Jobanputra, Vaidehi, Andrews, Peter, Felice, Vanessa, Abhyankar, Avinash, Kozon, Lukasz, Robinson, Dino, London, Ferrah, Hakker, Inessa, Wrzeszczynski, Kazimierz, Ronemus, Michael (December 2020) Detection of Copy Number Variants by Short Multiply Aggregated Sequence Homologies. The Journal of Molecular Diagnostics, 22 (12). pp. 1476-1481. ISSN 1525-1578
Abstract
Chromosomal microarray testing is indicated for patients with diagnoses including unexplained developmental delay or intellectual disability, autism spectrum disorders, and multiple congenital anomalies. The short multiply aggregated sequence homologies (SMASH) genomic assay is a novel next-generation sequencing technology that performs copy number analysis at resolution similar to high-coverage whole genome sequencing but requires far less capacity. We benchmarked the performance of SMASH on a panel of genomic DNAs containing known copy number variants (CNVs). SMASH was able to detect pathogenic copy number variants of ≥10 kb in 77 of 77 samples. No pathogenic events were seen in 32 of 32 controls, indicating 100% sensitivity and specificity for detecting pathogenic CNVs >10 kb. Repeatability (interassay precision) and reproducibility (intra-assay precision) were assessed with 13 samples and showed perfect concordance. We also established that SMASH had a limit of detection of 20% for detection of large mosaic CNVs. Finally, we analyzed seven blinded specimens by SMASH analysis and successfully identified all pathogenic events. These results establish the efficacy of the SMASH genomic assay as a clinical test for the detection of pathogenic copy number variants at a resolution comparable to chromosomal microarray analysis.
| Item Type: | Paper |
|---|---|
| Subjects: | diseases & disorders Investigative techniques and equipment diseases & disorders > mental disorders diseases & disorders > mental disorders > personality disorders Investigative techniques and equipment > assays diseases & disorders > mental disorders > personality disorders > autism bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > copy number variants bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > mutations Investigative techniques and equipment > assays > whole genome sequencing |
| CSHL Authors: | |
| Communities: | CSHL labs > Wigler lab |
| SWORD Depositor: | CSHL Elements |
| Depositing User: | CSHL Elements |
| Date: | December 2020 |
| Date Deposited: | 10 May 2021 13:35 |
| Last Modified: | 30 Jan 2024 21:06 |
| PMCID: | PMC7722526 |
| URI: | https://repository.cshl.edu/id/eprint/40071 |
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