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Rigor and Reproducibility in Genetics and Genomics
Peer-reviewed, Published, Cited
- 1st Edition - October 25, 2023
- Editors: George P. Patrinos, Douglas F. Dluzen, Monika Schmidt
- Language: English
- Paperback ISBN:9 7 8 - 0 - 1 2 - 8 1 7 2 1 8 - 6
- eBook ISBN:9 7 8 - 0 - 1 2 - 8 1 7 2 1 9 - 3
Rigor and Reproducibility in Genetics and Genomics: Peer-reviewed, Published, Cited provides a full methodological and statistical overview for researchers, clinicians, students,… Read more
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Request a sales quoteRigor 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 laboratory or classroom
- Presents illustrative case studies and training exercises, discussing common pitfalls and solutions for genotyping, gene expression analysis, epigenetic analysis, GWAS, 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
- Written to provide trainees and educators with highly applicable tools and strategies to learn or refine a method toward identifying meaningful results with high confidence in their reproducibility
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
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
- No. of pages: 502
- Language: English
- Edition: 1
- Published: October 25, 2023
- Imprint: Academic Press
- Paperback ISBN: 9780128172186
- eBook ISBN: 9780128172193
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George P. Patrinos
Dr. Patrinos is internationally renowned for his involvement in the field of pharmacogenomics research. His research includes discovery work and addresses the issue of clinical implementation of pharmacogenomics in a holistic manner, including wet- and dry-lab, as well as public health genomics approaches. Dr. Patrinos has also a keen interest in the clinical implementation of genomic medicine in resource-limited environments.
Affiliations and expertise
Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece; Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates; Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, United Arab EmiratesDD
Douglas F. Dluzen
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.
Affiliations and expertise
Assistant Professor of Biology, Morgan State University, Baltimore, MD, USAMS
Monika Schmidt
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.
Affiliations and expertise
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, CanadaRead Rigor and Reproducibility in Genetics and Genomics on ScienceDirect