Genomic Structural Variants: Methods and Protocols

ISBN-13: 9781617795060 / Twarda / 2012 / 400 str.

Feuk, Lars

Opis

The completion of a consensus draft sequence for the human genome was the starting point for more thorough investigations of individual genome variation. The development of array-based strategies made it possible to look at our genome in new ways and for new types of variation to be discovered and characterized. Characterization of copy number variation and other forms of structural genetic variation has highlighted the complexity of human genetic variation and also provided significant insight into the evolution and dynamic nature of our genome. Genomic Structural Variants: Methods and Protocols provides an in-depth description of the developments in our understanding of structural genetic variation and its implications for human disease, from the introduction of microarrays up to current state-of-the-art sequencing strategies. It covers the major technologies used for research and diagnostics as well as web-based resources for variation data, and it then goes into depth regarding specific regions of the genome that differ in variation content. Specific patient groups where copy number variation has been shown to be of great importance are highlighted, and implications for both pre-natal and standard diagnostics are described. Written in the highly successful Methods in Molecular Biology series format, chapters contain 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.Authoritative and accessible, Genomic Structural Variants: Methods and Protocols provides complete comprehensive coverage of this burgeoning field.

Spis treści

1. What Have Studies of Genomic Disorders Taught us about our Genome

                Alexandra D. Simmons N., Claudia M.B. Carvalho, and James R. Lupski

 

2. Microdeletion and Microduplication Syndromes

                Lisenka E.L.M Vissers and Pawel Stankiewicz

 

3. Structural Genomic Variation in Mental Retardation

                Rolph Pfundt and Joris A. Veltman

 

4. Copy Number Variation and Psychiatric Disease Risk

                Rebecca J. Levy, Bin Xu, Joseph A. Gogos, and Maria Karayiorgou

 

5. Detection and Characterization of Copy Number Variation (CNV) in Autism Spectrum Disorder (ASD)

                Christian R. Marshall and Stephen W. Scherer

 

6. Structural Variation in Subtelomeres

                M. Katharine Rudd

 

7. Array Based Approaches in Prenatal Diagnosis

                Paul D. Brady, Koenraad Devriendt, Jan Deprest, and Joris R. Vermeesch

 

8. Structural Variation and its Effect on Expression

                Louise Harewood, Evelyne Chaignat, and Alexandre Reymond

 

9. The Challenges of Studying Complex and Dynamic Regions of the Human Genome     

                Edward J. Hollox

 

10. Population Genetic Nature of Copy Number Variation

                Per Sjödin and Mattias Jakobsson

 

11. Detection and Interpretation of Genomic Structural Variation in Mammals

                Ira M. Hall and Aaron R. Quinlan

 

12. Structural Genetic Variation in the Context of Somatic Mosaicism

                Jan P. Dumanski and Arkadiusz Piotrowski

 

13. Online Resources for Genomic Structural Variation

                Tam P. Sneddon and Deanna M. Church

 

14. Algorithm Implementation for CNV Discovery using Affymetrix and Ilumina SNP Array Data

                Laura Winchester and Jiannis Ragoussis

 

15. Targeted Screening and Validation of Copy Nuber Variations

                Shana Ceulemans, Karlijn van der Ven, and Jurgen Del-Favero

 

16. High-resolution Copy Number Profiling by Array CGH using DNA Isolated from Formalin-Fixed Paraffin-Embedded Tissues

                Hendrik F. B. van Essen and Bauke Ylstra

 

17. Characterizing and Interpreting Genetic Variation from Personal Genome Sequencing

                Anna Johansson and Lars Feuk

 

18. Massively Parallel Sequencing Approaches for Characterization of Structural Variation

                Daniel C. Koboldt, David E. Larson, Ken Chen, Li Ding, and Richard K. Wilson