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Full Description
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.
Contents
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
