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Rowlands V, Rutkowski AJ, Meuser E, Carr TH, Harrington EA, Barrett JC. Optimisation of robust singleplex and multiplex droplet digital PCR assays for high confidence mutation detection in circulating tumour DNA. Sci Rep 2019; 9:12620. [PMID: 31477768 PMCID: PMC6718424 DOI: 10.1038/s41598-019-49043-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 08/12/2019] [Indexed: 12/20/2022] Open
Abstract
Liquid biopsies offer the potential to monitor cancer response and resistance to therapeutics in near real-time. However, the plasma cell free DNA (cfDNA) level can be low and the fraction of circulating tumour DNA (ctDNA) bearing a mutation - lower still. Detection of tumour-derived mutations in ctDNA is thus challenging and requires highly sensitive and specific assays. Droplet digital PCR (ddPCR) is a technique that enables exquisitely sensitive detection and quantification of DNA/RNA markers from very limiting clinical samples, including plasma. The Bio-Rad QX200 ddPCR system provides absolute quantitation of target DNA molecules using fluorescent dual-labelled probes. Critical to accurate sample analysis are validated assays that are highly specific, reproducible, and with known performance characteristics, especially with respect to false positives. We present a systematic approach to the development and optimisation of singleplex and multiplex ddPCR assays for the detection of point mutations with a focus on ensuring extremely low false positives whilst retaining high sensitivity. We also present a refined method to determine cfDNA extraction efficiency allowing for more accurate extrapolation of mutational levels in source samples. We have applied these approaches to successfully analyse many ctDNA samples from multiple clinical studies and generated exploratory data of high quality.
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Affiliation(s)
- Vicky Rowlands
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK.
| | - Andrzej J Rutkowski
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK.,Medicines Discovery Catapult, Block 35, Mereside, Alderley Park, Alderley Edge, Cheshire, SK10 4TG, UK
| | - Elena Meuser
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - T Hedley Carr
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | | | - J Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Boston, USA
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Cravero K, Medford A, Pallavajjala A, Canzoniero J, Hunter N, Chu D, Cochran RL, Waters I, Christenson ES, Kyker-Snowman K, Button B, Cole AJ, Park BH. Biotinylated amplicon sequencing: A method for preserving DNA samples of limited quantity. Pract Lab Med 2018; 12:e00108. [PMID: 30140723 PMCID: PMC6104457 DOI: 10.1016/j.plabm.2018.e00108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 07/06/2018] [Accepted: 08/08/2018] [Indexed: 11/24/2022] Open
Abstract
Background Genomic testing is often limited by the exhaustible nature of human tissue and blood samples. Here we describe biotinylated amplicon sequencing (BAmSeq), a method that allows for the creation of PCR amplicon based next-generation sequencing (NGS) libraries while retaining the original source DNA. Design and methods Biotinylated primers for different loci were designed to create NGS libraries using human genomic DNA from cell lines, plasma, and formalin-fixed paraffin embedded (FFPE) tissues using the BAmSeq protocol. DNA from the original template used for each BAmSeq library was recovered after separation with streptavidin magnetic beads. The recovered DNA was then used for end-point, quantitative and droplet digital PCR (ddPCR) as well as NGS using a cancer gene panel. Results Recovered DNA was analyzed and compared to the original DNA after one or two rounds of BAmSeq. Recovered DNA revealed comparable genomic distributions and mutational allelic frequencies when compared to original source DNA. Sufficient quantities of recovered DNA after BAmSeq were obtained, allowing for additional downstream applications. Conclusions We demonstrate that BAmSeq allows original DNA template to be recovered with comparable quality and quantity to the source DNA. This recovered DNA is suitable for many downstream applications and may prevent sample exhaustion, especially when DNA quantity or source material is limiting. Modification of targeted panel sequencing allows for recovery of original DNA template. Protocol provides value in the setting of scarce DNA template. Recovered DNA is suitable for NGS, ddPCR and qPCR. Recovered DNA shows no loss of genomic regions.
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Affiliation(s)
- Karen Cravero
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Arielle Medford
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Aparna Pallavajjala
- The Sidney Kimmel Comprehensive Cancer Center, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jenna Canzoniero
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Natasha Hunter
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - David Chu
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rory L Cochran
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ian Waters
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Eric S Christenson
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Kelly Kyker-Snowman
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Berry Button
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Alex J Cole
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ben Ho Park
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States.,The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
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