algorithm for the X chromosomal exact test for Hardy-Weinberg equilibrium with multiple alleles. Mol Ecol Resour 2021; 21:1547-1557. [PMID: 33687797 PMCID: PMC8251783 DOI: 10.1111/1755-0998.13373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 11/27/2022]
Abstract
Statistical methodology for testing the Hardy–Weinberg equilibrium at X chromosomal variants has recently experienced considerable development. Up to a few years ago, testing X chromosomal variants for equilibrium was basically done by applying autosomal test procedures to females only. At present, male alleles can be taken into account in asymptotic and exact test procedures for both the bi‐ and multiallelic case. However, current X chromosomal exact procedures for multiple alleles rely on a classical full enumeration algorithm and are computationally expensive, and in practice not feasible for more than three alleles. In this article, we extend the autosomal network algorithm for exact Hardy–Weinberg testing with multiple alleles to the X chromosome, achieving considerable reduction in computation times for multiallelic variants with up to five alleles. The performance of the X chromosomal network algorithm is assessed in a simulation study. Beyond four alleles, a permutation test is, in general, the more feasible approach. A detailed description of the algorithm is given, and examples of X chromosomal indels and microsatellites are discussed.
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Affiliation(s)
- Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain.,Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Leonardo Ortoleva
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain.,Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy
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Zubiaur P, Benedicto MD, Villapalos-García G, Navares-Gómez M, Mejía-Abril G, Román M, Martín-Vílchez S, Ochoa D, Abad-Santos F. SLCO1B1 Phenotype and CYP3A5 Polymorphism Significantly Affect Atorvastatin Bioavailability. J Pers Med 2021; 11:204. [PMID: 33805706 PMCID: PMC7999651 DOI: 10.3390/jpm11030204] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 02/07/2023] Open
Abstract
Atorvastatin, prescribed for the treatment of hypercholesterolemia, demonstrated overwhelming benefits in reducing cardiovascular morbidity and mortality. However, many patients discontinue therapy due to adverse reactions, especially myopathy. The Dutch Pharmacogenetics Working Group (DPWG) recommends an alternative agent to atorvastatin and simvastatin or a dose adjustment depending on other risk factors for statin-induced myopathy in SLCO1B1 rs4149056 CC or TC carriers. In contrast, the Clinical Pharmacogenetics Implementation Consortium (CPIC) published their guideline on simvastatin, but not on atorvastatin. In this work, we aimed to demonstrate the effect of SLCO1B1 phenotype and other variants (e.g., in CYP3A4/5, UGT enzymes or SLC transporters) on atorvastatin pharmacokinetics. For this purpose, a candidate-gene pharmacogenetic study was proposed. The study population comprised 156 healthy volunteers enrolled in atorvastatin bioequivalence clinical trials. The genotyping strategy comprised a total of 60 variants in 15 genes. Women showed higher exposure to atorvastatin compared to men (p = 0.001), however this difference disappeared after dose/weight (DW) correction. The most relevant pharmacogenetic differences were the following: AUC/DW and Cmax /DW based on (a) SLCO1B1 phenotype (p < 0.001 for both) and (b) CYP3A5*3 (p = 0.004 and 0.018, respectively). As secondary findings: SLC22A1 *2/*2 genotype was related to higher Cmax/DW (ANOVA p = 0.030) and SLC22A1 *1/*5 genotype was associated with higher Vd/F (ANOVA p = 0.032) compared to SLC22A1 *1/*1, respectively. Finally, UGT2B7 rs7439366 *1/*1 genotype was associated with higher tmax as compared with the *1/*3 genotype (ANOVA p = 0.024). Based on our results, we suggest that SLCO1B1 is the best predictor for atorvastatin pharmacokinetic variability and that prescription should be adjusted based on it. We suggest that the CPIC should include atorvastatin in their statin-SLCO1B1 guidelines. Interesting and novel results were observed based on CYP3A5 genotype, which should be confirmed with further studies.
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Affiliation(s)
- Pablo Zubiaur
- Pharmacogenetics Unit, Clinical Pharmacology Department, La Princesa University Hospital Research Institute, 28006 Madrid, Spain; (G.V.-G.); (M.N.-G.)
- Spanish Clinical Research Network (SCReN), La Princesa University Hospital Research Institute, 28006 Madrid, Spain;
| | | | - Gonzalo Villapalos-García
- Pharmacogenetics Unit, Clinical Pharmacology Department, La Princesa University Hospital Research Institute, 28006 Madrid, Spain; (G.V.-G.); (M.N.-G.)
| | - Marcos Navares-Gómez
- Pharmacogenetics Unit, Clinical Pharmacology Department, La Princesa University Hospital Research Institute, 28006 Madrid, Spain; (G.V.-G.); (M.N.-G.)
| | - Gina Mejía-Abril
- Spanish Clinical Research Network (SCReN), La Princesa University Hospital Research Institute, 28006 Madrid, Spain;
- Clinical Pharmacology Department, La Princesa University Hospital, 28006 Madrid, Spain;
| | - Manuel Román
- Clinical Trials Unit of La Princesa University Hospital (UECHUP), La Princesa University Hospital Research Institute, 28006 Madrid, Spain; (M.R.); (S.M.-V.)
| | - Samuel Martín-Vílchez
- Clinical Trials Unit of La Princesa University Hospital (UECHUP), La Princesa University Hospital Research Institute, 28006 Madrid, Spain; (M.R.); (S.M.-V.)
| | - Dolores Ochoa
- Clinical Pharmacology Department, La Princesa University Hospital, 28006 Madrid, Spain;
- Clinical Trials Unit of La Princesa University Hospital (UECHUP), La Princesa University Hospital Research Institute, 28006 Madrid, Spain; (M.R.); (S.M.-V.)
| | - Francisco Abad-Santos
- Pharmacogenetics Unit, Clinical Pharmacology Department, La Princesa University Hospital Research Institute, 28006 Madrid, Spain; (G.V.-G.); (M.N.-G.)
- Spanish Clinical Research Network (SCReN), La Princesa University Hospital Research Institute, 28006 Madrid, Spain;
- Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain;
- Clinical Pharmacology Department, La Princesa University Hospital, 28006 Madrid, Spain;
- Clinical Trials Unit of La Princesa University Hospital (UECHUP), La Princesa University Hospital Research Institute, 28006 Madrid, Spain; (M.R.); (S.M.-V.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), ICIII, 28006 Madrid, Spain
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Awab GR, Aaram F, Jamornthanyawat N, Suwannasin K, Pagornrat W, Watson JA, Woodrow CJ, Dondorp AM, Day NPJ, Imwong M, White NJ. Protective effect of Mediterranean-type glucose-6-phosphate dehydrogenase deficiency against Plasmodium vivax malaria. eLife 2021; 10:e62448. [PMID: 33543710 PMCID: PMC7884069 DOI: 10.7554/elife.62448] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/03/2021] [Indexed: 01/19/2023] Open
Abstract
X-linked glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common human enzymopathy. The severe Mediterranean variant (G6PD Med) found across Europe and Asia is thought to confer protection against malaria, but its effect is unclear. We fitted a Bayesian statistical model to observed G6PD Med allele frequencies in 999 Pashtun patients presenting with acute Plasmodium vivax malaria and 1408 population controls. G6PD Med was associated with reductions in symptomatic P. vivax malaria incidence of 76% (95% credible interval [CI], 58-88) in hemizygous males and homozygous females combined and 55% (95% CI, 38-68) in heterozygous females. Unless there is very large population stratification within the Pashtun (confounding these results), the G6PD Med genotype confers a very large and gene-dose proportional protective effect against acute vivax malaria. The proportion of patients with vivax malaria at risk of haemolysis following 8-aminoquinoline radical cure is substantially overestimated by studies measuring G6PD deficiency prevalence in healthy subjects.
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Affiliation(s)
- Ghulam R Awab
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
- Nangarhar Medical FacultyJalalabadAfghanistan
| | | | - Natsuda Jamornthanyawat
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
| | - Kanokon Suwannasin
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
| | - Watcharee Pagornrat
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
| | - James A Watson
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Charles J Woodrow
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Arjen M Dondorp
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Nicholas PJ Day
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
| | - Nicholas J White
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
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Novel directions in data pre-processing and genome-wide association study (GWAS) methodologies to overcome ongoing challenges. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Cerniglia L, Cimino S, Marzilli E, Pascale E, Tambelli R. Associations Among Internet Addiction, Genetic Polymorphisms, Family Functioning, and Psychopathological Risk: Cross-Sectional Exploratory Study. JMIR Ment Health 2020; 7:e17341. [PMID: 33361057 PMCID: PMC7790611 DOI: 10.2196/17341] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 10/02/2020] [Accepted: 10/20/2020] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND International research has emphasized that youths are at higher risk for the onset of internet addiction (IA), but studies investigating biological, psychological, and social factors associated with this condition are limited. OBJECTIVE This study aims to investigate the possible association between IA and genetic polymorphisms in monoamine oxidase A (MAO-A), serotonin-transporter (5-HTTPR), dopamine receptor (DRD4), and dopamine transporter (DAT1) genes by considering the role played by the perception of young adults in their family functioning and their depression, anxiety, and avoidant personality problems. METHODS In a sample of 104 male and female young adults aged between 19 and 23 years (mean age 21.87, SD 2.29 years) recruited from universities in the central southern part of Italy, we addressed the presence of IA using the Young criteria of the IA test. Moreover, the perception of young adults of their family functioning and their psychopathological symptoms were assessed through the Family Assessment Device (FAD) and the Adult Self-Report, respectively. RESULTS We found no significant association between IA and any genetic polymorphisms, neither among males or females. Young adults with IA reported significantly higher scores in the subscale of FAD affective responsiveness (AR; P=.01) and in depressive problems (P=.02), anxiety problems (P=.009), and avoidant personality problems (P=.003) than those in the control group. Results of mediation analyses showed a mediation role played by depressive symptoms (B=0.99; 95% CI 0.22 to 1.97) and avoidant personality problems (B=1.09; 95% CI 0.32 to 2.05) of young adults on the relationship between the FAD, AR, and IA. Finally, this relationship was moderated by the genotype of the 5-HTTLPR (P<.001), DAT1 (P<.001), and MAO-A (P<.001) genes in young adults. CONCLUSIONS This exploratory study supports the recent evidence on the mutual relationship among biological, individual, and social risk factors associated with IA in young adulthood. Our findings may have important clinical implications for the development of prevention and treatment programs.
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Affiliation(s)
- Luca Cerniglia
- International Telematic University Uninettuno, Rome, Italy
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Black MH, Li S, LaDuca H, Lo M, Chen J, Hoiness R, Gutierrez S, Tippin‐Davis B, Lu H, Gielzak M, Wiley K, Shi Z, Wei J, Zheng SL, Helfand BT, Isaacs W, Xu J. Validation of a prostate cancer polygenic risk score. Prostate 2020; 80:1314-1321. [PMID: 33258481 PMCID: PMC7590110 DOI: 10.1002/pros.24058] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/31/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND Genome-wide association studies have identified over 100 single-nucleotide polymorphisms (SNPs) associated with prostate cancer (PrCa), and polygenic risk scores (PRS) based on their combined genotypes have been developed for risk stratification. We aimed to assess the contribution of PRS to PrCa risk in a large multisite study. METHODS The sample included 1972 PrCa cases and 1919 unaffected controls. Next-generation sequencing was used to assess pathogenic variants in 14 PrCa-susceptibility genes and 72 validated PrCa-associated SNPs. We constructed a population-standardized PRS and tested its association with PrCa using logistic regression adjusted for age and family history of PrCa. RESULTS The mean age of PrCa cases at diagnosis and age of controls at testing/last clinic visit was 59.5 ± 7.2 and 57.2 ± 13.0 years, respectively. Among 1740 cases with pathology data, 57.4% had Gleason score ≤ 6, while 42.6% had Gleason score ≥ 8. In addition, 39.6% cases and 20.1% controls had a family history of PrCa. The PRS was significantly higher in cases than controls (mean ± SD: 1.42 ± 1.11 vs 1.02 ± 0.76; P < .0001). Compared with men in the 1st quartile of age-adjusted PRS, those in the 2nd, 3rd, and 4th quartile were 1.58 (95% confidence interval [CI]: 1.31-1.90), 2.36 (95% CI: 1.96-2.84), and 3.98 (95% CI: 3.29-4.82) times as likely to have PrCa (all P < .0001). Adjustment for family history yielded similar results. PRS predictive performance was consistent with prior literature (area under the receiver operating curve = 0.64; 95% CI: 0.62-0.66). CONCLUSIONS These data suggest that a 72-SNP PRS is predictive of PrCa, supporting its potential use in clinical risk assessment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Marta Gielzak
- Department of Urology, The James Buchanan Brady Urologic InstituteJohns Hopkins University School of MedicineBaltimoreMaryland
| | - Kathleen Wiley
- Department of Urology, The James Buchanan Brady Urologic InstituteJohns Hopkins University School of MedicineBaltimoreMaryland
| | - Zhuqing Shi
- Program for Personalized Cancer CareNorthShore University Health SystemEvanstonIllinois
| | - Jun Wei
- Program for Personalized Cancer CareNorthShore University Health SystemEvanstonIllinois
| | - Siqun Lilly Zheng
- Program for Personalized Cancer CareNorthShore University Health SystemEvanstonIllinois
| | - Brian T. Helfand
- Program for Personalized Cancer CareNorthShore University Health SystemEvanstonIllinois
| | - William Isaacs
- Department of Urology, The James Buchanan Brady Urologic InstituteJohns Hopkins University School of MedicineBaltimoreMaryland
| | - Jianfeng Xu
- Program for Personalized Cancer CareNorthShore University Health SystemEvanstonIllinois
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Mostafa T, Abdel-Hamid IA, Taymour M, Ali OI. Gene Variants in Premature Ejaculation: Systematic Review and Future Directions. Sex Med Rev 2020; 8:586-602. [PMID: 32800770 DOI: 10.1016/j.sxmr.2020.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/06/2020] [Accepted: 07/11/2020] [Indexed: 02/05/2023]
Abstract
INTRODUCTION A growing number of genetic association studies have been performed to investigate the association between the genetic susceptibility alleles and the risk of premature ejaculation (PE); however, the results remain inconclusive. OBJECTIVES This systematic review aimed: (i) to determine whether an association exists between gene(s) or allelic variant(s) and PE; (ii) to assess whether the associations are consistent across studies in magnitude and direction, and (iii) to identify any limitation, gap, or shortcoming in the included studies. METHODS The literature search was conducted in PubMed, MEDLINE, Scopus, Cochrane Library, EMBASE, Academic Search Complete, Google Scholar, and CINAHL databases. RESULTS Different gene variants associated with PE were assessed. 25 genetic association studies met the inclusion criteria that investigated 11 genes, 2,624 men with PE compared with 9,346 men as controls, twins, and siblings. 19 studies demonstrated a significant association with PE, whereas 4 studies denied such a relationship. SLC6A4 gene polymorphism was investigated in 11 studies (7 studies demonstrated a significant relationship with PE, and 4 studies denied such a relationship). Dopamine transporter gene (DAT1) polymorphism was investigated in 4 studies exhibiting a significant relationship. Androgen receptor gene polymorphisms were investigated in 2 studies, 1 with a significant relationship and the other with a non-significant relationship. Oxytocin gene polymorphisms and tryptophan hydroxylase 2 gene polymorphisms were investigated in 2 studies with a significant relationship. CONCLUSION While this review has highlighted several genes that may be potentially associated with PE such as SLC6A4, limitations such as variance in study methods, lack of robust findings, small sample sizes, lack of reproducibility, quality of reporting, and quality of assessment remain a major concern. Further efforts such as standardizing reporting, exploring complementary designs, and the use of genome-wide association studies technology are warranted to test the reproducibility of these early findings. Mostafa T, Abdel-Hamid IA, Taymour M, et al. Gene Variants in Premature Ejaculation: Systematic Review and Future Directions. Sex Med Rev 2020;8:586-602.
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Affiliation(s)
- Taymour Mostafa
- Andrology, Sexology & STIs Department, Faculty of Medicine, Cairo University, Cairo, Egypt.
| | | | - Mai Taymour
- Dermatology & Andrology, Private Sector, Cairo, Egypt
| | - Omar I Ali
- Faculty of Medicine and Surgery, 6th October University, Giza, Egypt
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Shin HR, Cho WK, Baek IC, Lee NY, Lee YJ, Kim SK, Ahn MB, Suh BK, Kim TG. Polymorphisms of IRAK1 Gene on X Chromosome Is Associated with Hashimoto Thyroiditis in Korean Children. Endocrinology 2020; 161:5851529. [PMID: 32498091 DOI: 10.1210/endocr/bqaa088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023]
Abstract
Autoimmune thyroid disease (AITD) is predominant in females and has been focused on the sexual diploid in immune response. The IL-1 receptor-associated kinase 1 (IRAK1) gene on the X chromosome was recently suggested as strong autoimmune disease-susceptible loci, second to the major histocompatibility complex region. We investigated the frequency of IRAK1 single-nucleotide polymorphisms (SNPs) in children with AITD. In this study, we observed that SNPs of IRAK1 including rs3027898, rs1059703, and rs1059702 in 115 Korean AITD pediatric patients (Graves' disease = 74 [females = 52/males = 22]; Hashimoto disease [HD] = 41 [females = 38/males = 3]; thyroid-associated ophthalmopathy [TAO] = 40 (females = 27/males = 13); without TAO = 75 (females = 63/males = 12); total males = 25, total females = 90; mean age = 11.9 years) and 204 healthy Korean individuals (males = 104/females = 100). The data from cases and controls were analyzed from separate sex-stratified or all combined by χ 2 test for categorical variables and Student t test for numerical variables. Our study revealed that SNPs of IRAK1-associated HD and without TAO but Graves' disease and TAO were not found significant. When cases and controls were analyzed by separate sex, we found that rs3027898 AA, rs1059703 AA, and rs1059702 GG showed disease susceptibility in female AITD, HD, and without TAO. Also, all rs3027898, rs1059703, and rs1059702 were found to be in strong linkage disequilibrium (D' = 0.96-0.98, r2 = 0.83-0.97). The haplotype of 3 SNPs was higher in AITD than in controls (CGA, r2 = 5.42, P = 0.019). Our results suggest that IRAK1 polymorphisms may contribute to the pathogenesis of HD, AITD, and without thyroid-associated ophthalmopathy for females.
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Affiliation(s)
- Hye-Ri Shin
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Won Kyoung Cho
- Department of Pediatrics, College of Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - In-Cheol Baek
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Na Yeong Lee
- Department of Pediatrics, College of Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yoon Ji Lee
- Department of Pediatrics, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seul Ki Kim
- Department of Pediatrics, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Moon Bae Ahn
- Department of Pediatrics, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Byung-Kyu Suh
- Department of Pediatrics, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Tai-Gyu Kim
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Cho WK, Shin HR, Lee NY, Kim SK, Ahn MB, Baek IC, Kim TG, Suh BK. GPR174 and ITM2A Gene Polymorphisms rs3827440 and rs5912838 on the X chromosome in Korean Children with Autoimmune Thyroid Disease. Genes (Basel) 2020; 11:genes11080858. [PMID: 32727090 PMCID: PMC7465061 DOI: 10.3390/genes11080858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 12/12/2022] Open
Abstract
(1) Background: Autoimmune thyroid diseases (AITDs) are female predominant and much attention has been focused on G protein-coupled receptor 174 (GPR174) and integral membrane protein 2A (ITM2A) on the X chromosome as Grave's disease (GD) susceptible locus. (2) Methods: We genotyped four single nucleotide polymorphisms (SNPs), rs3810712, rs3810711, rs3827440, and rs5912838, of GPR174 and ITM2A in 115 Korean children with AITD (M = 25 and F = 90; GD = 74 (14.7 ± 3.6 years), HD = 41 (13.4 ± 3.2 years); GD-thyroid-associated ophthalmopathy (TAO) = 40, GD-non-TAO=34) and 204 healthy Korean individuals (M = 104 and F = 100). The data were analyzed by sex-stratified or combined. (3) Results: Three SNPs, rs3810712, rs3810711 and rs3827440, were found to be in perfect linkage disequilibrium (D' = 1, r2 = 1). In AITD, HD, GD, GD-TAO, and GD-non-TAO patients, rs3827440 TT/T and rs5912838 AA/A were susceptible and rs3827440 CC/C and rs5912838 CC/C were protective genotypes. When analyzed by sex, rs3827440 TT and rs5912838 AA were susceptible and rs3827440 CC and rs5912838 CC were protective genotypes in female AITD, GD, GD-TAO, and GD-non-TAO subjects. In male AITD patients, rs3827440 T and rs5912838 A were susceptible and rs3827440 C and rs5912838 C were protective genotypes. (4) Conclusions: Polymorphisms in GPR174 and ITM2A genes on the X chromosome might be associated with AITD in Korean children.
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Affiliation(s)
- Won Kyoung Cho
- Department of Pediatrics, College of Medicine, St. Vincent’s Hospital, The Catholic University of Korea, Seoul 065941, Korea;
| | - Hye-Ri Shin
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul 065941, Korea; (H.-R.S.); (I.-C.B.)
| | - Na Yeong Lee
- Department of Pediatrics, College of Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 065941, Korea; (N.Y.L.); (S.K.K.); (M.B.A.)
| | - Seul Ki Kim
- Department of Pediatrics, College of Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 065941, Korea; (N.Y.L.); (S.K.K.); (M.B.A.)
| | - Moon Bae Ahn
- Department of Pediatrics, College of Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 065941, Korea; (N.Y.L.); (S.K.K.); (M.B.A.)
| | - In-Cheol Baek
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul 065941, Korea; (H.-R.S.); (I.-C.B.)
| | - Tai-Gyu Kim
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul 065941, Korea; (H.-R.S.); (I.-C.B.)
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 065941, Korea
- Correspondence: (T.-G.K.); (B.-K.S.); Tel.: +82-2-2258-7341 (T.-G.K.); +82-2-2258-6185 (B.-K.S.); Fax: +82-2-594-7355 (T.-G.K.); 82-2-532-6185 (B.-K.S.)
| | - Byung-Kyu Suh
- Department of Pediatrics, College of Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 065941, Korea; (N.Y.L.); (S.K.K.); (M.B.A.)
- Correspondence: (T.-G.K.); (B.-K.S.); Tel.: +82-2-2258-7341 (T.-G.K.); +82-2-2258-6185 (B.-K.S.); Fax: +82-2-594-7355 (T.-G.K.); 82-2-532-6185 (B.-K.S.)
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Peng Q, Shi L, Kong Y, Yan Y, Zhan J, Wen Y, Liu W, Yu D, Zhou Z, Yan H. CX3CL1 rs170364 gene polymorphism has a protective effect against major depression by enhancing its transcriptional activity. Brain Res 2020; 1738:146801. [PMID: 32234515 DOI: 10.1016/j.brainres.2020.146801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/05/2020] [Accepted: 03/21/2020] [Indexed: 01/10/2023]
Abstract
Studies have shown that adult hippocampal neurogenesis may be a cause of depression. CX3CL1 is a chemokine that plays an important role in adult neurogenesis. This study aimed to investigate the relationship between CX3CL1 polymorphisms (rs170364) and the risk of depression. A case-control study of 502 patients with major depression and 504 gender-matched and age-matched healthy controls was performed. All subjects were recruited from the Chinese Han population. Next-generation sequencing was used to genotype the CX3CL1 rs170364 locus. In addition, the effect of the rs170364 polymorphism on transcription of CX3CL1 was investigated through the use of luciferase reporter constructs and in vitro analysis in SH-SY5Y cells. Our results demonstrated that the T allele and GT + TT genotype of the CX3CL1 rs170364 locus were associated with a reduced risk of major depression. Subgroup analysis found that this significant association was consistently found in females but not in males. In vitro experiments found that the rs170364 mutation enhanced the transcriptional activity of CX3CL1. These results suggest that T allele and GT + TT genotypes of the CX3CL1 rs170364 locus may be a protective factor against the onset of depression in the Chinese Han population, especially in females. SNP rs170364 enhances the transcriptional activity of CX3CL1.
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Affiliation(s)
- Qiuju Peng
- Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Lei Shi
- Department of Pharmacy, General Hospital of Southern Theatre Command, Guangzhou 510010, China
| | - Yanying Kong
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yuan Yan
- Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jielin Zhan
- Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yuguan Wen
- Department of Pharmacy, Guangzhou Brain Hospital, Guangzhou 510370, China
| | - Wenyi Liu
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Southern Theatre Command, Guangzhou 510507, China
| | - Dexian Yu
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Southern Theatre Command, Guangzhou 510507, China
| | - Zhijian Zhou
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Southern Theatre Command, Guangzhou 510507, China
| | - Huacheng Yan
- Department of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Southern Theatre Command, Guangzhou 510507, China.
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Sex linkage of the skeletal muscle sodium channel gene (SCN4A) explains apparent deviations from Hardy-Weinberg equilibrium of tetrodotoxin-resistance alleles in garter snakes (Thamnophis sirtalis). Heredity (Edinb) 2020; 124:647-657. [PMID: 32111979 DOI: 10.1038/s41437-020-0300-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 01/01/2023] Open
Abstract
The arms race between tetrodotoxin-bearing Pacific newts (Taricha) and their garter snake predators (Thamnophis) in western North America has become a classic example of coevolution, shedding light on predator-prey dynamics, the molecular basis of adaptation, and patterns of convergent evolution. Newts are defended by tetrodotoxin (TTX), a neurotoxin that binds to voltage-gated sodium channels (Nav proteins), arresting electrical activity in nerves and muscles and paralyzing would-be predators. However, populations of the common garter snake (T. sirtalis) have overcome this defense, largely through polymorphism at the locus SCN4A, which renders the encoded protein (Nav1.4) less vulnerable to TTX. Previous work suggests that SCN4A commonly shows extreme deviations from Hardy-Weinberg equilibrium (HWE) in these populations, which has been interpreted as the result of intense selection imposed by newts. Here we show that much of this apparent deviation can be attributed to sex linkage of SCN4A. Using genomic data and quantitative PCR, we show that SCN4A is on the Z chromosome in Thamnophis and other advanced snakes. Taking Z-linkage into account, we find that most apparent deviations from HWE can be explained by female hemizygosity rather than low heterozygosity. Sex linkage can affect mutation rates, selection, and drift, and our results suggest that Z-linkage of SCN4A may make significant contributions to the overall dynamics of the coevolutionary arms race between newts and snakes.
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Stanković B, Kotur N, Gašić V, Klaassen K, Ristivojević B, Stojiljković M, Pavlović S, Zukić B. Pharmacogenomics landscape of COVID-19 therapy response in Serbian population and comparison with worldwide populations. J Med Biochem 2020; 39:488-499. [PMID: 33312066 DOI: 10.5937/jomb0-26725] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022] Open
Abstract
Background Since there are no certified therapeutics to treat COVID-19 patients, drug repurposing became important. With lack of time to test individual pharmacogenomics markers, population pharmacogenomics could be helpful in predicting a higher risk of developing adverse reactions and treatment failure in COVID-19 patients. Aim of our study was to identify pharmacogenes and pharmacogenomics markers associated with drugs recommended for COVID-19 treatment, chloroquine/hydroxychloroquine, azithromycin, lopinavir and ritonavir, in population of Serbia and other world populations. Methods Genotype information of 143 individuals of Serbian origin was extracted from database previously obtained using TruSight One Gene Panel (Illumina). Genotype data of individuals from different world populations were extracted from the 1000 Genome Project. Fisher's exact test was used for comparison of allele frequencies. Results We have identified 11 potential pharmacogenomics markers in 7 pharmacogenes relevant for COVID-19 treatment. Based on high alternative allele frequencies in population and the functional effect of the variants, ABCB1 rs1045642 and rs2032582 could be relevant for reduced clearance of azithromycin, lopinavir and ritonavir drugs and UGT1A7 rs17868323 for hyperbilirubinemia in ritonavir treated COVID-19 patients in Serbian population. SLCO1B1 rs4149056 is a potential marker of lopinavir response, especially in Italian population. Our results confirmed that pharmacogenomics profile of African population is different from the rest of the world. Conclusions Considering population specific pharmacogenomics landscape, preemptive testing for pharmacogenes relevant for drugs used in COVID-19 treatment could contribute to better understanding of the inconsistency in therapy response and could be applied to improve the outcome of the COVID-19 patients.
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Affiliation(s)
- Biljana Stanković
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Nikola Kotur
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Vladimir Gašić
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Kristel Klaassen
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Bojan Ristivojević
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Maja Stojiljković
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Sonja Pavlović
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Branka Zukić
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
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Puig X, Ginebra J, Graffelman J. Bayesian model selection for the study of Hardy-Weinberg proportions and homogeneity of gender allele frequencies. Heredity (Edinb) 2019; 123:549-564. [PMID: 31142813 DOI: 10.1038/s41437-019-0232-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/15/2019] [Accepted: 05/02/2019] [Indexed: 12/24/2022] Open
Abstract
Standard statistical tests for Hardy-Weinberg equilibrium assume the equality of allele frequencies in the sexes, whereas tests for the equality of allele frequencies in the sexes assume Hardy-Weinberg equilibrium. This produces a circularity in the testing of genetic variants, which has recently been resolved with new frequentist likelihood and exact procedures. In this paper, we tackle the same problem by posing it as a Bayesian model comparison problem. We formulate an exhaustive set of ten alternative scenarios for biallelic genetic variants. Using Dirichlet and Beta priors for genotype and allele frequencies, we derive marginal likelihoods for all scenarios, and select the most likely scenario using the posterior probabilities that each of these scenarios is the one in place. Different from the usual frequentist testing approach, the Bayesian approach allows one to compare any number of models, and not just two at a time, and the models compared do not have to be nested. We illustrate our Bayesian approach with genetic data from the 1,000 genomes project and through a simulation study.
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Affiliation(s)
- Xavier Puig
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Josep Ginebra
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain. .,Department of Biostatistics, University of Washington, Seattle, WA, USA.
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Backenroth D, Carmi S. A test for deviations from expected genotype frequencies on the X chromosome for sex-biased admixed populations. Heredity (Edinb) 2019; 123:470-478. [PMID: 31101879 DOI: 10.1038/s41437-019-0233-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/19/2019] [Accepted: 04/29/2019] [Indexed: 11/09/2022] Open
Abstract
Genome-wide scans for deviations from expected genotype frequencies, as determined by the Hardy-Weinberg equilibrium (HWE), are commonly applied to detect genotyping errors and deviations from random mating. In contrast to the autosomes, genotype frequencies on the X chromosome do not reach HWE within a single generation. Instead, if allele frequencies in males and females initially differ, they oscillate for a few generations toward equilibrium. Allele frequency differences between the sexes are expected in populations that have experienced recent sex-biased admixture, namely, their male and female founders differed in ancestry. Sex-biased admixture does not allow testing for HWE on X, because deviations are naturally expected, even under random mating (post admixture) and error-free genotyping. In this paper, we develop a likelihood ratio test and a χ2 test to detect deviations from expected genotype frequencies on X, beyond natural deviations due to sex-biased admixture. We demonstrate by simulations that our tests are powerful for detecting deviations due to non-random mating, while at the same time they do not reject the null under historical sex-biased admixture and random mating thereafter. We also demonstrate that when applied to 1000 Genomes project populations, our likelihood ratio test rejects fewer SNPs than other tests, but we describe limitations in the interpretation of the results.
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Affiliation(s)
- Daniel Backenroth
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Motawi TMK, Sadik NAH, Sabry D, Shahin NN, Fahim SA. rs2267531, a promoter SNP within glypican-3 gene in the X chromosome, is associated with hepatocellular carcinoma in Egyptians. Sci Rep 2019; 9:6868. [PMID: 31053802 PMCID: PMC6499880 DOI: 10.1038/s41598-019-43376-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/23/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a major health concern in Egypt owing to the high prevalence of hepatitis C virus (HCV) infection. HCC incidence is characterized by obvious male predominance, yet the molecular mechanisms behind this gender bias are still unidentified. Functional variations in X-linked genes have more impact on males than females. Glypican-3 (GPC3) gene, located in the Xq26 region, has lately emerged as being potentially implicated in hepatocellular carcinogenesis. The current study was designed to examine the association of -784 G/C single nucleotide polymorphism (SNP) in GPC3 promoter region (rs2267531) with HCC susceptibility in male and female Egyptian HCV patients. Our results revealed a significant association between GPC3 and HCC risk in both males and females, evidenced by higher C allele and CC/C genotype frequencies in HCC patients when compared to controls. However, no such association was found when comparing HCV patients to controls. Moreover, GPC3 gene and protein expression levels were significantly higher in CC/C than in GG/G genotype carriers in males and females. The CC/C genotype exhibited a significant shorter overall survival than GG/G genotype in HCC patients. In conclusion, GPC3 rs2267531 on the X chromosome is significantly associated with HCC, but not with HCV infection, in the Egyptian population.
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Affiliation(s)
| | | | - Dina Sabry
- Medical Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Nancy Nabil Shahin
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Sally Atef Fahim
- Biochemistry Department, Faculty of Pharmacy, Ahram Canadian University, Cairo, Egypt.
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Wellek S, Ziegler A. Testing for goodness rather than lack of fit of an X-chromosomal SNP to the Hardy-Weinberg model. PLoS One 2019; 14:e0212344. [PMID: 30789927 PMCID: PMC6383894 DOI: 10.1371/journal.pone.0212344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/31/2019] [Indexed: 02/01/2023] Open
Abstract
The problem of checking the genotype distribution obtained for some diallelic marker for compatibility with the Hardy-Weinberg equilibrium (HWE) condition arises also for loci on the X chromosome. The possible genotypes depend on the sex of the individual in this case: for females, the genotype distribution is trinomial, as in the case of an autosomal locus, whereas a binomial proportion is observed for males. Like in genetic association studies with autosomal SNPs, interest is typically in establishing approximate compatibility of the observed genotype frequencies with HWE. This requires to replace traditional methods tailored for detecting lack of fit to the model with an equivalence testing procedure to be derived by treating approximate compatibility with the model as the alternative hypothesis. The test constructed here is based on an upper confidence bound and a simple to interpret combined measure of distance between true and HWE conforming genotype distributions in female and male subjects. A particular focus of the paper is on the derivation of the asymptotic distribution of the test statistic under null alternatives which is not of the usual Gaussian form. A closed sample size formula is also provided and shown to behave satisfactorily in terms of the approximation error.
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Affiliation(s)
- Stefan Wellek
- Department of Biostatistics, CIMH Mannheim, Mannheim Medical School of the University of Heidelberg, Mannheim, Germany
- Department of Medical Biostatistics, Epidemiology & Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Andreas Ziegler
- Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck, Germany
- StatSol, Moenring 2, Lübeck, Germany
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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Poriswanish N, Neumann R, Wetton JH, Wagstaff J, Larmuseau MHD, Jobling MA, May CA. Recombination hotspots in an extended human pseudoautosomal domain predicted from double-strand break maps and characterized by sperm-based crossover analysis. PLoS Genet 2018; 14:e1007680. [PMID: 30296256 PMCID: PMC6193736 DOI: 10.1371/journal.pgen.1007680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 10/18/2018] [Accepted: 09/05/2018] [Indexed: 01/11/2023] Open
Abstract
The human X and Y chromosomes are heteromorphic but share a region of homology at the tips of their short arms, pseudoautosomal region 1 (PAR1), that supports obligate crossover in male meiosis. Although the boundary between pseudoautosomal and sex-specific DNA has traditionally been regarded as conserved among primates, it was recently discovered that the boundary position varies among human males, due to a translocation of ~110 kb from the X to the Y chromosome that creates an extended PAR1 (ePAR). This event has occurred at least twice in human evolution. So far, only limited evidence has been presented to suggest this extension is recombinationally active. Here, we sought direct proof by examining thousands of gametes from each of two ePAR-carrying men, for two subregions chosen on the basis of previously published male X-chromosomal meiotic double-strand break (DSB) maps. Crossover activity comparable to that seen at autosomal hotspots was observed between the X and the ePAR borne on the Y chromosome both at a distal and a proximal site within the 110-kb extension. Other hallmarks of classic recombination hotspots included evidence of transmission distortion and GC-biased gene conversion. We observed good correspondence between the male DSB clusters and historical recombination activity of this region in the X chromosomes of females, as ascertained from linkage disequilibrium analysis; this suggests that this region is similarly primed for crossover in both male and female germlines, although sex-specific differences may also exist. Extensive resequencing and inference of ePAR haplotypes, placed in the framework of the Y phylogeny as ascertained by both Y microsatellites and single nucleotide polymorphisms, allowed us to estimate a minimum rate of crossover over the entire ePAR region of 6-fold greater than genome average, comparable with pedigree estimates of PAR1 activity generally. We conclude ePAR very likely contributes to the critical crossover function of PAR1. 95% of our genome is contained in 22 pairs of chromosomes shared by all humans. However, women and men differ in their sex chromosomes: while women have two X chromosomes, men have an X and a smaller, sex-determining Y chromosome. To ensure correct partition of X and Y into sperm, genetic exchange (crossover) must occur between these very different chromosomes in a short, shared region. The location of the boundary of this region was thought to have been conserved since before the divergence from old world monkeys at least 27 million years ago, but recently it has been shown that some human males carry an extended version on their Y chromosomes, thanks to the transposition of a piece of DNA from the X chromosome. Here, we asked if genetic exchange occurs in this newly extended region. To do this, we used previously published information that signposted the positions within the X chromosome segment which exhibit the hallmarks of crossover initiation. We then sought direct evidence of crossover in the sperm of men carrying the extension. This work showed that the signposts were accurate, pointing to frequent crossover in this novel shared sex-chromosomal domain.
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Affiliation(s)
- Nitikorn Poriswanish
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Forensic Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Jon H. Wetton
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - John Wagstaff
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Maarten H. D. Larmuseau
- Laboratory of Forensic Genetics and Molecular Archaeology, Department of Imaging and Pathology, KU Leuven, Belgium
| | - Mark A. Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Celia A. May
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
- * E-mail:
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Messmer AM, Leong JS, Rondeau EB, Mueller A, Despins CA, Minkley DR, Kent MP, Lien S, Boyce B, Morrison D, Fast MD, Norman JD, Danzmann RG, Koop BF. A 200K SNP chip reveals a novel Pacific salmon louse genotype linked to differential efficacy of emamectin benzoate. Mar Genomics 2018; 40:45-57. [PMID: 29673959 DOI: 10.1016/j.margen.2018.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 02/28/2018] [Accepted: 03/27/2018] [Indexed: 11/28/2022]
Abstract
Antiparasitic drugs such as emamectin benzoate (EMB) are relied upon to reduce the parasite load, particularly of the sea louse Lepeophtheirus salmonis, on farmed salmon. The decline in EMB treatment efficacy for this purpose is an important issue for salmon producers around the world, and particularly for those in the Atlantic Ocean where widespread EMB tolerance in sea lice is recognized as a significant problem. Salmon farms in the Northeast Pacific Ocean have not historically experienced the same issues with treatment efficacy, possibly due to the relatively large population of endemic salmonid hosts that serve to both redistribute surviving lice and dilute populations potentially under selection by introducing naïve lice to farms. Frequent migration of lice among farmed and wild hosts should limit the effect of farm-specific selection pressures on changes to the overall allele frequencies of sea lice in the Pacific Ocean. A previous study using microsatellites examined L. salmonis oncorhynchi from 10 Pacific locations from wild and farmed hosts and found no population structure. Recently however, a farm population of sea lice was detected where EMB bioassay exposure tolerance was abnormally elevated. In response, we have developed a Pacific louse draft genome that complements the previously-released Atlantic louse sequence. These genomes were combined with whole-genome re-sequencing data to design a highly sensitive 201,279 marker SNP array applicable for both subspecies (90,827 validated Pacific loci; 153,569 validated Atlantic loci). Notably, kmer spectrum analysis of the re-sequenced samples indicated that Pacific lice exhibit a large within-individual heterozygosity rate (average of 1 in every 72 bases) that is markedly higher than that of Atlantic individuals (1 in every 173 bases). The SNP chip was used to produce a high-density map for Atlantic sea louse linkage group 5 that was previously shown to be associated with EMB tolerance in Atlantic lice. Additionally, 478 Pacific louse samples from farmed and wild hosts obtained between 2005 and 2014 were also genotyped on the array. Clustering analysis allowed us to detect the apparent emergence of an otherwise rare genotype at a high frequency among the lice collected from two farms in 2013 that had reported elevated EMB tolerance. This genotype was not observed in louse samples collected from the same farm in 2010, nor in any lice sampled from other locations prior to 2013. However, this genotype was detected at low frequencies in louse samples from farms in two locations reporting elevated EMB tolerance in 2014. These results suggest that a rare genotype present in Pacific lice may be locally expanded in farms after EMB treatment. Supporting this hypothesis, 437 SNPs associated with this genotype were found to be in a region of linkage group 5 that overlaps the region associated with EMB resistance in Atlantic lice. Finally, five of the top diagnostic SNPs within this region were used to screen lice that had been subjected to an EMB survival assay, revealing a significant association between these SNPs and EMB treatment outcome. To our knowledge this work is the first report to identify a genetic link to altered EMB efficacy in L. salmonis in the Pacific Ocean.
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Affiliation(s)
- Amber M Messmer
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - Jong S Leong
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - Eric B Rondeau
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - Anita Mueller
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - Cody A Despins
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - David R Minkley
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - Matthew P Kent
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Brad Boyce
- Marine Harvest Canada, Campbell River, BC, Canada.
| | | | - Mark D Fast
- Department of Pathology and Microbiology, University of Prince Edward Island, Charlottetown, PEI C1A 4P3, Canada.
| | - Joseph D Norman
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; Present address: The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 0A4, Canada.
| | - Roy G Danzmann
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada; Centre for Biomedical Research, University of Victoria, Victoria, BC V8W 3N5, Canada.
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Guilherme JPLF, Silva MS, Bertuzzi R, Lancha Junior AH. TheAGTR2rs11091046 (A>C) polymorphism and power athletic status in top-level Brazilian athletes. J Sports Sci 2018; 36:2327-2332. [DOI: 10.1080/02640414.2018.1455260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
| | - Mariana Sussi Silva
- Laboratory of Applied Nutrition and Metabolism, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo, Brazil
| | - Rômulo Bertuzzi
- Endurance Performance Research Group, School of Physical Education and Sport, University of São Paulo, Sao Paulo, Brazil
| | - Antonio Herbert Lancha Junior
- Laboratory of Applied Nutrition and Metabolism, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo, Brazil
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42
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Paternal lineage early onset hereditary ovarian cancers: A Familial Ovarian Cancer Registry study. PLoS Genet 2018; 14:e1007194. [PMID: 29447163 PMCID: PMC5813894 DOI: 10.1371/journal.pgen.1007194] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/09/2018] [Indexed: 11/19/2022] Open
Abstract
Given prior evidence that an affected woman conveys a higher risk of ovarian cancer to her sister than to her mother, we hypothesized that there exists an X-linked variant evidenced by transmission to a woman from her paternal grandmother via her father. We ascertained 3,499 grandmother/granddaughter pairs from the Familial Ovarian Cancer Registry at the Roswell Park Cancer Institute observing 892 informative pairs with 157 affected granddaughters. We performed germline X-chromosome exome sequencing on 186 women with ovarian cancer from the registry. The rate of cancers was 28.4% in paternal grandmother/granddaughter pairs and 13.9% in maternal pairs consistent with an X-linked dominant model (Chi-square test X2 = 0.02, p = 0.89) and inconsistent with an autosomal dominant model (X2 = 20.4, p<0.001). Paternal grandmother cases had an earlier age-of-onset versus maternal cases (hazard ratio HR = 1.59, 95%CI: 1.12–2.25) independent of BRCA1/2 status. Reinforcing the X-linked hypothesis, we observed an association between prostate cancer in men and ovarian cancer in his mother and daughters (odds ratio, OR = 2.34, p = 0.034). Unaffected mothers with affected daughters produced significantly more daughters than sons (ratio = 1.96, p<0.005). We performed exome sequencing in reported BRCA negative cases from the registry. Considering age-of-onset, one missense variant (rs176026 in MAGEC3) reached chromosome-wide significance (Hazard ratio HR = 2.85, 95%CI: 1.75–4.65) advancing the age of onset by 6.7 years. In addition to the well-known contribution of BRCA, we demonstrate that a genetic locus on the X-chromosome contributes to ovarian cancer risk. An X-linked pattern of inheritance has implications for genetic risk stratification. Women with an affected paternal grandmother and sisters of affected women are at increased risk for ovarian cancer. Further work is required to validate this variant and to characterize carrier families. Our article uses the largest familial study of ovarian cancer to argue that there exists an ovarian cancer susceptibility gene on the X-chromosome acting independently of BRCA1 and BRCA2. This observation implies that there may be many cases of seemingly sporadic ovarian cancer that are actually inherited; for example, only daughters who inherit risk from their fathers. This X-linked pattern implies novel ways to prioritize families for screening even without additional testing—sisters must both be carriers or neither; fathers of women with potentially inherited ovarian cancer may receive new attention. In addition, we found evidence that other cancers affect fathers and sons in these families. Using sequencing technology, we isolated a candidate gene, MAGEC3, that may be associated with earlier onset of ovarian cancer. The further study of this gene and the X-linked pattern will require additional study.
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Graffelman J, Weir BS. Multi-allelic exact tests for Hardy-Weinberg equilibrium that account for gender. Mol Ecol Resour 2018; 18:461-473. [PMID: 29288525 PMCID: PMC5969302 DOI: 10.1111/1755-0998.12748] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 11/29/2022]
Abstract
Statistical tests for Hardy–Weinberg equilibrium are important elementary tools in genetic data analysis. X‐chromosomal variants have long been tested by applying autosomal test procedures to females only, and gender is usually not considered when testing autosomal variants for equilibrium. Recently, we proposed specific X‐chromosomal exact test procedures for bi‐allelic variants that include the hemizygous males, as well as autosomal tests that consider gender. In this study, we present the extension of the previous work for variants with multiple alleles. A full enumeration algorithm is used for the exact calculations of tri‐allelic variants. For variants with many alternate alleles, we use a permutation test. Some empirical examples with data from the 1,000 genomes project are discussed.
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Affiliation(s)
- Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain.,Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, Seattle, WA, USA
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44
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Mirfakhraie R. The association between FOXP3 gene variations and autism: True or false positive? Gene X 2017; 635:1-2. [DOI: 10.1016/j.gene.2017.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 09/04/2017] [Indexed: 11/16/2022] Open
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45
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Graffelman J, Weir BS. On the testing of Hardy-Weinberg proportions and equality of allele frequencies in males and females at biallelic genetic markers. Genet Epidemiol 2017; 42:34-48. [PMID: 29071737 PMCID: PMC5813254 DOI: 10.1002/gepi.22079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/22/2017] [Accepted: 08/17/2017] [Indexed: 01/21/2023]
Abstract
Standard statistical tests for equality of allele frequencies in males and females and tests for Hardy‐Weinberg equilibrium are tightly linked by their assumptions. Tests for equality of allele frequencies assume Hardy‐Weinberg equilibrium, whereas the usual chi‐square or exact test for Hardy‐Weinberg equilibrium assume equality of allele frequencies in the sexes. In this paper, we propose ways to break this interdependence in assumptions of the two tests by proposing an omnibus exact test that can test both hypotheses jointly, as well as a likelihood ratio approach that permits these phenomena to be tested both jointly and separately. The tests are illustrated with data from the 1000 Genomes project.
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Affiliation(s)
- Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain.,Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
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46
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Genome-wide genetic structure and differentially selected regions among Landrace, Erhualian, and Meishan pigs using specific-locus amplified fragment sequencing. Sci Rep 2017; 7:10063. [PMID: 28855565 PMCID: PMC5577042 DOI: 10.1038/s41598-017-09969-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 08/02/2017] [Indexed: 12/22/2022] Open
Abstract
As typical Chinese indigenous pig breeds, Erhualian and Meishan have been widely used to produce new strain or breed in the world. However, the genetic basis of characteristics of these pig breeds is still limited. Moreover, considering cost and output of sequencing, it is necessary to further develop cost-effective method for pig genome screening. To contribute on this issue, we developed a SLAF-seq (specific-locus amplified fragment sequencing) method for pigs and applied it to analyze the genetic difference among Landrace, Erhualian, and Meishan pigs. A total of 453.75 million reads were produced by SLAF-seq. After quality-control, 165,670 SNPs (single nucleotide polymorphisms) were used in further analysis. The results showed that Landrace had distinct genetic relationship compared to Erhualian (FST = 0.5480) and Meishan (FST = 0.5800), respectively, while Erhualian and Meishan held the relatively close genetic relationship (FST = 0.2335). Furthermore, a genome-wide scanning revealed 268 differentially selected regions (DSRs) with 855 genes and 256 DSRs with 347 genes between Landrace and the two Chinese indigenous pig breeds and between Erhualian and Meishan, respectively. This study provides a new cost-effective method for pig genome study and might contribute to a better understanding on the formation mechanism of genetic difference among pigs with different geographical origins.
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47
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Puig X, Ginebra J, Graffelman J. A Bayesian test for Hardy-Weinberg equilibrium of biallelic X-chromosomal markers. Heredity (Edinb) 2017; 119:226-236. [PMID: 28900292 PMCID: PMC5597779 DOI: 10.1038/hdy.2017.30] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 05/08/2017] [Indexed: 12/29/2022] Open
Abstract
The X chromosome is a relatively large chromosome, harboring a lot of genetic information. Much of the statistical analysis of X-chromosomal information is complicated by the fact that males only have one copy. Recently, frequentist statistical tests for Hardy-Weinberg equilibrium have been proposed specifically for dealing with markers on the X chromosome. Bayesian test procedures for Hardy-Weinberg equilibrium for the autosomes have been described, but Bayesian work on the X chromosome in this context is lacking. This paper gives the first Bayesian approach for testing Hardy-Weinberg equilibrium with biallelic markers at the X chromosome. Marginal and joint posterior distributions for the inbreeding coefficient in females and the male to female allele frequency ratio are computed, and used for statistical inference. The paper gives a detailed account of the proposed Bayesian test, and illustrates it with data from the 1000 Genomes project. In that implementation, a novel approach to tackle multiple testing from a Bayesian perspective through posterior predictive checks is used.
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Affiliation(s)
- X Puig
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - J Ginebra
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - J Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain.,Department of Biostatistics, University of Washington, Seattle, WA, USA
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48
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Graffelman J, Jain D, Weir B. A genome-wide study of Hardy-Weinberg equilibrium with next generation sequence data. Hum Genet 2017; 136:727-741. [PMID: 28374190 PMCID: PMC5429372 DOI: 10.1007/s00439-017-1786-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/22/2017] [Indexed: 12/03/2022]
Abstract
Statistical tests for Hardy–Weinberg equilibrium have been an important tool for detecting genotyping errors in the past, and remain important in the quality control of next generation sequence data. In this paper, we analyze complete chromosomes of the 1000 genomes project by using exact test procedures for autosomal and X-chromosomal variants. We find that the rate of disequilibrium largely exceeds what might be expected by chance alone for all chromosomes. Observed disequilibrium is, in about 60% of the cases, due to heterozygote excess. We suggest that most excess disequilibrium can be explained by sequencing problems, and hypothesize mechanisms that can explain exceptional heterozygosities. We report higher rates of disequilibrium for the MHC region on chromosome 6, regions flanking centromeres and p-arms of acrocentric chromosomes. We also detected long-range haplotypes and areas with incidental high disequilibrium. We report disequilibrium to be related to read depth, with variants having extreme read depths being more likely to be out of equilibrium. Disequilibrium rates were found to be 11 times higher in segmental duplications and simple tandem repeat regions. The variants with significant disequilibrium are seen to be concentrated in these areas. For next generation sequence data, Hardy–Weinberg disequilibrium seems to be a major indicator for copy number variation.
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Affiliation(s)
- Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Avinguda Diagonal 647, 08028, Barcelona, Spain. .,Department of Biostatistics, University of Washington, University Tower, 15th Floor, 4333 Brooklyn Avenue, Seattle, WA, 98105-9461, USA.
| | - Deepti Jain
- Department of Biostatistics, University of Washington, University Tower, 15th Floor, 4333 Brooklyn Avenue, Seattle, WA, 98105-9461, USA
| | - Bruce Weir
- Department of Biostatistics, University of Washington, University Tower, 15th Floor, 4333 Brooklyn Avenue, Seattle, WA, 98105-9461, USA
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49
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Abstract
The Hardy-Weinberg principle, one of the most important principles in population genetics, was originally developed for the study of allele frequency changes in a population over generations. It is now, however, widely used in studies of human diseases to detect inbreeding, population stratification, and genotyping errors. For assessment of deviation from Hardy-Weinberg proportions in data, the most popular approaches include the asymptotic Pearson's chi-squared goodness-of-fit test and the exact test. Pearson's chi-squared goodness-of-fit test is simple and straightforward, but is very sensitive to a small sample size or rare allele frequency. The exact test of Hardy-Weinberg proportions is preferable in these situations. The exact test can be performed through complete enumeration of heterozygote genotypes or on the basis of the Markov chain Monte Carlo procedure. In this chapter, we describe the Hardy-Weinberg principle and the commonly used Hardy-Weinberg proportion tests and their applications, and we demonstrate how the chi-squared test and exact test of Hardy-Weinberg proportions can be performed step-by-step using the popular software programs SAS, R, and PLINK, which have been widely used in genetic association studies, along with numerical examples. We also discuss approaches for testing Hardy-Weinberg proportions in case-control study designs that are better than traditional approaches for testing Hardy-Weinberg proportions in controls only. Finally, we note that deviation from the Hardy-Weinberg proportions in affected individuals can provide evidence for an association between genetic variants and diseases.
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Affiliation(s)
- Jian Wang
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sanjay Shete
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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