1. Stephen W. Scherer and Lars Feuk are at The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, 14^th Floor, Toronto Medical Discovery Tower, MaRS Discovery District, 101 College Street, Room 14-701, Ontario M5G 1L7, Canada.
2. Stephen W. Scherer is in the Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5G 1L7, Canada. e-mail: steve@genet.sickkids.on.ca
3. Charles Lee is in the Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.
4. Ewan Birney is at the European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
5. Nigel P. Carter and Matthew E. Hurles are at the Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
6. David M. Altshuler is in the Program in Medical and Population Genetics, Broad Institute of Harvard University and the Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
7. Evan E. Eichler is in the Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, Washington 98195, USA.

Abstract

There has been an explosion of data describing newly recognized structural variants in the human genome. In the flurry of reporting, there has been no standard approach to collecting the data, assessing its quality or describing identified features. This risks becoming a rampant problem, in particular with respect to surveys of copy number variation and their application to disease studies. Here, we consider the challenges in characterizing and documenting genomic structural variants. From this, we derive recommendations for standards to be adopted, with the aim of ensuring the accurate presentation of this form of genetic variation to facilitate ongoing research.

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