Advantages and pitfalls in the application of mixed-model association methods

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2. Statistical properties of simple random-effects models for genetic heritability
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3. Genome-wide barebones regression scan for mixed-model association analysis
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4. Genetic architecture modulates diet-induced hepatic mRNA and miRNA expression profiles in Diversity Outbred mice
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5. Analysis of Heritability Using Genome‐Wide Data
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6. Estimating inflation in GWAS summary statistics due to variance distortion from cryptic relatedness
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8. Performing Genome-Wide Association Studies Using rMVP
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9. Archetypal clustering reveals physiological mechanisms linking milk yield and fertility in dairy cattle
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10. Genetic and genomic analysis of reproduction traits in holstein cattle using SNP chip data and imputed sequence level genotypes
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11. An integrative approach to prioritize candidate causal genes for complex traits in cattle
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12. Leveraging ancestral recombination graphs for scalable mixed-model analysis of complex traits
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13. Predictors of smoking reduction outcomes in a sample of 287 patients with schizophrenia spectrum disorders
    Bo-Jian Wu, Tsuo‐Hung Lan · 2015 · European Archives of Psychiatry and Clinical Neuroscience
14. Genetic Influences on Evening Preference Overlap with Those for Bipolar Disorder in a Sample of Mexican Americans and American Indians
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15. Deshrinking ridge regression for genome-wide association studies
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16. Penalized linear mixed models for structured genetic data
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17. Polygenic influences associated with adolescent cognitive skills
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18. A genome‐wide association study for eumelanin pigmentation in chicken plumage using a computer vision approach
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19. Effect of veterinary feed directive rule changes on tetracycline-resistant and erythromycin-resistant bacteria (Salmonella, Escherichia, and Campylobacter) in retail meats in the United States
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20. Genome-Wide Association Studies and Heritability Estimation in the Functional Genomics Era
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21. PolyQTL: Bayesian multiple eQTL detection with control for population structure and sample relatedness
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22. Linear mixed models for association analysis of quantitative traits with next‐generation sequencing data
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23. Gene-Based Association Testing of Dichotomous Traits With Generalized Functional Linear Mixed Models Using Extended Pedigrees: Applications to Age-Related Macular Degeneration
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24. Simultaneous test and estimation of total genetic effect in eQTL integrative analysis through mixed models
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25. Sustained Effects of Muscle Calpain System Genotypes on Tenderness Phenotypes of South African Beef Bulls during Ageing up to 20 Days
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26. Discovery and refinement of muscle weight QTLs in B6 × D2 advanced intercross mice
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27. Association Between NEDD4L Variation and the Genetic Risk of Acute Appendicitis
    Apostolos Gaitanidis, Haytham M. A. Kaafarani, Mathias Aagaard Christensen, Kerry Breen, April E. Mendoza, Peter J. Fagenholz, George C. Velmahos, Maha Reda Farhat · 2021 · JAMA Surgery
28. Quantitative Genetic Analysis of the Maize Leaf Microbiome
    Jason G. Wallace, Karl A. G. Kremling, Edward S. Buckler · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
29. Scalable analysis of large multi-ancestry biobanks by leveraging sparse ancestry-adjusted sample-relatedness
    Xihong Lin, Rounak Dey, Xihao Li, Zilin Li · 2024 · Research Square
30. Meta-GWAS Accuracy and Power (MetaGAP) Calculator Shows that Hiding Heritability Is Partially Due to Imperfect Genetic Correlations across Studies
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31. Evaluation and characterization of expression quantitative trait analysis methods in the Hybrid Rat Diversity Panel
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32. Long-Term Results of a Digital Diabetes Self-Management and Education Support Program Among Adults With Type 2 Diabetes: A Retrospective Cohort Study
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33. Comparison of machine learning methods for genomic prediction of selected Arabidopsis thaliana traits
    Ciaran Michael Kelly, Russell Lewis McLaughlin · 2024 · PLoS ONE
34. Genetic parameters and genome-wide association studies including the X chromosome for various reproduction and semen quality traits in Nellore cattle
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35. Alzheimer disease is (sometimes) highly heritable: Drivers of variation in heritability estimates for binary traits, a systematic review
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36. Genomic approaches to accelerate American chestnut restoration
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37. The Liability Threshold Model for Predicting the Risk of Cardiovascular Disease in Patients with Type 2 Diabetes: A Multi-Cohort Study of Korean Adults
    Eun Pyo Hong, Seong Gu Heo, Ji Wan Park · 2020 · Metabolites
38. Genetic mapping of renal glutathione suggests a novel regulatory locus on the murine X chromosome and overlap with hepatic glutathione regulation
    Rebecca Lizabeth Gould, Steven Wesley Craig, Susan McClatchy, Gary A. Churchill, Robert Pazdro · 2021 · Free Radical Biology and Medicine
39. Multi-phenotype genome-wide association studies of the Norfolk Island isolate implicate pleiotropic loci involved in chronic kidney disease
    Ngan K. Tran, Rod A. Lea, Samuel E. Holland, Quan Hoang Nguyen, Arti M. Raghubar, Heidi G. E. Sutherland, Miles C. Benton, Larisa Margaret Haupt, Nicholas B. Blackburn, Joanne E. Curran et al. · 2021 · Scientific Reports
40. Comparison of mixed model based approaches for correcting for population substructure with application to extreme phenotype sampling
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41. Genomic Selection in Chinese Holsteins Using Regularized Regression Models for Feature Selection of Whole Genome Sequencing Data
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42. Genetic Structure and Diversity Study of Cassava (Manihot esculenta) Germplasm for African Cassava Mosaic Disease and Fresh Storage Root Yield
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43. Accurate genomic selection using low-density SNP panels preselected by maximum likelihood estimation
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44. Genetic basis of maize stalk strength decoded via linkage and association mapping
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45. On the impact of relatedness on SNP association analysis
    Arnd Gross, Anke Tönjes, Markus R. Scholz · 2017 · BMC Genetics
46. A fast-linear mixed model for genome-wide haplotype association analysis: application to agronomic traits in maize
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47. Scalable and Robust Regression Methods for Phenome-Wide Association Analysis on Large-Scale Biobank Data
    Wenjian Bi, Seunggeun Lee · 2021 · Frontiers in Genetics
48. Gene-based whole genome sequencing meta-analysis of 250 circulating proteins in three isolated European populations
    Gilly, Arthur, Klaric, Lucija, Park, Young-Chan, Png, Grace, Barysenka, Andrei, Marsh, Joseph A., Tsafantakis, Emmanouil, Karaleftheri, Maria, Dedoussis, George, Wilson, James F. et al. · 2022 · Molecular Metabolism
49. Longitudinal Associations between Alcohol Intake and Arterial Stiffness, Pressure Wave Reflection, and Inflammation
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50. Behavioral phenotypes revealed during reversal learning are linked with novel genetic loci in diversity outbred mice
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51. Genetic association models are robust to common population kinship estimation biases
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52. Further advances on Bayesian Ying-Yang harmony learning
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53. The Relation Between Inflation in Type-I and Type-II Error Rate and Population Divergence in Genome-Wide Association Analysis of Multi-Ethnic Populations
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54. Replication and discovery of musculoskeletal QTLs in LG/J and SM/J advanced intercross lines
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55. Mapping QTL for production traits in segregating Piétrain pig populations using genome‐wide association study results of F2 crosses
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56. Fast and powerful genome wide association of dense genetic data with high dimensional imaging phenotypes
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57. New Entries in the Lottery of Facial GWAS Discovery
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58. Inference for High-Dimensional Linear Mixed-Effects Models: A Quasi-Likelihood Approach
    Sai Li, Tommaso Cai, Hongzhe Li · 2019 · arXiv (Cornell University)
59. Multi-scale Inference of Genetic Trait Architecture using Biologically Annotated Neural Networks
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60. Discovery of genomic loci for liver health and steatosis reveals overlap with glutathione redox genetics
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61. Unraveling metabolic stress response in dairy cows: Genetic control of plasma biomarkers throughout lactation and the transition period
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62. GWAS and multi-omics integrative analysis reveal novel loci and their molecular mechanisms for circulating fatty acids
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63. Efficient Mendelian randomization analysis with self-adaptive determination of sample structure and multiple pleiotropic effects
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64. Genome-wide association study and genomic selection for growth-related traits in Eastern oyster (Crassostrea virginica)
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65. OmiGA for ultra-efficient molecular quantitative trait loci mapping
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66. Identification of Genomic Loci Controlling Grain Macro and Micronutrient Variation in a Wild Barley (Hordeum vulgare spp. spontaneum) Diversity Panel
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67. Maternal and fetal origins of offspring blood pressure: statistical analysis using genetic correlation and genetic risk score-based Mendelian randomization
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68. Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs
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69. The quantitative genetics of gene expression in Mimulus guttatus
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70. Multi-trait modeling and machine learning discover new markers associated with stem traits in alfalfa
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71. Proteomic Data Integration Highlights Central Actors Involved in Einkorn (Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition
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72. Integrative genomic analysis in African American children with asthma finds three novel loci associated with lung function
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73. Genetic Architecture of Depression: Where Do We Stand Now?
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74. Genome-wide association study reveals novel loci associated with feeding behavior in Pekin ducks
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75. Bos taurus haplotypes segregating in Nellore (Bos indicus) cattle
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76. Ratios of Acetaminophen Metabolites Identify New Loci of Pharmacogenetic Relevance in a Genome-Wide Association Study
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77. Metabolic drivers of dysglycemia in pregnancy: ethnic-specific GWAS of 146 metabolites and 1-sample Mendelian randomization analyses in a UK multi-ethnic birth cohort
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78. Defining a Contemporary Ischemic Heart Disease Genetic Risk Profile Using Historical Data
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79. Recent developments in statistical methods for GWAS and high-throughput sequencing association studies of complex traits
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80. RETRACTED: Genetic Architecture Modulates Diet-Induced Hepatic mRNA and miRNA Expression Profiles in Diversity Outbred Mice
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81. Little Evidence of Modified Genetic Effect of rs16969968 on Heavy Smoking Based on Age of Onset of Smoking
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82. Genome-wide hierarchical mixed model association analysis
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83. The genetics of resistance to infectious pancreatic necrosis virus in rainbow trout unveiled through survival and virus load data
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84. Genetic and metabolic characterization of individual differences in liver fat accumulation in Atlantic salmon
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85. Mendelian randomisation to uncover causal associations between conformation, metabolism, and production as potential exposure to reproduction in German Holstein dairy cattle
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86. Genetic control of prickles in tetraploid blackberry
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87. Genome-wide association study identifies novel genes for plant architecture and yield traits in cassava (Manihot esculenta Crantz)
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88. Fine-mapping methods for complex traits: essential adaptations for samples of related individuals
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89. Genome-wide meta-analysis of 92 cardiometabolic protein serum levels
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90. Dissecting heritability, environmental risk, and air pollution causal effects using > 50 million individuals in MarketScan
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91. Transiently elevated expression of different forms of brain-derived neurotrophic factor in the neonatal medial prefrontal cortex affected anxiety and depressive-like behaviors in adolescence
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92. Genetic risk assessment of the joint effect of several genes: Critical appraisal
    Alexander V. Rubanovich, Хромов-Борисов Никита Николаевич · 2016 · Russian Journal of Genetics
93. MicroRNA-eQTLs in the developing human neocortex link miR-4707-3p expression to brain size
    Lafferty, Michael J, Aygün, Nil, Patel, Niyanta K, Krupa, Oleh, Liang, Dan, Wolter, Justin M, Geschwind, Daniel H, de la Torre-Ubieta, Luis, Stein, Jason L · 2023 · eLife
94. Polygenic influences on the behavioral effects of alcohol withdrawal in a mixed-ancestry population from the collaborative study on the genetics of alcoholism (COGA)
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95. GWAS meta-analysis of resistance against Piscirickettsia salmonis in Atlantic salmon
    Rodrigo Marín-Nahuelpi, Baltasar F. García, Agustin Piña-Elgueda, Jousepth Gallardo-Hidalgo, Paulina López, Daniela Cichero, Thomas Moen, Jørgen Ødegård, José Manuel Yañez · 2023 · Aquaculture
96. Modeling within and between Sub-Genomes Epistasis of Synthetic Hexaploid Wheat for Genome-Enabled Prediction of Diseases
    Jaime Cuevas, David O. González-Diéguez, Susanne Dreisigacker, Johannes W. R. Martini, Leonardo Crespo‐Herrera, Nérida Lozano-Ramírez, Pawan Kumar Singh, Xinyao He, Julio Huerta‐Espino, José Luis Crossa · 2024 · Genes
97. Chromosome-scale Reference Genome and RAD-based Genetic Map of Yellow Starthistle ( Centaurea solstitialis ) Reveal Putative Structural Variation and QTL Associated With Invader Traits
    Bryan Reatini, Jessie A. Pelosi, F. Alice Cang, Qiuyu Jiang, Michael T. W. McKibben, Michael S. Barker, Loren H. Rieseberg, Katrina M. Dlugosch · 2024 · Genome Biology and Evolution
98. Marker-Based Estimation of Genetic Parameters in Genomics
    Zhiqiu Hu, Rong‐Cai Yang · 2014 · PLoS ONE
99. Using Stochastic Approximation Techniques to Efficiently Construct Confidence Intervals for Heritability
    Regev Schweiger, Eyal Fisher, Elior Rahmani, Liat Shenhav, Saharon Rosset, Eran Halperin · 2017 · Lecture notes in computer science
100. TCAP FAC‐WIN6 Elite Barley GWAS Panel QTL. II. Malting Quality QTL in Elite North American Facultative and Winter Six‐Rowed Barley Identified via GWAS
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