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Section 1: Introduction
1. Review of reproducibility in genetic studies (John Ioannidis, PhD)
2. Review of common statistical practices and assumptions (Daniel Benjamin, PhD)
3. Rigor in the classroom and in the mentor/mentee relationship (Douglas F. Dluzen, PhD)
Section 2: Genotyping
4. Review of GWAS studies (Naomi Wray, PhD)
5. Best practices in GWAS and pitfalls to avoid (Daniel Benjamin, PhD)
6. GWAS learning and training activities (Bethany Bowling, PhD, Northern Kentucky University)
7. DNA sequencing for genotyping and best practices for comparative genomics (Heidi Rehm, PhD)
8. Statistical approaches for rigorous genome sequence analyses and genotype imputations (Nianjun Liu, PhD, Indiana University)
9. DNA sequencing activities; classroom case studies (Rivka Glaser, PhD, Stevenson University)
Section 3: Gene Expression
10. Review of gene expression using microarray and RNA-seq (Alexandra Soboleva)
11. Best statistical approaches for analysis of gene expression data (Purvesh Katri, PhD)
12. Validating approaches to gene expression studies (Yaov Benjamin, PhD)
13. Misconceptions in the classroom and case studies (Dina Newman, PhD)
Section 4: Epigenetic Analyses
14. Review of DNA methylation and other omits data resources (Thomas Jenuwein)
15. Statistical approaches to improve rigor in Chip-Seq, methyl-seq, and epi datasets (Olga Troyanskaya, PhD)
16. Best methods for combining DNA, RNA, and methylation data (Jennie Williams, PhD)
17. Teaching epigenetics in the classroom (Louisa Stark, PhD)
Section 5: Gene Editing Technologies
18. Review of current gene editing technologies, including CRISPR (Lei Stanley Qi, PhD)
19. Best strategies to design and implement CRISPR-based genetic analysis (Kathy Niakan, Phd)
20. CRISPR classroom activities and/or case studies (Sylvain Moineau, PhD)
Section 6: Conclusion
Appendix: Links to supplementary resources
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
Active researchers, basic and translational scientists, clinicians, postgraduates, and students in the areas of genetics, human genomics, pathology, cellular biology, organismal biology, molecular biology, biochemistry, and bioinformatics
- No. of pages:
- © Academic Press 2021
- 1st July 2021
- Academic Press
- Paperback ISBN:
Douglas F. Dluzen is an Assistant Professor of Biology at Morgan State University, Baltimore, MD, United States.
Assistant Professor of Biology, Morgan State University, Baltimore, MD, USA
Monika Schmidt is a PhD Candidate in the Lab of Dr. C.E. Pearson at The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Genetics & Genome Biology in Toronto, Ontario, Canada.
PhD Candidate, Lab of Dr. C.E. Pearson, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Genetics and Genome Biology, Toronto, ONT, Canada
George Patrinos is Professor of Pharmacogenomics at the University of Patras School of Health Sciences (Department of Pharmacy) in Patras, Greece with Adjunct positions in Rotterdam, the Netherlands and Al-Ain, United Arab Emirates. His research interests span the fields of pharmacogenomics and personalised medicine, focused on psychiatric diseases and hemoglobinopathies, the implementation of genomics into healthcare, particularly for health systems in developing countries, the development of genomic databases and web-based translational tools for personalised medicine and the application of genomics in public health. George Patrinos has published more than 270 scientific papers in peer reviewed journals on topics related to genetics, genomic medicine, pharmacogenomics, molecular diagnostics, and social and economic evaluation for genomic medicine. He is also the editor of several textbooks published by Elsevier/Academic Press, including the renowned textbook "Molecular Diagnostics", published by Elsevier now in its third edition. He serves as Editor-In-Chief and Communicating and Associate Editor for several high impact scientific journals and he is co-organizer of the international meeting series “Golden Helix Conferences”.
Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece; United Arab Emirates University, College of Medicine and Health Sciences, Department of Pathology, Al-Ain, UAE, United Arab Emirates University, Zayed Center of Health Sciences, Al-Ain, UAE and Erasmus University Medical Center, School of Medicine and Health Sciences, Department of Pathology – Bioinformatics Unit, Rotterdam, The Netherlands
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