Rigor and Reproducibility in Genetics and Genomics

George P. Patrinos is Professor of Pharmacogenomics and Pharmaceutical Biotechnology in the University of Patras (Greece), Department of Pharmacy, Head of Division of Pharmacology and Biosciences of the same Department and holds adjunct Full Professorships at Erasmus MC, Faculty of Medicine, Rotterdam (the Netherlands) and the United Arab Emirates University, College of Medicine, Department of Genetics and Genomics, Al-Ain (UAE). Also, since March 2018, he is Chair of the Global Genomic Medicine Collaborative (G2MC) and since May 2023 Chairman of the Scientific Advisory Board of the ASPIRE Abu Dhabi Precision Medicine Research Institute. He has ample regulatory experience, as he served for 12.5 years as Full Member and Greece’s National representative in the CHMP Pharmacogenomics Working Party of the European Medicines Agency (EMA) and he is still an active member of the European Medicines Agency participating in expert panels to provide scientific advice where needed. George is currently Director of the Laboratory of Pharmacogenomics and Individualized Therapy, the first officially established academic pharmacogenomics laboratory in Greece. His group has keen interest in research covering disciplines from wet and dry lab and public health genomics projects, all focusing on pharmacogenomics and personalized medicine. In particular, his research interests involve discovery work and clinical implementation of pharmacogenomics, focusing in particular in psychiatry but also cardiology and oncology, genomics of rare disorders and transcriptional regulation of human fetal globin genes. Moreover, George’s group is internationally recognized for its involvement in developing National/Ethnic Genetic databases to document the genetic heterogeneity in different populations worldwide and of genome informatics tools to translate genomic information into a clinically meaningful format. Also, George’s group has a keen interest in public health genomics to critically assess the impact of genomics to society and public health. George has more than 330 publications in peer-reviewed scientific journals, some of them in leading scientific journals, such as The Lancet and Lancet EBioMedicine. Also, he has co-authored and co-edited more than 15 textbooks, among which the renowned textbook “Molecular Diagnostics”, published by Academic Press, now in its 3rd edition, while he is the editor of “Translational and Applied Genomics” book series, published by Elsevier. Furthermore, since September 2020, he serves as Editor-In-Chief of the prestigious Pharmacogenomics Journal (TPJ), published by Nature Publishing Group, Associate Editor and member of the editorial board of several scientific journals and has been a member of several international boards and advisory and evaluation committees. Apart from that, George is the main co-organizer of the Golden Helix Conferences, an international meeting series on Pharmacogenomics and Genomic Medicine with more than 50 conferences organized in more than 25 countries worldwide. Douglas F. Dluzen is a geneticist and has previously studied the genetic contributors to aging, drug metabolism, hypertension, and inflammation. Dluzen is particularly interested in how social determinants of health influence gene expression in the immune system. Currently, he is the director of the Professional Development and Career Office at the Johns Hopkins University School of Medicine and has worked previously at the National Institutes of Health and Morgan State University. He enjoys writing science fiction and hiking with his family. Monika Schmidt completed her doctoral work in the realm of tandem repeat-associated neuromuscular/neurodegenerative diseases, with a focus upon fragile X syndrome, amyotrophic lateral sclerosis, and DNA metabolism. Monika has a particular interest in wet lab validation of in silico findings, with a penchant for Southern blotting of structurally complex repetitive DNA sequences. Currently, she is a freelance scientific editor, private healthcare liaison, and event organizer. Monika enjoys traveling on a shoestring, working with her hands on home or cottage improvements, and spending time with her spouse and children.

SECTION 1 Introduction 1. Rigor and reproducibility in genetic research and the effects on scientific reporting and public discourse 2. Unveiling the hidden curriculum: Developing rigor and reproducibility values through teaching and mentorship SECTION 2 Genotyping 3. Genome-wide association studies (GWAS): hat are they, when to use them? 4. GWAS in the learning environment 5. Polygenic risk scores and comparative genomics: Best practices and statistical considerations 6. DNA sequencing and genotyping in the classroom 7. Classroom to career: Implementation considerations for engaging students with meaningful DNA sequencing learning opportunities SECTION 3 Next-generation sequencing & gene expression 8. Review of gene expression using microarray and RNA-seq 9. Guidelines and important considerations for ‘omics-level studies 10. Best practices for statistical analysis of omics data 11. Validation of gene expression by quantitative PCR SECTION 4 Epigenetic analyses 12. Best practices for epigenome-wide DNA modification data collection and analysis 13. Best practices for the ATAC-seq assay and its data analysis 14. Best practice for ChIP-seq and its data analysis 15. A practical guide for essential analyses of Hi-C data 16. Epigenetics in the classroom SECTION 5 Gene editing technologies 17. Genome editing technologies 18. Genetic modification of mice using CRISPR-Cas9: Best practices and practical concepts explained 19. CRISPR classroom activities and case studies