Small Multiply Aggregated Sequence Homologies (SMASH)
Overview
The NYGC’s Small Multiply Aggregated Sequence Homologies (SMASH) assay is available as proband only, duo, or trio. The SMASH assay is a low-coverage whole genome sequencing based method for detection of copy number variants (CNVs) with higher resolution than is currently available with most microarray methodologies, including CNVs as small as 10kb. SMASH data is analyzed in the context of the phenotype indication for testing and any available inheritance information from affected or unaffected relatives of the proband.
The rapid pace with which knowledge of current and evolving gene-disease associations is developing necessitates methodologies that can keep pace. SMASH utilizes genome sequencing at low pass coverage to significantly increase the resolution of copy number variant calling up to 10kb. Currently, copy number variant analysis with CMA is the first-tier test for individuals with a variety of undiagnosed diseases with suspected genetic etiologies, including individuals with autism or neurodevelopmental anomalies. However, the SMASH assay enables this analysis at significantly better resolution, enabling the identification of small copy number variants below the threshold of detection for current CMA methodologies.
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Deliverables
The NYGC’s Clinical Laboratory returns SMASH results within 6-8 weeks. Results are sent to the physician and/or principal investigator. A report is released indicating CNVs that were identified which may explain the patient’s phenotype. Additional methods of data delivery for larger projects are available and may be discussed with the clinical lab.
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Ordering Instructions
A physician can order the test using the NYGC’s test requisition form and must obtain informed consent from each family member (in pediatric cases, the child’s parents) being tested. This test requires at least 2ml of blood drawn in an EDTA tube, saliva specimen collected in an Oragene Dx collection kit, or DNA extracted in a CLIA-certified laboratory from the proband and each family member being tested (all samples submitted together whenever possible). Samples should be shipped to the NYGC overnight via FedEx. A courier service may also be feasible.
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