Rigor and Reproducibility in Genetics and Genomics: Peer-reviewed, Published, Cited provides a full methodological and statistical overview for researchers, clinicians, students and post-doctoral fellows conducting genetic and genomic research. Here, active geneticists, clinicians and bioinformaticists offer practical solutions for a variety of challenges associated with several modern approaches in genetics and genomics, including genotyping, gene expression analysis, epigenetic analysis, GWAS, EWAS, genomic sequencing and gene editing. Emphasis is placed on rigor and reproducibility throughout, with each section containing laboratory case-studies and classroom activities covering step-by-step protocols, best practices and common pitfalls.
Specific genetic and genomic technologies discussed include microarray analysis, DNA-seq, RNA-seq, Chip-Seq, methyl-seq, CRISPR gene editing, and CRISPR-based genetic analysis. Training exercises, supporting data, and in-depth discussions of rigor, reproducibility, and ethics in research together deliver a solid foundation in research standards for the next generation of genetic and genomic scientists.
- Provides practical approaches and step-by-step protocols to strengthen genetic and genomic research conducted in the lab or classroom
- Presents illustrative case studies and training exercises and discusses common pitfalls and solutions for genotyping, gene expression analysis, epigenetic analysis, GWAS, EWAS, genomic sequencing, and gene editing, among other genetic and genomic approaches
- Examines best practices for microarray analysis, DNA-seq, RNA-seq, gene expression validation, Chip-Seq, methyl-seq, CRISPR gene editing, and CRISPR-based genetic analysis
Section 1: Introduction
Chapter 1: Review of reproducibility in genetic studies (John Ioannidis, PhD)
Chapter 2: Review of common statistical practices and assumptions (Daniel Benjamin, PhD)
Chapter 3: Rigor in the classroom and in the mentor/mentee relationship (Douglas F. Dluzen, PhD) Section 2: Genotyping
Chapter 4: Review of GWAS studies (Naomi Wray, PhD)
Chapter 5: Best practices in GWAS and pitfalls to avoid (Daniel Benjamin, PhD)
Chapter 6: GWAS learning and training activities (Bethany Bowling, PhD, Northern Kentucky University)
Chapter 7: DNA sequencing for genotyping and best practices for comparative genomics (Heidi Rehm, PhD)
Chapter 8: Statistical approaches for rigorous genome sequence analyses and genotype imputations (Nianjun Liu, PhD, Indiana University)
Chapter 9: DNA sequencing activities; classroom case studies (Rivka Glaser, PhD, Stevenson University) Section 3: Gene Expression
Chapter 10: Review of gene expression using microarray and RNA-seq (Alexandra Soboleva)
Chapter 11: Best statistical approaches for analysis of gene expression data (Purvesh Katri, PhD)
Chapter 12: Validating approaches to gene expression studies (Yaov Benjamin, PhD)
Chapter 13: Misconceptions in the classroom and case studies (Dina Newman, PhD) Section 4: Epigenetic Analyses
Chapter 14: Review of DNA methylation and other omits data resources (Thomas Jenuwein)
Chapter 15: Statistical approaches to improve rigor in Chip-Seq, methyl-seq, and epi datasets (Olga Troyanskaya, PhD)
Chapter 16: Best methods for combining DNA, RNA, and methylation data (Jennie Williams, PhD)
Chapter 17: Teaching epigenetics in the classroom (Louisa Stark, PhD) Section 5: Gene Editing Technologies
Chapter 18: Review of current gene editing technologies, including CRISPR (Lei Stanley Qi, PhD)
Chapter 19: Best strategies to design and implement CRISPR-based genetic analysis (Kathy Niakan, Phd)
Chapter 20: CRISPR classroom activities and/or case studies (Sylvain Moineau, PhD) Section 6: Conclusion Appendix: Links to supplementary resources
George P. Patrinos is a Professor of Pharmacogenomics and Pharmaceutical Biotechnology in the University of Patras (Greece), Department of Pharmacy, and Head of Division of Pharmacology and Biosciences of the same department and holds adjunct Full Professorships at Erasmus MC, Faculty of Medicine, and Health Sciences, Rotterdam (the Netherlands), and the United Arab Emirates University, College of Medicine, Department of Genetics and Genomics, Al-Ain (UAE). Also, from 2018 until the end of 2024, he was Chair of the Global Genomic Medicine Collaborative (G2MC). He served 12.5 years as a full member and Greeces National representative in the CHMP Pharmacogenomics Working Party of the European Medicines Agency (EMA). George has more than 340 publications in peer-reviewed scientific journals, some of them in leading scientific journals, such as The Lancet, Nature Genetics, Nature Reviews Genetic, Nucleic Acids Research, Genes & Development. He has also coauthored and coedited 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, he serves as the 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 advisory and evaluation committees. Apart from that, George is the main coorganizer 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.
