Assessment of Structural and Copy Number Variants in Constitutional Samples using Electronic Genome Mapping

Cytogenetic laboratories rely on chromosomal microarray analysis (CMA), fluorescence in situ hybridization, and chromosome banding analysis to characterize structural variants (SVs) and copy number variants (CNVs), but each method is limited in the types and sizes of SVs it can resolve. Researchers at Labcorp asked whether electronic genome mapping (EGM) could be used to assess SVs and CNVs genome-wide in a single workflow.

A cohort of constitutional and prenatal blood samples with abnormalities previously characterized by CMA, quantitative PCR, chromosome banding, and optical genome mapping (OGM) was analyzed on the OhmX™ Platform. SVs were identified by de novo assembly with SV-Discover™ (previously Human Chromosome Explorer®), available in Nabsys Navigator™, and copy number alterations were assessed with a CNV analysis pipeline. EGM results were highly concordant with array and OGM, from an ~89 kb deletion on 10q21.1 to multi-megabase events. An ~8.9 Mb inversion on 6q, flanked by two duplications, was resolved by both EGM and OGM; array cannot detect a balanced rearrangement of this kind. Coverage across the repetitive chromosome 9 pericentromere was also greater with EGM and OGM than with array.

Explore how EGM can electrify genome-wide SV and CNV assessment in your constitutional and prenatal research.