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August 12, 2022

Optical Genome Mapping Gains Momentum for Clinical Applications in Hematologic Disorders

BALTIMORE – Researchers at the University of Texas MD Anderson Cancer Center have demonstrated the prognostication utility of optical genome mapping (OGM) in a large cohort of patients with myelodysplastic syndromes (MDS), boosting OGM as an alternative to cytogenetic analysis in hematologic disorders.

In a study published earlier this month in Leukemia , the MD Anderson team showed that, when paired with targeted next-generation sequencing for mutation analysis, OGM achieved congruous structural variant profiling with standard-of-care cytogenetic analysis combined with targeted NGS.

In addition, OGM helped uncover additional cryptic aberrations in MDS patients that were of prognostic and therapeutic value but missed by conventional karyotyping.

A group of related disorders that prevent bone marrow from producing enough healthy blood cells, MDS is a very heterogeneous disease that can cause conditions such as anemia and acute leukemia, said Rashmi Kanagal-Shamanna, a hematopathologist and molecular genetic pathologist at MD Anderson and the lead investigator of this study.

While patients with anemia can go on to live for decades with close disease monitoring, Kanagal-Shamanna said, those who suffer from acute leukemia are likely to experience very poor outcomes.

Therefore, to extrapolate a patient’s prognostic risk and establish appropriate treatment plans, clinicians often rely on the Revised International Prognostic Scoring System (IPSS-R), a widely adopted risk stratification system for MDS patients that is currently largely determined by a patient’s chromosomal abnormality features.

“When a patient comes in at the beginning, we decide whether the patient needs therapy or not or if we can just watch and wait [based on] this IPSS-R score,” said Kanagal-Shamanna, adding that, under the current standard of care, chromosomal abnormalities are obtained by conventional metaphase karyotyping techniques, where bone marrow cells are cultured and observed under the microscope.

Compared with the traditional cytogenic analysis technique, OGM has several advantages, Kanagal-Shamanna said. For one, she noted that diagnostic time using OGM can be faster. According to her, the average turnaround time for a karyotyping analysis can be seven days, whereas for OGM, the average is five days.

Even when cytogenetics is carried out, Kanagal-Shamanna said, clinicians often follow up the results with confirmatory tests, such as the fluorescence in situ hybridization (FISH) assay, which can further the turnaround time for diagnosis. On the other hand, OGM can consolidate all these tests and provide “much more comprehensive” results in one assay, she added.

Additionally, because traditional karyotyping requires cell culturing, the technique cannot effectively analyze hypocellular MDS cases, where bone marrow cells are difficult to grow, Kanagal-Shamanna pointed out. In contrast, OGM, which is a DNA-based assay, can circumvent such limitations.

For this study, Kanagal-Shamanna’s team applied OGM to 101 consecutive, newly diagnosed MDS patients from MD Anderson who underwent standard-of-care cytogenetic and targeted NGS analysis.

“My hypothesis was that optical genome mapping will be able to better prognosticate these patients by identifying additional smaller aberrations missed by karyotype and uncovering some of the cryptic, actionable alterations,” said Kanagal-Shamanna. “That's exactly what we showed in our study.”

Specifically, the results showed that, in addition to performing commensurately with the conventional cytogenetic assays, OGM, paired with targeted NGS designed for mutation analysis, identified 224 structural variants that were cryptic to the standard-of-care chromosome banding analysis techniques and targeted NGS in 34 percent of patients. These cryptic structural variants changed the comprehensive cytogenetic scoring system (CCSS) score in 21 percent of the participants and the IPSS-R risk category in 17 percent of patients.

These findings “translated to better patient risk stratification,” said Kanagal-Shamanna, adding that improved disease prognostication could help better inform clinicians whether to initiate disease-modifying treatment, including using hypomethylating agents, or simply observe the patients while carrying out mitigations such as blood transfusions.

“Hypomethylating agent is chemotherapy, every chemotherapy has side effects, [and] you do not want to overburden patients with unnecessary treatments,” Kanagal-Shamanna said. More importantly, she said a subset of MDS patients may even develop hypomethylating agent failure. “Once the patients fail hypomethylating agents, there is no treatment,” she added. “You want to push the therapy out as much as possible."

In addition to improved risk stratification, the study also showed that OGM helped uncover actionable structural alterations, such as MECOM rearrangements and biallelic TP53 alterations, that could open up opportunities for the patients to qualify for certain clinical trials for targeted therapies, Kanagal-Shamanna noted.

What is “even more astonishing,” she said, is that the team found OGM can not only detect gene-level alterations but also pick out structural alterations at the exon level, such as partial tandem duplications involving KMT2A.

This study “agrees with the expectations that cytogenetics is not a high-resolution methodology,” said Eric Duncavage, a molecular oncology pathologist at the Washington University School of Medicine in St. Louis who was not involved in this study. “It’s a technology that predates touch-tone phones; it’s one of the oldest laboratory methods that we still use on a daily basis.”

Last year, Duncavage and his team published a study in the New England Journal of Medicine exploring the use of whole-genome sequencing (WGS) as an alternative to cytogenetic analysis in MDS. Mirroring this study, his group reported that WGS also delivered rapid and accurate genomic profiling in MDS and acute myeloid leukemia (AML) patients, while providing a greater diagnostic yield and more efficient risk stratification compared with conventional cytogenetic analysis.

Commenting on WGS and the OGM-based approach, Duncavage said each method has pros and cons. For instance, while WGS can provide single-base resolution of the genome and promise “a one-stop assay” for clinicians to obtain all the information needed for risk stratification, Duncavage said the downside of the technology right now is that it is more expensive.

“I think for most labs, the big advantage [of OGM] is that the equipment is cheaper to buy, and the assays are cheaper to run compared to whole-genome sequencing,” he said, adding that the disadvantages of OGM include that it requires “very high molecular weight DNA” as an input and that it requires targeted NGS in conjunction to analyze mutations on the base level.

As sequencing costs continue to drop, Duncavage said he believes WGS will eventually become a more cost-effective technology in the long run for MDS analysis. However, in the short term, he said he still sees a need for OGM to fill the void.

In addition to WGS and OGM, researchers are also tapping long-read sequencing technologies to achieve real-time detection of copy number variants (CNVs) in patients with genetic disorders.

Commenting on these emerging sequencing-focused technologies, Kanagal-Shamanna said one major advantage for OGM is that clinicians can implement it quickly with minimal bioinformatics infrastructure. For long-read and short-read sequencing, people tend to need dedicated analysis pipelines and bioinformaticians, whereas with OGM’s analysis interface, researchers can manually visualize the abnormalities even without extensive bioinformatic knowledge, she said.

Moving forward, Kanagal-Shamanna said the team has already started a prospective study to further validate OGM’s performance in MDS and AML patients. The group also plans to incorporate OGM into some of the ongoing MDS clinical trials.

Additionally, encouraged by the existing results, Kanagal-Shamanna said MD Anderson also plans to adopt OGM as part of routine cancer diagnostics. Toward that goal, she said the institution now houses three Bionano Genomics Saphyr instruments, including one for its CLIA-certified laboratory, which is currently validating the OGM assay for hematological malignancies and will potentially explore solid tumors. “We hope to get it up and running for routine patient care in the next six months or so,” Kanagal-Shamanna said.

As for insurance coverage, she said, now that OGM has shown it can be a powerful alternative to conventional cytogenetic analysis, “it would just be a matter of time before the reimbursement issue is sorted out.”

Echoing Kanagal-Shamanna’s point, Duncavage thinks methods like OGM and NGS will become more common in the next five years as they become more widely covered by insurance carriers.

“I think it's a testament to the fact that the world is ready to move forward from cytogenetics,” Duncavage said.