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Droplet Digital PCR (ddPCR) in Precision Oncology and MRD: Perspectives from the Trenches
Wednesday, November 20
9:00 – 9:50 AM, Room 116 & 117, Level 1
- Droplet Digital PCR
- Molecular Quality Controls & Standards
- Real-Time PCR
- Rare Cell and Circulating Tumor Cell (CTC) Capture
We Advance Science and Save Lives Together
Our mission is to propel scientific discovery forward through innovative solutions and partnership.
We continue to make great strides in cancer research, but the journey is far from over. There are still many unanswered questions and challenges in the fight against cancer. At Bio-Rad, we support this important work with a comprehensive suite of genomics and proteomics solutions.
Our offerings are designed to assist researchers in discovering new methods for cancer detection, treatment and monitoring.
For Research Use Only. Not for use in diagnostic procedures.
Detection
Variant Detection
Effective mutation detection, copy number, and gene expression analysis require high sensitivity and precision to identify and quantify rare genetic variants and low-abundance transcripts precisely.
Signaling Pathway Analysis
Unraveling the intricate web of cancer signaling pathways necessitates protein analysis with sensitive detection and precise quantitation to elucidate the subtleties of these complex cascades to propel knowledge forward.
Treatment
Biomarker Discovery and Validation
Discovering biomarkers with high sensitivity, validating across diverse populations, and obtaining reproducible results are key to identifying new treatment targets.
Targeted Therapy Development
Developing targeted therapies in oncology requires molecular techniques that deliver precision profiling, navigate tumor heterogeneity, detect low-frequency mutations, and enable high-throughput screening.
Monitoring
Biomarker Quantification and Monitoring
Effective monitoring relies on molecular techniques with high specificity and a broad dynamic range to accurately track biomarker changes over time.
Drug Resistance Monitoring
Precise quantification of gene variant and protein levels is necessary to monitor changes over time, especially in response to drug treatment, to assess drug efficacy and resistance development.
Consult with a specialist about how Bio‑Rad can help you discover the ideal solutions for your research needs.
Have a Specialist Contact MeDroplet Digital PCR
Droplet Digital PCR (ddPCR) is the Premier Solution for Serial ctDNA Analysis
Our performance-leading systems and assays deliver deeper and earlier insights into cancer research around treatment response, progression, and risk of relapse to detect cancer recurrence well before current standards of care, using a simple blood draw to monitor trace levels of circulating tumor DNA (ctDNA).
Droplet Digital PCR is a precise and sensitive tool with favorable turnaround time, cost, and results reporting compared to NGS, providing a lab-friendly workflow for ctDNA analysis.
Our customers are advancing the field of oncology with ddPCR-powered ctDNA analysis!
Learn HowExplore our Kits, Assays, and Custom Design Engine
Bio‑Rad offers validated kits and assays for oncology applications and custom assays for detection of key biomarkers with high sensitivity, precision and multiplexing.
Bio‑Rad's database and design engine optimize oncology experiments - take advantage of 24/7 service at your fingertips to design an assay on demand for your application or search or browse our curated lists of predesigned assays, such as these cancer-focused lists of targets aligned to the National Comprehensive Cancer Network (NCCN) guidelines.
Breast Cancer
Emerging ESR1 mutations are a common mechanism of acquired resistance following endocrine therapy which highlights the criticality of analyzing mutations for advancing clinical research in breast cancer. The ddPLEX ESR1 Mutation Detection Kit maximizes precious liquid biopsy or FFPE samples by interrogating seven key ESR1 mutations in a single well. Additional, relevant biomarkers are shown for breast cancer many of which align with NCCN guidelines.
Colorectal Cancer (CRC)
Microsatellite instability (MSI) is a frequent molecular hallmark for certain types of colorectal cancer and is characterized by accumulation of mutations in microsatellite regions. The ddPCR Microsatellite Instability Kit provides sensitive, reproducible and qualitative results for five mononucleotide microsatellite markers in plasma or tumor tissue samples without the need for normal tissue. The characterization of MSI and relevant genetic alterations can contribute to the understanding of colorectal cancer disease progression and potential interventions.
| Mutation Detection and Copy Number Assays* | |||
|---|---|---|---|
| APC | PIK3CA | PTEN | EGFR |
| TP53 | FBXW7 | CDKN2A | IDH1 |
| KRAS | MET | STK11 | CTNNB1 |
| BRAF | SMAD4 | KIT | NRAS |
* >200 wet-lab validated mutation detection and >700 wet-lab validated copy number determination assays
| Multiplex Mutation Screening Kits | ||
|---|---|---|
| MSI | BAT25/26, NR21/24, Mono27 | |
| BRAF V600 | V600E, V600K, V600R | |
| KRAS G12/G13 | G12A, G12C, G12D, G12R, G12S, G12V, G13D | |
| EGFR exon 19 deletion | >15 EGFR exon19 deletions | |
Heme Oncology
Bio‑Rad offers several heme oncology kits and assays that include markers found on many established guidelines. Read testimonials from customers and review compelling studies demonstrating the high sensitivity and unmatched precision that ddPCR provides to labs.
Read MoreMethylation Expert Design Assays
DNA methylation, an essential epigenetic modification, involves adding a methyl group to cytosine bases within CpG dinucleotides. These CpG islands are concentrated in specific regions of the genome. In normal cells, DNA methylation ensures proper gene regulation and stable gene silencing. However, irregularities in methylation can lead to tumor development. Hypermethylation within promoter regions can lead to tumor-suppressor gene inactivation, while global hypomethylation contributes to genomic instability.
Methylation-Sensitive Restriction Enzymes (MSRE) digestion method offers a straightforward approach to DNA methylation quantification, bypassing the limitations of traditional bisulfite conversion. This method requires minimal input sample requirements. Explore our selection of Expert Design methylation assays to enhance your research. Our ddPCR Expert Design Assays are tailored for Droplet Digital PCR.
Read More
ddPCR Technology
Droplet Digital PCR technology is a digital PCR method utilizing a water-oil emulsion droplet system. Droplets are formed in a water-oil emulsion to form the partitions that separate the template DNA molecules. The droplets serve essentially the same function as individual test tubes or wells in a plate in which the PCR reaction takes place, albeit in a much smaller format. The massive sample partitioning is a key aspect of the ddPCR technique.
Absolute Quantification
Eliminate reliance on standard curves
Easy Multiplexing
Multiplex up to 12 targets per well
Unmatched Performance
Sensitivity as low as 0.001% precision confirmed by the National Measurement Institute
Broad Variant Detection
Easily detect single/multiple nucleotide variations, copy number variations, structural variants, loss of heterozygosity
Real-Time PCR
Real-Time PCR (qPCR) has been explored and widely implemented to study the expression of gene patterns for cancer development, predicting response and resistance to therapy. Due to its sensitivity, accuracy, and robustness, qPCR has become a cost-effective molecular technique for clinical trials and routine lab use. We offer a wide range of optimized instruments, reagents, and tools empowering your cancer research.
Real-Time PCR Systems
CFX Opus Real-Time PCR Systems offer workflow flexibility and throughput with industry leading reliability and uniformity.
PCR Reagents and Plastics
- Formulated with advanced enzyme technology, buffer, and universal reference dyes for reliable amplification
- Delivers higher processivity and inhibitor tolerance without comprising qPCR data
- Large selection of warp-free Hard-shell PCR plates designed for optimum performance with automation
- Plates certified free of Dnase, Rnase, and human gDNA
Stain-Free Western Blotting
Elucidating aberrant signaling cascades is critical in characterizing cancer cells and identifying novel biomarkers. Researchers turn to western blotting as the established technique to quickly determine differential protein expression or phosphorylation states in apoptotic signaling.
Stain-Free Western Blotting Workflow
Stain-Free Western Blotting speeds up the process of quantifying differential protein expression by reducing electrophoresis and transfer time to less than 30 minutes. Incorporating total protein normalization enhances efficiency and accuracy of protein quantitation.
Separate Proteins
Speed with flexibility: TGX Stain-Free Gel chemistry available in precast and handcast formats
Visualize Protein Separation
Coomassie-like performance with no background variability and no staining/destaining
Protein Transfer
Fast, efficient, and uniform protein transfer Throughput: transfer 4 mini or 2 midi gels at onceConvenience: choose from ready-to-use transfer packs of nitrocellulose or PVDF
Assess Transfer Efficiency
Quickly verify quality of transfer by imaging gel post transfer
Normalize Total Protein and Analyze Western Blot Data
Easy Multiplexing
Stain-Free Western Blotting Workflow can speed up the process of quantifying crucial proteins within the signaling pathway. You can increase throughput compared to traditional blotting by reducing electrophoresis and transfer time to less than 30 minutes, enhancing efficiency and accuracy of protein quantitation.
Total protein detection with chemiluminescence
Total protein detection with fluorescence
Stain-free blot (from step 4) for normalization
Benefits of Using Stain-Free Blot Image as Total Protein Loading Control
- Eliminates the need to strip then reprobe, or cut the blot
- More precise normalization method compared to traditional methods which use a single housekeeping protein
- Produces reliable and accurate quantitation
CTC Capture and Recovery
The investigation of circulating tumor cells (CTCs) is a rapidly emerging area of cancer research that holds promise for insights into metastasis. Because of their presence in the bloodstream and other body fluids, CTCs can be collected by liquid biopsy. In contrast to circulating tumor DNA (ctDNA) which is also found in blood, analysis of living CTCs can yield in-depth information about cancer genomics, gene expression, gene regulation, and cancer progression. A challenge to CTC analysis, however, is their heterogeneity and paucity in blood samples (typically 1-5 cells/mL of blood). Thus, a major obstacle for cancer researchers lies in the need for efficient and unbiased selective enrichment of CTCs from the many other cell components in blood (e.g. RBCs, WBCs).
The Genesis System with Celselect Slides™ stands out as an innovative solution for the unbiased capture, enrichment and enumeration of CTCs. The unique microfluidics design of Celselect Slides captures individual CTCs and clusters ranging from 8-30 um in size, within microchannel chambers with high efficiency, eliminating over 99% of RBCs, WBCs and other components found in blood samples. Captured CTCs can be recovered for culture or downstream analysis (e.g. NGS, ddPCR), or alternatively immunostained on-slide for detection of cell surface biomarkers and enumeration.
- Capture and recovery of >80% of CTCs from liquid biopsy samples
- Removal of >99% of red and white blood cells and other blood components
- Easy on-slide immunostaining of captured CTCs
- Imaging compatible with automated microscopes
Referenced with permission from the NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines®) for Breast Cancer V.5.2023. © National Comprehensive Cancer Network, Inc. 2023. All rights reserved. Accessed December 5th, 2023. To view the most recent and complete version of the guideline, go online to NCCN.org.
Referenced with permission from the NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines®) for Colon Cancer V.4.2023. © National Comprehensive Cancer Network, Inc. 2023. All rights reserved. Accessed November 16th, 2023. To view the most recent and complete version of the guideline, go online to NCCN.org.
NCCN makes no warranties of any kind whatsoever regarding their content, use or application and disclaims any responsibility for their application or use in any way.