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Bio-Rad (BIO) Release: Highly Sensitive Cancer Mutation Profiling And Single-Cell Genomics Research Using Droplet Digital Technology Presented At ASHG 2016



11/2/2016 8:58:25 AM

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New research demonstrating the power of Bio-Rad’s Droplet DigitalTM technology for cancer mutation and single-cell transcriptome profiling was presented at Bio-Rad’s Exhibitor Education Event during The American Society of Human Genetics (ASHG) Annual Meeting in Vancouver, British Columbia, October 18 – 22.

Bio-Rad’s Exhibitor Education Event entitled “Advanced Applications of Droplet Digital Technology: Liquid Biopsies to Single-Cell Transcriptome Profiling” featured three researchers from universities in the U.S. and Canada. Two of the presentations illustrated the robust ability of Droplet Digital PCR (ddPCRTM) technology to rapidly detect and quantify somatic cancer mutations in both tissues and cell-free DNA. The third presentation demonstrated the utility of the Illumina®|Bio-Rad® Single-Cell Sequencing Solution, which is used to understand human pluripotent stem cell (hPSC) population heterogeneity.

New Approaches to Detect and Profile Diverse Cancers

Dr. Curtis B. Hughesman, postdoctoral researcher in Dr. Charles Haynes’ laboratory at the Michael Smith Laboratories, University of British Columbia, presented recent work demonstrating the utility of ddPCR for the clinical detection and quantification of cancerous DNA biomarkers. Dr. Hughesman’s talk was entitled “Thinking ‘inside’ the droplet: Re-envisioned molecular diagnostic assays using ddPCR for the detection of somatic mutations in cancer.”

The Haynes laboratory has developed novel methods that achieve exceptional sensitivity in ddPCR quantification of closely related alleles. Differentiating between wild-type and mutant genes with only a single base-pair difference can be very challenging. Their work demonstrates a novel model for predicting melting thermodynamics of dual-labeled hydrolysis probes, which they used to discriminate between and quantify clinically relevant mutant alleles such as BRAF V600E and KIT D816V in a ddPCR assay.

In addition, the Haynes laboratory has demonstrated a robust method for measuring copy number alterations (CNAs) in DNA extracted from frozen or formalin-fixed paraffin embedded (FFPE) tissue biopsy samples. These common clinical samples typically have a low quantity and quality of genomic DNA making it difficult to quantify gene copy numbers. The group’s strategy involves a novel experimental design, data analysis tool, and optimized primer and probe design in a multiplexed ddPCR assay offering reliable quantification of biomarker CNAs.

The Haynes laboratory has also achieved reliable and accurate quantification of the frequency of the fusion gene BCR-ABL. Using a novel ddPCR assay, this known chronic myelogenous leukemia (CML) oncogene can be quantified with a detection limit of 0.25 percent. In contrast, the standard approach for detecting BCR-ABL, fluorescence in situ hybridization (FISH), is a tedious assay that requires direct visualization and has a limit of detection of roughly two percent. The more sensitive and specific ddPCR assay provides a basis for the development of a potential molecular diagnostic for CML.

Multiplexing to Quantify Somatic Mutations in Lymphoma

Dr. Miguel Alcaide, research associate in the laboratory of Dr. Ryan Morin at the Simon Fraser University, presented a novel approach for detecting multiple recurrent somatic mutations in B-cell non-Hodgkin lymphoma (NHLs) samples in a talk entitled “Novel Droplet Digital PCR assays to detect and quantify somatic mutations in cancer tissues and cell-free DNA.”

Research from the Morin laboratory has produced a suite of ddPCR assays for detecting prevalent mutations in B-cell NHLs in fresh tumor, FFPE and liquid biopsies samples. These assays allow for differentiation between and counting of mutant and wild-type molecules using a single hydrolysis probe. Multiplexing was also implemented in assay design, allowing for the simultaneous detection of distinct mutations. These novel techniques overcome limitations in analytical sensitivity, cost, and scalability seen in current mutation detection options and offer a superior option for potential prognosis and therapeutic management in B-cell NHLs.

Scalable Single-Cell Sequencing

Dr. Maroof Adil, postdoctoral researcher in the laboratory of Dr. David Schaffer at the University of California, Berkeley, presented the final talk entitled “Investigating population heterogeneity in 3-D biomaterial human pluripotent stem cell (hPSC) cultures.” This unpublished research aims to understand hPSC population heterogeneity using the Illumina®|Bio-Rad® Single-Cell Sequencing Solution.

Human pluripotent stem cells (hPSCs) can be an unlimited cell source for a variety of biomedical applications including cell replacement therapy, disease modeling, drug and toxicology screening, and in vitro organogenesis. Dr. Adil will present exciting new findings in which single-cell RNA sequencing is used to determine population variation among human induced pluripotent stem cells. The cells were expanded within a chemically-defined 3-D biomaterial platform, which has the potential for scalable production for biomedical and clinical application.

For more information about the Illumina®|Bio-Rad® Single-Cell Sequencing Solution, visit bio-rad.com/ddSEQ.

To learn about additional applications for ddPCR, please visit bio-rad.com/digitalPCR.

The QX200™ Droplet Digital PCR System is intended for research use only.

Read at BioSpace.com


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