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New book presents successful strategies for probing genetic variation
Date:9/25/2007

COLD SPRING HARBOR, N.Y. -- The first manual specifically geared towards genetic variation studies has just been released by Cold Spring Harbor Laboratory Press (www.cshlpress.com). Genetic Variation: A Laboratory Manual unites key concepts from bioinformatics, technology, statistics, and biology, to provide a comprehensive yet detailed guide for performing genetic variation studies that are feasible for a wide range of laboratories. It was edited by leading scientists Michael P. Weiner, Stacey B. Gabriel, and J. Claiborne Stephens, and includes 35 chapters by experts in the field.

With the genome sequences of many organisms now catalogued, geneticists are turning their attention to natural variation among individuals. Physical characteristics such as eye or hair color, as well as susceptibility to diseases such as diabetes, autism, and heart disease, are often linked to specific DNA variants. However, designing and executing studies to identify such variants is a complicated endeavor, as it involves testing large numbers of individuals, employing powerful modern technologies, and generating enormous amounts of data. Genetic Variation thoroughly addresses all of these issues.

[T]he editors have assembled a remarkable team and generated a solid foundation for novices and experts alike, writes Dr. Thomas Hudson in the foreword to the book. [T]he founding principles that are outlined by world-class specialists will have lasting value, and help connect new facts and datasets into rational explanations.

The manual describes the power of high-throughput approaches for whole-genome genotyping as well as strategies and solutions for laboratory-scale genotyping. From study design and population choice to experimental analysis and data interpretation, Genetic Variation will function as a valuable handbook for any scientist using methods to probe genetic differences among individuals. Many of the methods included in the manual are feasible for average-sized labs. These will be particularly useful for graduate students and professional scientists in clinical and research settings.

Detailed step-by-step protocols cover all levels of analysis, including sample handling and extraction, whole-genome amplification, high-density genotyping, and comparative genomic hybridization. The protocols can be applied to the complete spectrum of genetic variationfrom SNPs, indels, and microsatellites to more complex structural alterations, including chromosomal rearrangements and copy number variation. Recent advances in genome technologies are discussed, as are available tools for analyzing the data and resources such as HapMap and dbSNP.

The sheer capacity for generating genomic variation data has an addictive effect: The more you see, the more you want, write the editors in the preface to the book. However, the sheer volume of data cannot overcome poorly planned studies.

To overcome the obstacles of designing studies that are often enormous in size and scope, the manual also includes substantial background information and advice on topics such as marker selection, sample size, population choice, and statistical power. Ethical issues are also considered: procedures and requirements for obtaining informed consent are included, and appropriate measures for maintaining privacy protection when handling the associated samples and data are discussed.

The methods can be applied to virtually any animal or plant system, but eight model organisms are given special consideration, including three plant species (Arabidopsis, corn, and rice) and five mammalian species (mouse, rat, cat, dog, and chimpanzee). For each species, available genetic maps, resources, and tools are described; strains and sources of genetic material are outlined; and large-scale projects and ongoing studies are reviewed.

The final chapters of Genetic Variation discuss recent advances in human genetic ancestry, forensics, population genetics, and human evolution.


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Contact: Ingrid Benirschke
benirsch@cshl.edu
619-275-6021
Cold Spring Harbor Laboratory
Source:Eurekalert

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