December 4, 2024
The Leukemia & Lymphoma Society estimates that by year end, 2024 will have seen 187,740 Americans diagnosed with a blood cancer—or about one person every three minutes.
This unfortunate statistic belies the difficulty of arriving at a diagnosis and treatment. Current diagnostic workflows use multiple lab technologies, such as karyotyping, fluorescence in situ hybridization, microarrays, gene panels, and PCR testing. The process is complex, the technology is limited, and the results can be conflicting.
A growing number of researchers are finding that whole-genome sequencing (WGS) can, with unprecedented sensitivity and accuracy, identify variants and biomarkers that are critical for prognosis, risk stratification, and treatment decisions in research cohorts.
“Sequencing technology has really improved risk stratification in cancer research,” says Illumina bioinformatician Weida Gong. “For acute myeloid leukemia, or AML, in particular, sequencing is essential to understanding the mutational profile.” Some mutational patterns more significantly impact how the disease progresses, and if these mutations or abnormalities were to go undetected, the individual would suffer a lower survival rate.
The standard of care for bone marrow or blood cancer patients often involves multiple tests. “Conventionally, physicians have been using karyotyping or cytogenetics to profile just the genomic abnormality for hematology patients,” Gong says. Unfortunately, these methods cannot provide a high-resolution picture of the disease. Cytogenetics may only detect chromosomal aberrations larger than five megabases (5 million genetic base pairs). Hematology patients, Gong explains, can have mutations that affect just one or a few base pairs—small insertions or deletions (indels) far from the megabase scale. Infinitesimal differences like these prove there are still gaps that we can address through research. WGS provides researchers opportunities to explore and identify important information that standard testing would miss.
Last month at the American Society of Human Genetics (ASHG) annual meeting in Denver, Gong presented a poster on a study evaluating the analytical performance of WGS (limit of detection, sensitivity, specificity, and reproducibility) in identifying somatic small variants, structural variants (SV), and copy number alterations (CNA) specific to AML, in a research cohort of AML patients. (Illumina coauthor Guidantonio Malagoli Tagliazucchi had just presented the same poster at the European Society for Medical Oncology annual meeting in September.)
The researchers used a combination of 23 clinical samples from collaborators at Washington University in St. Louis, plus a cohort of 30 AML clinical samples from Discovery Life Sciences, and more than 500 samples, including both cell lines and clinical samples, from their in-house development and optimization work with the assay.
The demonstration study compared the data from a WGS workflow with reference sets from Washington University and Discovery Life Sciences. Overall, they found an improved and more complete picture of each tumor, and the new data provided greater insights.
“When you look at AML patients, there are mutations that have low variant allele frequency [VAF], from 5% to 20%,” Gong says. “This means that if you sequence a specific location, 5% or 20% of the time, you’re going to see that mutation.” The previous Washington University paper used approximately 60× coverage. In their study, Gong and his colleagues sequenced at 200× coverage, which helped reveal mutations that are more difficult to find using conventional technologies such as microarrays.
“The analytical sensitivity was 100%, including hard-to-find indels,” Gong says. “There’s one particular mutation that is very, very important for AML risk stratification, and that is FLT3-ITD. There are also AML specific SVs and CNAs. We were able to detect all of them from the clinical samples.” The researchers also carried out a limit-of-detection study in which they were able to report a 95% detection rate for 5% VAF at a coverage of 140×. This is the same VAF percentage as the recently FDA-approved TruSight Oncology Comprehensive test.
“WGS is definitely very sensitive and we don’t need to apply multiple different technologies to profile the genetic risk for AML cases,” says Gong.
Industry leaders understand the power of WGS to provide a comprehensive genomic characterization for heme malignancies, well beyond what cytogenetics applications can achieve.
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