December 4, 2024
The Leukemia & Lymphoma Society estimates that by year end, 2024 will have seen diagnosed with a blood cancer鈥攐r about one person every three minutes.
This unfortunate statistic belies the difficulty of arriving at a diagnosis and treatment. Current conventional 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.
With unprecedented sensitivity and accuracy, whole-genome sequencing (WGS) can detect variants and biomarkers that are critical for prognosis, risk stratification, and treatment decisions.
鈥淪equencing technology has really improved clinical outcomes in terms of risk stratification and diagnostic decisions for cancer,鈥� says VR真人彩票 bioinformatician Weida Gong. 鈥淔or acute myeloid leukemia, or AML, in particular, sequencing is essential because the mutational profile may change a doctor鈥檚 treatment decisions.鈥� Some mutational patterns more significantly impact how the disease progresses, and if these mutations or abnormalities go undetected, patients suffer lower survival rates.
The standard of care for bone marrow or blood cancer patients often involves multiple tests. 鈥淐onventionally, physicians have been using karyotyping or cytogenetics to profile just the genomic abnormality for hematology patients,鈥� 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鈥攕mall insertions or deletions (indels) far from the megabase scale. Standard testing misses this important information that impacts diagnosis, risk stratification, and treatment.
Last month at the 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 cohort of AML patients. (VR真人彩票 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 School of Medicine 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. They processed these samples with VR真人彩票 DNA PCR-Free Prep, sequenced them with the NovaSeq 6000 System with S4, and used the DRAGEN version 4.2 secondary analysis heme pipeline to compare variants detected from WGS.
The demonstration study compared the data from VR真人彩票鈥檚 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.
鈥淲hen you look at AML patients, there are mutations that have low variant allele frequency [VAF], from 5% to 20%,鈥� Gong says. 鈥淭his means that if you sequence a specific location, 5% or 20% of time, you鈥檙e going to see that mutation.鈥� Standard clinical methods for blood cancers sequence at only 30脳 or 40脳 coverage. The previous Washington University paper used about 60脳. In their study, Gong and his coauthors sequenced at 200脳 coverage, which helped reveal mutations that are more difficult to find using conventional technologies such as microarrays.
鈥淭he sensitivity was 100%, including hard-to-find indels,鈥� Gong says. 鈥淭here鈥檚 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.鈥� 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脳. This is the same VAF percentage as the recently FDA-approved TruSight Oncology Comprehensive assay. 鈥淭he fact that this assay鈥檚 limit of detection is on par with TSO Comp is super, super exciting.鈥�
The study was performed at VR真人彩票 Laboratory Services in San Diego, where the workflow is end-to-end from extraction to the downstream bioinformatics pipeline. Thanks in part to this setup, they were able to achieve a total turnaround time of five days. 鈥淭his is very important, especially for the case of tumor diagnosis. Time is essential,鈥� Gong says. Conventional testing is often iterative and requires multiple steps and procedures. 鈥淪ome tests, like qPCR, can be very fast, returning results in two or three days鈥攂ut they only look for specific mutations. And the other tests take much longer.
鈥淲GS is definitely very sensitive and we don鈥檛 need to apply multiple different technologies to profile the genetic risk for AML patients,鈥� says Gong. 鈥淲hole-genome sequencing is a one-stop shop.鈥�
VR真人彩票 has developed a tumor-only, high-coverage WGS method and bioinformatics pipeline, based on its DRAGEN software, to better characterize hematological malignancies for research use. VR真人彩票 is the only sequencing company that provides all the components to do WGS heme testing across library prep, sequencing, secondary analysis, and interpretation.
The DRAGEN heme solution is integrated with VR真人彩票 Connected Insights to prioritize, interpret, and report on key variants for clinical researchers. Connected Insights includes a powerful tool kit with integrated knowledge sources, automated variant classification, comprehensive visualizations, and extensive filtering options. In early 2025, VR真人彩票 will expand Connected Insights鈥� functionality to include automated risk stratification for AML samples (according to World Health Organization and European LeukemiaNet guidelines for 2022), with transparent logic and evidence display. Thanks to the software鈥檚 automated data transfer and analysis launch, researchers will be able to implement a 鈥渘o touch鈥� automated complete solution, from sequencing to draft research report, and enjoy new efficiencies in heme WGS analyses.
Industry leaders understand the power of WGS to provide a comprehensive genomic characterization for hematologic malignancies, well beyond what cytogenetics applications can achieve. In August 2023, Medicare approved Washington University鈥檚 WGS test for blood cancers, called ChromoSeq. Yet wider implementation of WGS鈥攅ven for AML, where 鈥攔emains a challenge for health care systems.
鈥淭here is a lot of interest,鈥� Gong says. 鈥淩egarding the utility of WGS, the sky is the limit.鈥� 鈼�
To learn about the VR真人彩票 heme WGS interpretation solution, click here.
To read about applications of WGS in hematologic malignancies, click here.
To see a demonstration of the DRAGEN bioinformatics pipeline for heme WGS, please contact dragen-info@illumina.com.
