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.
1. Section 1: Introduction - p. xx 2. Chapter 1. Rigor and reproducibility in genetic research and the effects on scientific reporting and public discourse - p. 3 3. Chapter 2. Unveiling the hidden curriculum: Developing rigor and reproducibility values through teaching and mentorship - p. 27 4. Section 2: Genotyping - p. 47 5. Chapter 3. Genome-wide association studies (GWAS): What are they, when to use them? - p. 51 6. Chapter 4. GWAS in the learning environment - p. 85 7. Chapter 5. Polygenic risk scores and comparative genomics: Best practices and statistical considerations - p. 91 8. Chapter 6. Sequence analysis and genomics in the classroom - p. 115 9. Chapter 7. Classroom to career: Implementation considerations for engaging students with meaningful DNA sequencing learning opportunities - p. 137 10. Section 3: Next-generation sequencing & gene expression - p. 155 11. Chapter 8. Review of gene expression using microarray and RNA-seq - p. 159 12. Chapter 9. Guidelines and important considerations for ‘omics-level studies - p. 189 13. Chapter 10. Rigor and reproducibility of RNA sequencing analyses - p. 211 14. Chapter 11. Validation of gene expression by quantitative PCR - p. 247 15. Section 4: Epigenetic analyses - p. 257 16. Chapter 12. Best practices for epigenome-wide DNA modification data collection and analysis - p. 261 17. Chapter 13. Best practices for the ATAC-seq assay and its data analysis - p. 305 18. Chapter 14. Best practices for ChIP-seq and its data analysis - p. 319 19. Chapter 15. A practical guide for essential analyses of Hi-C data - p. 343 20. Chapter 16. Epigenetics in the classroom - p. 363 21. Section 5: Gene editing technologies - p. 393 22. Chapter 17. Genome editing technologies - p. 397 23. Chapter 18. Genetic modification of mice using CRISPR-Cas9: Best practices and practical concepts explained - p. 425 24. Chapter 19. CRISPR classroom activities and case studies - p. 453 25. Index - p. 473
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.
1. Section 1: Introduction - p. xx 2. Chapter 1. Rigor and reproducibility in genetic research and the effects on scientific reporting and public discourse - p. 3 3. Chapter 2. Unveiling the hidden curriculum: Developing rigor and reproducibility values through teaching and mentorship - p. 27 4. Section 2: Genotyping - p. 47 5. Chapter 3. Genome-wide association studies (GWAS): What are they, when to use them? - p. 51 6. Chapter 4. GWAS in the learning environment - p. 85 7. Chapter 5. Polygenic risk scores and comparative genomics: Best practices and statistical considerations - p. 91 8. Chapter 6. Sequence analysis and genomics in the classroom - p. 115 9. Chapter 7. Classroom to career: Implementation considerations for engaging students with meaningful DNA sequencing learning opportunities - p. 137 10. Section 3: Next-generation sequencing & gene expression - p. 155 11. Chapter 8. Review of gene expression using microarray and RNA-seq - p. 159 12. Chapter 9. Guidelines and important considerations for ‘omics-level studies - p. 189 13. Chapter 10. Rigor and reproducibility of RNA sequencing analyses - p. 211 14. Chapter 11. Validation of gene expression by quantitative PCR - p. 247 15. Section 4: Epigenetic analyses - p. 257 16. Chapter 12. Best practices for epigenome-wide DNA modification data collection and analysis - p. 261 17. Chapter 13. Best practices for the ATAC-seq assay and its data analysis - p. 305 18. Chapter 14. Best practices for ChIP-seq and its data analysis - p. 319 19. Chapter 15. A practical guide for essential analyses of Hi-C data - p. 343 20. Chapter 16. Epigenetics in the classroom - p. 363 21. Section 5: Gene editing technologies - p. 393 22. Chapter 17. Genome editing technologies - p. 397 23. Chapter 18. Genetic modification of mice using CRISPR-Cas9: Best practices and practical concepts explained - p. 425 24. Chapter 19. CRISPR classroom activities and case studies - p. 453 25. Index - p. 473
