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Leveraging Rapid NGS to Advance Hemato-Oncology Research

In a recent Association for Molecular Pathology (AMP) workshop, Dr. Cecilia Yeung shared how her lab is implementing rapid next-generation sequencing (NGS) to help advance hemato-oncology research and expand access to underserved populations.

cecilia-yeungCecilia CS Yeung, MD
Associate Professor – Fred Hutchinson Cancer Center, Clinical Research Division
Associate Professor – UW Medicine, Department of Laboratory Medicine & Pathology
Medical Director – Fred Hutch CLIA Laboratories

She introduced her lab’s exciting collaborations with The Max Foundation and National Cancer Institute (NCI), which are leveraging the latest NGS technology to help create a better future for patients diagnosed with myeloid disorders. 


Making a Global Impact: Spot on CML + The Max Foundation

Dr. Yeung began her presentation by highlighting the challenges that low- and middle-income countries (LMIC) face in combating cancer. Seventy percent of cancer deaths occur in these countries, where access to pathology services for timely, accurate diagnosis is extremely limited.

The Fred Hutchinson Cancer Center (FHCC) is collaborating with The Max Foundation on a program called Spot on CML, which intends to provide access to low-cost advanced laboratory diagnostics for chronic myeloid leukemia (CML) and free lifesaving treatment for patients in underserved countries. Since the program started, the molecular oncology lab at FHCC has processed nearly 1000 samples from 23 countries.

Recently, the lab started using rapid NGS for its dried blood spot (DBS) samples, which can be more easily obtained from patients in LMICs with limited access to pathology services. Dr. Yeung remarked on how well amplicon-based sequencing performs, even with challenging samples that contain very limited amounts of nucleic acid (e.g., as low as 1.25 ng DNA and 7.76 ng RNA).

She went on to share a case study where they employed rapid NGS with a targeted DNA sequencing panel on a DBS specimen and identified a tyrosine kinase inhibitor (TKI)–resistant mutation that altered treatment plans. Together, the Spot on CML program and The Max Foundation are helping improve the survival of CML patients in LMICs.


MyeloMATCH: Precision Medicine AML/MDS Trial

In the second portion of her presentation, Dr. Yeung introduced the MyeloMATCH trial, a precision medicine umbrella trial for acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) with multiple sub studies for current and investigational agents.

Patients are enrolled at diagnosis, and their blood samples are sent to Fred Hutch CLIA Laboratories for flow cytometry, cytogenetics, and NGS. Results are typically delivered within 72 hours, and patients are assigned to an initial sub study based on clinical information and molecular features.

The goal of the trial is to help accelerate therapeutic advances for myeloid malignancies through the creation of a collaborative network and portfolio of rationally designed treatment sub studies that patients sequentially enroll in over their entire treatment journey. As tumor burden decreases, the focus shifts to targeting residual disease more effectively.



Ongoing Research with the Oncomine™ Myeloid Assay GX

As part of the ongoing study, the molecular oncology lab at FHCC and the National Institutes of Health (NIH) Molecular Characterization (MoCha) Laboratory evaluated the Oncomine™ Myeloid Assay GX on the Genexus™ System. They analytically validated the assay for the feasibility of reporting clinical-grade results.

The assay was selected for the study because of its ability to rapidly detect both RNA fusions and DNA variants in the same sequencing run and produce harmonized data across the sister labs.

Dr. Yeung highlighted the advantages of the Ion Torrent™ GX5™ Chip, a 4-lane chip with 12 to 15 million reads per lane. She noted that you can multiplex up to 8 samples per lane and use the lanes over 2 weeks.

NGS on the Genexus™ System delivers rapid results—just 14 hours for a single-lane run and 24 to 30 hours for a full chip of 32 samples. The fully automated system uses Ion AmpliSeq™ technology, which eliminates the need for cluster generation and is a faster method than other sequencing methods. She noted that her lab technicians appreciate that they can load and walk away.


Oncomine™ Myeloid Assay: Feasibility, Harmonization, and FLT3 ITD Detection

Next, Dr. Yeung shared data from the feasibility and harmonizing studies that her lab and the NIH MoCha Lab conducted, including the following quality control (QC) metrics for V1 of the assay over 86 runs and 1182 samples.

QC Metrics

  •    98.2% of samples passed QC
  •    Sensitivity: 99%
  •    Specificity: 100% 
  •    LOD: <1% single nucleotide variants (SNVs), 3% insertions-  deletions (indels), 20 read counts for fusions
  •    Reproducibility: 99.4% over 154 libraries
  •    Concordance with reference assay in 8 blinded samples: 100%

Dr. Yeung and her team also evaluated the FLT3-internal tandem duplication (ITD) detection performance of the Oncomine™ Myeloid Assay GX. They chose 69 samples from their FLT3-ITD archival data with large ITDs, multiple peaks, and low AR and variant allele fractions (VAFs). In 19 runs, the assay demonstrated 100% QC, 100% sensitivity, and 100% specificity with a detectable range of 21 bp to 117 bp.  


Oncomine Myeloid Assay FLT3-ITD Performance

Sensitivity: 100%
Specificity: 100%
Detectable range: 21 bp–117 bp (up to 126 bp was detected in this study cohort)

Dr. Yeung shared some of the details of their ongoing analytical data validation including informatics, reporting, and laboratory information management system (LIMS). In addition, she highlighted the QA/QC dashboards of the Genexus™ System and the advantages of the Key Findings page, and reviewed their lab’s data workflow for the clinical trial.

Dr. Yeung concluded that the Genexus™ System and Oncomine™ Myeloid Assay GX demonstrated strong performance with challenging samples and that they have the potential to make a significant impact on global oncology. 

Watch the full webinar on demand.

*For Research Use Only. Not for use in diagnostic procedures.

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Leveraging Rapid NGS to Advance Hemato-Oncology Research

In a recent Association for Molecular Pathology (AMP) workshop, Dr. Cecilia Yeung shared how her lab is implementing rapid next-generation sequencing (NGS) to help advance hemato-oncology research and expand access to underserved populations.