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Hensel C, Vanzo R, Martin M, Dixon S, Lambert C, Levy B, Nelson L, Peiffer A, Ho KS, Rushton P, Serrano M, South S, Ward K, Wassman E. Analytical and Clinical Validity Study of FirstStepDx PLUS: A Chromosomal Microarray Optimized for Patients with Neurodevelopmental Conditions. PLoS Curr 2017; 9. [PMID: 28357155 PMCID: PMC5346028 DOI: 10.1371/currents.eogt.7d92ce775800ef3fbc72e3840fb1bc22] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Introduction: Chromosomal microarray analysis (CMA) is recognized as the first-tier test in the genetic evaluation of children with developmental delays, intellectual disabilities, congenital anomalies and autism spectrum disorders of unknown etiology. Array Design: To optimize detection of clinically relevant copy number variants associated with these conditions, we designed a whole-genome microarray, FirstStepDx PLUS (FSDX). A set of 88,435 custom probes was added to the Affymetrix CytoScanHD platform targeting genomic regions strongly associated with these conditions. This combination of 2,784,985 total probes results in the highest probe coverage and clinical yield for these disorders. Results and Discussion: Clinical testing of this patient population is validated on DNA from either non-invasive buccal swabs or traditional blood samples. In this report we provide data demonstrating the analytic and clinical validity of FSDX and provide an overview of results from the first 7,570 consecutive patients tested clinically. We further demonstrate that buccal sampling is an effective method of obtaining DNA samples, which may provide improved results compared to traditional blood sampling for patients with neurodevelopmental disorders who exhibit somatic mosaicism.
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Affiliation(s)
| | - Rena Vanzo
- Clinical Genetic Services, Lineagen, Inc., Salt Lake City, Utah, USA
| | | | - Sean Dixon
- Operations, Lineagen, Inc., Salt Lake City, Utah, USA
| | - Christophe Lambert
- Department of Internal Medicine, Center for Global Health, Division of Translational Informatics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Brynn Levy
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - Lesa Nelson
- Affiliated Genetics Laboratory, Inc., Salt Lake City, Utah, USA
| | - Andy Peiffer
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA; Lineagen, Inc., Salt Lake City, Utah, USA
| | - Karen S Ho
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA; Lineagen, Inc., Salt Lake City, Utah, USA
| | | | | | - Sarah South
- ARUP Laboratories, Salt Lake City, Utah, USA; 23andMe, Inc., Mountain View, California, USA
| | - Kenneth Ward
- Affiliated Genetics Laboratory, Inc., Salt Lake City, Utah, USA
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