Chapter 6: Structural Variation and Medical Genomics

Benjamin J. Raphael mail

Abstract

Differences between individual human genomes, or between human and cancer genomes, range in scale from single nucleotide variants (SNVs) through intermediate and large-scale duplications, deletions, and rearrangements of genomic segments. The latter class, called structural variants (SVs), have received considerable attention in the past several years as they are a previously under appreciated source of variation in human genomes. Much of this recent attention is the result of the availability of higher-resolution technologies for measuring these variants, including both microarray-based techniques, and more recently, high-throughput DNA sequencing. We describe the genomic technologies and computational techniques currently used to measure SVs, focusing on applications in human and cancer genomics.

Citation: Raphael BJ (2012) Chapter 6: Structural Variation and Medical Genomics. PLoS Comput Biol 8(12): e1002821. doi:10.1371/journal.pcbi.1002821
Editors: Fran Lewitter ( Whitehead Institute, United States of America ), and Maricel Kann ( University of Maryland, Baltimore County, United States of America )
Published: December 27, 2012
Copyright: © 2012 Benjamin J. Raphael. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work is supported by National Institutes of Health (R01 HG005690). BJR is supported by an National Science Foundation CAREER Award (CCF-1053753), a Career Award from the Scientific Interface from the Burroughs Wellcome Fund and an Alfred P. Sloan Research Fellowship. The funders had no role in the preparation of the manuscript.
Competing interests: The author has declared that no competing interests exist.
* E-mail: braphael@brown.edu