American Association for Cancer Research® (AACR) Annual Meeting 2024

Visit us at booth #547

Reveal the power of the 6-base genome. Introducing duet multiomics solution evoC.

Distinguish 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) together with all four canonical bases to measure multiple modes of biology from a single low-input DNA sample in a single experiment. Identify novel multimodal biomarkers to gain transformative insights into current and future states of disease.

7 April 2024
to 10 April 2024

San Diego Convention Center, San Diego

About the event

The American Association for Cancer Research® (AACR) Annual Meeting 2024 is the focal point of the cancer research community, where scientists, clinicians, other health care professionals, survivors, patients, and advocates gather to share the latest advances in cancer science and medicine. From population science and prevention; to cancer biology, translational, and clinical studies; to survivorship and advocacy; the American Association for Cancer Research® (AACR) Annual Meeting 2024 highlights the work of the best minds in cancer research from institutions all over the world.

Comprehensive Genetic and Epigenetic Analysis Using Limited DNA Samples

Joon Seon Lee, Ph.D.

Computational Biologist

Michael Smith Laboratories, University of British Columbia

Monday, April 8, 2024 | 3:00 PM - 4:00 PM | Spotlight Theater E - Sails Pavilion

Presentation abstract

Joon Seon Leea, Misha Bilenkya,b, Qi Caoa, Michelle Moksaa, Martin Hirsta,b 

aMichael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada; bCanada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada 

One challenge in precision medicine is limited DNA availability making it challenging to construct representative libraries for (epi)genomic measurements. The biomodal duet multiomics solution +modC allows for the quantitative measurement of genotype and modified cytosines simultaneously from a single DNA sample. In this study, we applied the biomodal multiomics assay to DNA extracted from two primary pre-treatment synovial sarcoma (SyS) tumor tissue and six cell-free DNA samples (cfDNA). Following library construction, the indexed libraries were pooled together and sequenced on NovaSeq 6000 S4 chip. To benchmark the performance of the biomodal assay, we compared the resulting CpG calls (for gDNA libraries with >94% CpG calls at 5X per sample) to our inhouse post bisuflite adapter ligation (PBAL) method capable of generating bisulfite libraries down to a single cell (Hui et al., 2018). The biomodal duet assay showed lower coverage bias across a range of CpG densities compared to PBAL with 95% of CpGs covered at >=10X with the biomodal assay. CpG methylation calls across the two methods were significantly correlated with (R > 0.94 at CpG coverage >= 5), and this concordance increased in CpG dense regions (R > 0.98 at CpG coverage >= 5). An average of 3.7 million variants were called in the cfDNA and SyS samples. For the SyS tumor samples, most of the somatic variants called by mutect2 from whole genome shotgun sequencing were detected by duet +modC (93% of 1,943 in sample1 and 85% of 3,676 in sample 2). For all eight samples analysed by duet+modC we found overall concordance between variants called and dbSNP higher than 90%. The application of duet +modC to limiting DNA samples provides significant efficiency in sample handling by enabling comprehensive and accurate genetic and epigenetic measurement. 

Multimodal features of cell-free DNA from breast cancer preclinical models for CDK4/6 inhibitor resistance liquid biopsy biomarker discovery

Sasha Main

PhD Candidate

Princess Margaret Cancer Centre

Monday, April 8, 2024 | 3:00 PM - 4:00 PM | Spotlight Theater E - Sails Pavilion

Presentation abstract

Sasha Main (1,2), Dr. Mitchell Elliott (1,3,4), Zhen Zhao (1), Althaf Singhawansa (1), Dr. Jinfeng Zou (1), Dr. Scott Bratman(1,2,5), Dr. David Cescon (1,3,4) 



1) Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C1, Ontario, Canada.  

2) Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada.  

3) Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Toronto M5S 1A8, Ontario, Canada.  

4) Institute of Medical Science, University of Toronto, Toronto M5S 1A8, Ontario, Canada.  

5) Department of Radiation Oncology, University of Toronto, Toronto M5T 1P5, Ontario, Canada.  

Background:  CDK4/6 inhibitors (CDK4/6i), in combination with endocrine therapy, are the standard first-line treatment for patients with ER+/HER2- metastatic breast cancer. Acquired resistance to therapy is inevitable for patients, highlighting the need for novel biomarkers to predict non-responders and identify rational next lines of therapy. Analyzing circulating tumor DNA (ctDNA) through liquid biopsy offers a minimally invasive method for discovering biomarkers of CDK4/6i resistance and capturing disease heterogeneity at multiple metastatic sites. While most studies have primarily focused on genetic alterations in ctDNA, expanding the scope to include epigenetic features—such as methylation, hydroxymethylation, and nucleosome positioning—may uncover novel biomarkers of CDK4/6i resistance. Here, we assess the feasibility of simultaneously evaluating multiple epigenetic features with a single sequencing platform on ctDNA derived from preclinical models for CDK4/6i resistance biomarker discovery.   

Methods: We applied methods to simulate ctDNA in tissue culture models, utilizing a nuclease treatment to mimic nucleosomal distributions found in plasma. Using matched CDK4/6 inhibitor (CDK4/6i) sensitive and resistant breast cancer cell lines (n=10), we generated simulated ctDNA samples. We conducted six-letter sequencing (6L-seq) on simulated ctDNA derived from a single initial cell line (CAMA-1), with biological replicates and shallow sequencing coverage (average 1.5X). We then evaluated paired RNA-seq, ATAC-seq, and simulated ctDNA WGS relative to simulated ctDNA 6L-seq. 

Technical evaluation and comparison of duet evoC data from head and neck cancer gDNA samples

Claudia Lalancette

Director BRCF Epigenomics Core

University of Michigan Medicine

Monday, April 8, 2024 | 3:00 PM - 4:00 PM | Spotlight Theater E - Sails Pavilion

Presentation abstract

Stay tuned!

One sample. One workflow. One solution.

Here are the relevant biomodal resources for information. Find poster presentation information, case studies, interviews, and more.

duet multiomics solution evoC product sheet

duet multiomics solution evoC product sheet

Novel single-base-resolution solution that delivers the standard four-base sequencing (A, C, G, and T), and distinguishes between 5‑methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), on the same DNA molecule.

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Director of Sales and Business Development for North America
AACR April 2024

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