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Genetic Variation

Methods and Protocols

Series: Methods in Molecular Biology

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by Michael R. Barnes and Gerome Breen

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Main description:

“Your genome is an email attachment” What a difference a few years can make? In 2001, to a global fanfare, the completion of the frst draft sequence of the human genome was announced. This had been a Herculean effort, involving thousands of researchers and millions of dollars. Today, a project to re-sequence 1,000 genomes is well underway, and within a year or two, your own “personal genome” is likely to be available for a few thousand pounds, a price that will undoubtedly decrease further. We are fast approaching the day when your genome will be available as an email attachment (about 4 Mb). The key to this feat is the fact that any two human genomes are more than 99% identical, so rather than representing every base, there is really only a requirement to store the 1% of variable sequence judged against a common reference genome. This brings us directly to the focus of this edition of Methods in Molecular Biology, Genetic Variation. The human genome was once the focus of biology, but now individual genome var- tion is taking the center stage. This new focus on individual variation ultimately democ- tizes biology, offering individuals insight into their own phenotype. But these advances also raise huge concerns of data misuse, misinterpretation, and misunderstanding. The immediacy of individual genomes also serves to highlight our relative ignorance of human genetic variation, underlining the need for more studies of the nature and impact of genetic variation on human phenotypes.

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Division of Psychological Medicine and Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, UK

Back cover:

With the continuing advances in sequencing technologies and the availability of thousands of distinct human genomes, we are fast approaching the day when "personal genomes" become a standard study measure and a routine component of personal health records. In Genetic Variation: Methods and Protocols, expert researchers address the rising importance of genome variation, both at the level of the individual and in population-based studies of disease, with a collection of detailed protocols reflecting the nature and impact of genetic variation on human phenotypes. The contributions cover a majority of the most important forms of genetic variation studied today, including single nucleotide polymorphisms (SNPs), insertions/deletion (indels), copy number variation (CNVs), variable number tandem repeats (VNTRs), mitochondrial variation, mobile elements, and epigenetic variation. As a volume in the highly successful Methods in Molecular Biology™ series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.

Convenient and cutting-edge, Genetic Variation: Methods and Protocols aims to bring bench scientists, clinicians, and bioinformaticians together in order to aid progress toward a greater understanding of the full impact of variation on human health and disease.

Contents:

1. Genetic Variation Analysis for Biomedical Researchers: A Primer
Michael R. Barnes

2. Exploring the Landscape of the Genome
Michael R. Barnes

3. Asking Complex Questions of the Genome without Programming
Peter M. Woollard

4. Laboratory Methods for the Detection of Chromosomal Abnormalities
Jacqueline Schoumans and Claudia Ruivenkamp

5. Cancer Genome Analysis Informatics
Ian P. Barrett

6. Copy Number Variations in the Human Genome and Strategies for Analysis
Emily A. Vucic, Kelsie L. Thu, Ariane C. Williams, Wan L. Lam, and Bradley P. Coe

7. A Short Primer on the Functional Analysis of Copy Number Variation for Biomedical Scientists
Michael R. Barnes and Gerome Breen

8. Computational Methods for the Analysis of Primate Mobile Elements
Richard Cordaux, Shurjo K. Sen, Miriam K. Konkel, and Mark A. Batzer

9. Laboratory Methods for the Analysis of Primate Mobile Elements
David A. Ray, Kyudong Han, Jerilyn A. Walker, and Mark A. Batzer

10. Practical Informatics Approaches to Microsatellite and Variable Number Tandem Repeat Analysis
Gerome Breen

11. Assessing the Impact of Genetic Variation on Transcriptional Regulation in vitro
Fahad R. Ali, Kate Haddley, and John P. Quinn

12. Whole Genome Sequencing
Pauline C. Ng and Ewen F. Kirkness

13. Detection of Mitochondrial DNA Variation in Human Cells
Kim J. Krishnan, John K. Blackwood, Amy K. Reeve, Douglass M. Turnbull, and Robert W. Taylor

14. An Introduction to Mitochondrial Informatics
Hsueh-Wei Chang, Li-Yeh Chuang, Yu-Huei Cheng, De-Leung Gu, Hurng-Wern Huang, and Cheng-Hong Yang

15. Web-Based Analysis of (Epi-) Genome Data Using EpiGRAPH and Galaxy
Christoph Bock, Greg Von Kuster, Konstantin Halachev, JamesTaylor, Anton Nek-rutenko, and Thomas Lengauer

16. Short Tandem Repeats and Genetic Variation
Bo Eskerod Madsen, Palle Villesen, and Carsten Wiuf

17. Bioinformatic Tools for Identifying Disease Gene and SNP Candidates
Sean D. Mooney, Vidhya G. Krishnan, and Uday S. Evani

18. Analysis of the Impact of Genetic Variation on Human Gene Expression
Elin Grundberg, Tony Kwan, and Tomi M. Pastinen

19. Quality Control for Genome-Wide Association Studies
Michael E. Weale

20. Gaining a Pathway Insight into Genetic Association Data
Inti Pedroso

PRODUCT DETAILS

ISBN-13: 9781603273664
Publisher: Springer (Humana Press)
Publication date: September, 2010
Pages: 366
Weight: 2010g
Availability: Not available (reason unspecified)
Subcategories: Biochemistry, Genetics

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From the reviews:

“Genetic variation is addressed in this volume of Methods in Molecular Biology that provides an overview of all forms of human genomic variation … . present tools for interpretation and quality control of the genome-wide association studies (GWAS). This book is recommended for researchers and students interested in concepts, applications and tools to study human genetics and bioinformatics.” (Rosario Dominguez Crespo Hirata, Brazilian Journal of Pharmaceutical Sciences, Vol. 47 (2), Summer, 2011)