Genetic Variation

1. Front Matter

   Pages i-xi

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2. Genetic Variation Analysis for Biomedical Researchers: A Primer

   • Michael R. Barnes

   Pages 1-20

3. Exploring the Landscape of the Genome

   • Michael R. Barnes

   Pages 21-38

4. Asking Complex Questions of the Genome Without Programming

   • Peter M. Woollard

   Pages 39-52

5. Laboratory Methods for the Detection of Chromosomal Abnormalities

   • Jacqueline Schoumans, Claudia Ruivenkamp

   Pages 53-73

6. Cancer Genome Analysis Informatics

   • Ian P. Barrett

   Pages 75-102

7. Copy Number Variations in the Human Genome and Strategies for Analysis

   • Emily A. Vucic, Kelsie L. Thu, Ariane C. Williams, Wan L. Lam, Bradley P. Coe

   Pages 103-117

8. A Short Primer on the Functional Analysis of Copy Number Variation for Biomedical Scientists

   • Michael R. Barnes, Gerome Breen

   Pages 119-135

9. Computational Methods for the Analysis of Primate Mobile Elements

   • Richard Cordaux, Shurjo K. Sen, Miriam K. Konkel, Mark A. Batzer

   Pages 137-151

10. Laboratory Methods for the Analysis of Primate Mobile Elements

    • David A. Ray, Kyudong Han, Jerilyn A. Walker, Mark A. Batzer

    Pages 153-179

11. Practical Informatics Approaches to Microsatellite and Variable Number Tandem Repeat Analysis

    • Gerome Breen

    Pages 181-194

12. Assessing the Impact of Genetic Variation on Transcriptional Regulation In Vitro

    • Fahad R. Ali, Kate Haddley, John P. Quinn

    Pages 195-214

13. Whole Genome Sequencing

    • Pauline C. Ng, Ewen F. Kirkness

    Pages 215-226

14. Detection of Mitochondrial DNA Variation in Human Cells

    • Kim J. Krishnan, John K. Blackwood, Amy K. Reeve, Douglass M. Turnbull, Robert W. Taylor

    Pages 227-257

15. An Introduction to Mitochondrial Informatics

    • Hsueh-Wei Chang, Li-Yeh Chuang, Yu-Huei Cheng, De-Leung Gu, Hurng-Wern Huang, Cheng-Hong Yang

    Pages 259-274

16. Web-Based Analysis of (Epi-) Genome Data Using EpiGRAPH and Galaxy

    • Christoph Bock, Greg Von Kuster, Konstantin Halachev, James Taylor, Anton Nekrutenko, Thomas Lengauer

    Pages 275-296

17. Short Tandem Repeats and Genetic Variation

    • Bo Eskerod Madsen, Palle Villesen, Carsten Wiuf

    Pages 297-306

18. Bioinformatic Tools for Identifying Disease Gene and SNP Candidates

    • Sean D. Mooney, Vidhya G. Krishnan, Uday S. Evani

    Pages 307-319

19. Analysis of the Impact of Genetic Variation on Human Gene Expression

    • Elin Grundberg, Tony Kwan, Tomi M. Pastinen

    Pages 321-339

20. Quality Control for Genome-Wide Association Studies

    • Michael E. Weale

    Pages 341-372

“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.

• Bioinformatics
• Copy number variation (CNVs)
• DNA
• Genome sequencing
• Human phenotypes
• Personalized medicine
• Radiologieinformationssystem
• Single Nucleotide Polymorphism
• Single nucleotide polymorphisms (SNPs)
• Variable number tandem repeats (VNTRs)
• chromosome
• gene expression
• genes
• genome
• transcription

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)

• Medicines Research Centre, GlaxoSmithKline R&D Limited, Stevenage, Hertfordshire, United Kingdom

  Michael R. Barnes

• Institute of Psychiatry, Social, Genetic & Developmental, King's College, London, United Kingdom

  Gerome Breen

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