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Review
. 2012 May;81(5):403-12.
doi: 10.1111/j.1399-0004.2011.01818.x. Epub 2011 Dec 13.

Towards an evidence-based process for the clinical interpretation of copy number variation

E R Riggs  1 , D M Church, K Hanson, V L Horner, E B Kaminsky, R M Kuhn, K E Wain, E S Williams, S Aradhya, H M Kearney, D H Ledbetter, S T South, E C Thorland, C L Martin
Affiliations
Review

Towards an evidence-based process for the clinical interpretation of copy number variation

E R Riggs et al. Clin Genet. 2012 May.

Abstract

The evidence-based review (EBR) process has been widely used to develop standards for medical decision-making and to explore complex clinical questions. This approach can be applied to genetic tests, such as chromosomal microarrays, in order to assist in the clinical interpretation of certain copy number variants (CNVs), particularly those that are rare, and guide array design for optimal clinical utility. To address these issues, the International Standards for Cytogenomic Arrays Consortium has established an EBR Work Group charged with building a framework to systematically assess the potential clinical relevance of CNVs throughout the genome. This group has developed a rating system enumerating the evidence supporting or refuting dosage sensitivity for individual genes and regions that considers the following criteria: number of causative mutations reported; patterns of inheritance; consistency of phenotype; evidence from large-scale case-control studies; mutational mechanisms; data from public genome variation databases; and expert consensus opinion. The system is designed to be dynamic in nature, with regions being reevaluated periodically to incorporate emerging evidence. The evidence collected will be displayed within a publically available database, and can be used in part to inform clinical laboratory CNV interpretations as well as to guide array design.

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Conflict of interest statement

S. A. is employed by GeneDx (a subsidiary of Bioreference Laboratories, Inc.). S. S. is the Medical Director at ARUP Laboratories, a not-for-profit organization owned by the University of Utah offering among other tests genomic microarray. She also serves as a consultant to Lineagen, Inc., a for-profit company, which offers genomic microarray testing. Dr S. S. has received honoraria for speaking engagements on behalf of Affymetrix Inc. D. L. is a consultant for Roche Nimblegen. The other authors declare no conflict of interest.

Figures

Fig. 1
Fig. 1
Framework for an evidence-based process by which to evaluate dosage sensitivity.
Fig. 2
Fig. 2
Levels of evidence suggesting that dosage-sensitivity results in clinical phenotype.
See this image and copyright information in PMC

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