• Home/
  • Blog/
  • January 10, 2022 – OGM in Constitutional Cytogenetics Applications Reveals More Genome Variants that Matter with Greater Sensitivity and Better Resolution than Traditional Workflows Which Increases Success Rates and Improves Stratification of Subjects

Bionano Genomics kicked off its 2022 Symposium today with speakers from around the world sharing their experiences using optical genome mapping (OGM) with the Saphyr® system for genomic analysis of constitutional genetic diseases.

Cytogenetic techniques, such as karyotyping, fluorescent in situ hybridization (FISH) and chromosomal microarray analysis (CMA) have traditionally been used to identify and report chromosomal aberrations in constitutional genetic disease research. Today’s session included studies on a wide range of constitutional genetic diseases in pre- and postnatal genetics and offered insight into applications in infertility and reproductive medicine. Together they overwhelmingly supported OGM as a strong alternative to these traditional workflows.

The OGM workflow in constitutional cytogenetics reveals more clinically relevant variants from genomic data at a higher resolution than traditional workflows. This streamlined workflow shortens turn-around times, increases success rates, improves stratification and yields critical new genetic insights. The identification of disease-causing genetic variants depends on researchers’ ability to assemble pieces of the genome across millions of base pairs. OGM makes those puzzle pieces larger, making it easier to complete the puzzle and construct a fuller picture of the genome. As a result, researchers using OGM can find structural rearrangements that may be causing a rare disease that have previously gone undetected. Today’s presenters agreed that OGM provides a more complete view of the genome and should be used as a standard tool for identification of variants in genetic diseases.


Why is this research so important?


According to the National Organization for Rare Disorders (NORD), there are approximately 7,000 rare diseases and most are thought to be genetic or have a genetic component. Although many of these rare diseases present at birth or in early childhood, determining the actual cause of the rare disease often takes years.

Both Dr. Iqbal, from the University of Rochester Medical Center, and Dr. Shirley Heggarty compared the performance of OGM in the evaluation of pre- and postnatal samples with known chromosomal aberrations. Both studies found a high concordance of OGM results compared to traditional methods. In addition. OGM was able to identify both unbalanced structural chromosome abnormalities and balanced structural variants (SVs), like translocations and inversions, that CMA could not.

Dr. Alexander Hoischen explored repeat disorders and specifically the capabilities of OGM to map repeat expansions, which are particularly challenging types of SVs, in subjects with Canvas syndrome and myotonic dystrophy types 1 and 2. The OGM workflow was able to immediately call very large insertions, probably even with greater precision than some of the standard cytogenetic techniques, and with a very high concordance. Not only does OGM allow researchers to be able to see more of the genome, but it is also less time-consuming and labor-intensive than other molecular methodologies like Southern blotting, as Dr. Nikhil Sahajpal discovered. Results from his validation study were 100% concordant with traditional methods and demonstrated a streamlined laboratory workflow for different sample types.

In addition to pre- and postnatal applications, two speakers, Dr. Laila El-Khattabi and Chaim Jalas, shared how the OGM workflow plays a significant role in their research in infertility and reproductive disorders. In her study, Dr. El-Khattabi used OGM to characterize apparently balanced SVs related to male infertility and identify new genes involved in reproductive disorders. Jalas shared how OGM used in preimplantation genetic diagnosis can identify structural rearrangements, including balanced translocations and inversions, in embryos prior to transfer, which could improve pregnancy and delivery rates in an IVF setting.

“The power of researchers to discover important genomic variants and develop treatments for those born with genetic disorders is why I believe that OGM has the potential for significant growth,” said Alka Chaubey, PhD, FACMG, Chief Medical Officer at Bionano. “Being able to identify causative variants and see the whole genome at a much higher resolution, could make all the difference in the world to parents awaiting a diagnosis for their child or others planning to have a family.”


Today’s presenters:


Chaim Jalas

Chief Operations Officer and Director of Technology Development, The Foundation for Embryonic Competence

“Clinical Validation of Optical Genome Mapping for Preimplantation Genetic Diagnosis – Structural Rearrangement (PGD-SR) Applications”


Laila El-Khattabi, PharmD, PhD

Associate Professor of Genomic Technologies and Immuno-Genomics, APHP Université de Paris

“Balanced translocations associated with male infertility: How optical genome mapping could lead to new discoveries?”


Shirley Heggarty, BSc, PhD

Principal Clinical Scientist, Belfast Health and Social Care Trust

“Clinical Utility of Optical Genome Mapping in a Constitutional Cytogenetics Laboratory”


Alexander Hoischen, PhD

Associate Professor of Genomic Technologies and Immuno-Genomics, Radboud University Medical Center, The Netherlands

“Optical genome mapping to map difficult structural variant type – repeat expansions”


Anwar Iqbal, PhD, FACMG

Director, Microarray CGH Laboratory, Director of Clinical Cytogenetics Development, University of Rochester Medical Center

“Validation study of Optical Genome Mapping for Postnatal and Prenatal Clinical Testing according to established NYSDOH guidelines”


Nikhil Sahajpal, PhD

Post-Doctoral Fellow, Department of Pathology, Augusta University

“Enhanced Structural Variation Detection with Optical Genome Mapping in Constitutional Genetic Disorders”


Symposium presentations will be available online after January 14, 2022 at




This website stores cookies on your computer. These cookies are used to collect information about how you interact with our website and allow us to remember you. We use this information in order to improve and customize your browsing experience and for analytics and metrics about our visitors both on this website and other media. To find out more about the cookies we use, see our Privacy Policy.