Multisite Assessment of Optical Genome Mapping for Analysis of Structural Variants in Constitutional Postnatal Cases

M. Anwar Iqbal, Ulrich Broeckel, Brynn Levy, Steven Skinner, Nikhil S. Sahajpal, Vanessa Rodriguez, Aaron Stence, Kamel Awayda, Gunter Scharer, Cindy Skinner, Roger Stevenson, Aaron Bossler, Peter L. Nagy, Ravindra Kolhe

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


This study compares optical genome mapping (OGM) performed at multiple sites with current standard-of-care (SOC) methods used in clinical cytogenetics. This study included 50 negative controls and 359 samples from individuals (patients) with suspected genetic conditions referred for cytogenetic testing. OGM was performed using the Saphyr system and Bionano Access software version 1.7. Structural variants, including copy number variants, aneuploidy, and regions of homozygosity, were detected and classified according to American College of Medical Genetics and Genomics guidelines. Repeated expansions in FMR1 and contractions in facioscapulohumeral dystrophy 1 were also analyzed. OGM results were compared with SOC for technical concordance, clinical classification concordance, intrasite and intersite reproducibility, and ability to provide additional, clinically relevant information. Across five testing sites, 98.8% (404/409) of samples yielded successful OGM data for analysis and interpretation. Overall, technical concordance for OGM to detect previously reported SOC results was 99.5% (399/401). The blinded analysis and variant classification agreement between SOC and OGM was 97.6% (364/373). Replicate analysis of 130 structural variations was 100% concordant. On the basis of this demonstration of the analytic validity and clinical utility of OGM by this multisite assessment, the authors recommend this technology as an alternative to existing SOC tests for rapid detection and diagnosis in postnatal constitutional disorders.

Original languageEnglish (US)
Pages (from-to)175-188
Number of pages14
JournalJournal of Molecular Diagnostics
Issue number3
StatePublished - Mar 2023

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Molecular Medicine


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