Ben O'Leary1,2, Sarah Hrebien1, Matthew Beaney1, Charlotte Fribbens1,2, Isaac Garcia-Murillas1, John Jiang3, Yuan Li3, Cynthia Huang Bartlett3, Fabrice André4, Sibylle Loibl5, Sherene Loi6, Massimo Cristofanilli7, Nicholas C Turner8,2. 1. Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK. 2. Breast Unit, Royal Marsden Hospital, London, UK. 3. Pfizer, New York, NY. 4. Department of Medical Oncology, Institut Gustave Roussy, Villejuif, France. 5. German Breast Group, Neu-Isenburg, Germany. 6. Division of Research and Cancer Medicine, University of Melbourne, Peter MacCallum Cancer Centre, Melbourne, Australia. 7. Robert H. Lurie Comprehensive Cancer Centre, Feinberg School of Medicine, Chicago, IL. 8. Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK; nicholas.turner@icr.ac.uk.
Abstract
BACKGROUND: Circulating tumor DNA (ctDNA) assays are increasingly used for clinical decision-making, but it is unknown how well different assays agree. We aimed to assess the agreement in ctDNA mutation calling between BEAMing (beads, emulsion, amplification, and magnetics) and droplet digital PCR (ddPCR), 2 of the most commonly used digital PCR techniques for detecting mutations in ctDNA. METHODS: Baseline plasma samples from patients with advanced breast cancer enrolled in the phase 3 PALOMA-3 trial were assessed for ESR1 and PIK3CA mutations in ctDNA with both BEAMing and ddPCR. Concordance between the 2 approaches was assessed, with exploratory analyses to estimate the importance of sampling effects. RESULTS: Of the 521 patients enrolled, 363 had paired baseline ctDNA analysis. ESR1 mutation detection was 24.2% (88/363) for BEAMing and 25.3% (92/363) for ddPCR, with good agreement between the 2 techniques (κ = 0.9l; 95% CI, 0.85-0.95). PIK3CA mutation detection rates were 26.2% (95/363) for BEAMing and 22.9% (83/363) for ddPCR, with good agreement (κ = 0.87; 95% CI, 0.81-0.93). Discordancy was observed for 3.9% patients with ESR1 mutations and 5.0% with PIK3CA mutations. Assessment of individual mutations suggested higher rates of discordancy for less common mutations (P = 0.019). The majority of discordant calls occurred at allele frequency <1%, predominantly resulting from stochastic sampling effects. CONCLUSIONS: This large, clinically relevant comparison showed good agreement between BEAMing and ddPCR, suggesting sufficient reproducibility for clinical use. Much of the observed discordancy may be related to sampling effects, potentially explaining many of the differences in the currently available ctDNA literature.
BACKGROUND: Circulating tumor DNA (ctDNA) assays are increasingly used for clinical decision-making, but it is unknown how well different assays agree. We aimed to assess the agreement in ctDNA mutation calling between BEAMing (beads, emulsion, amplification, and magnetics) and droplet digital PCR (ddPCR), 2 of the most commonly used digital PCR techniques for detecting mutations in ctDNA. METHODS: Baseline plasma samples from patients with advanced breast cancer enrolled in the phase 3 PALOMA-3 trial were assessed for ESR1 and PIK3CA mutations in ctDNA with both BEAMing and ddPCR. Concordance between the 2 approaches was assessed, with exploratory analyses to estimate the importance of sampling effects. RESULTS: Of the 521 patients enrolled, 363 had paired baseline ctDNA analysis. ESR1 mutation detection was 24.2% (88/363) for BEAMing and 25.3% (92/363) for ddPCR, with good agreement between the 2 techniques (κ = 0.9l; 95% CI, 0.85-0.95). PIK3CA mutation detection rates were 26.2% (95/363) for BEAMing and 22.9% (83/363) for ddPCR, with good agreement (κ = 0.87; 95% CI, 0.81-0.93). Discordancy was observed for 3.9% patients with ESR1 mutations and 5.0% with PIK3CA mutations. Assessment of individual mutations suggested higher rates of discordancy for less common mutations (P = 0.019). The majority of discordant calls occurred at allele frequency <1%, predominantly resulting from stochastic sampling effects. CONCLUSIONS: This large, clinically relevant comparison showed good agreement between BEAMing and ddPCR, suggesting sufficient reproducibility for clinical use. Much of the observed discordancy may be related to sampling effects, potentially explaining many of the differences in the currently available ctDNA literature.
Authors: Sukhkaran S Aulakh; Dustin A Silverman; Kurtis Young; Steven K Dennis; Andrew C Birkeland Journal: Cancers (Basel) Date: 2022-06-16 Impact factor: 6.575
Authors: Georgios Nteliopoulos; Karen Page; Allison Hills; Karen Howarth; Warren Emmett; Emma Green; Luke J Martinson; Daniel Fernadez-Garcia; Robert Hastings; David S Guttery; Laura Kenny; Justin Stebbing; Susan Cleator; Farah Rehman; Kelly L T Gleason; Andrijac Sanela; Charlotte Ion; Amelia J Rushton; Nitzan Rosenfeld; R Charles Coombes; Jacqueline A Shaw Journal: Breast Cancer Res Treat Date: 2021-06-07 Impact factor: 4.872
Authors: Elisa Izquierdo; Paula Proszek; Giulia Pericoli; Sara Temelso; Matthew Clarke; Diana M Carvalho; Alan Mackay; Lynley V Marshall; Fernando Carceller; Darren Hargrave; Birgitta Lannering; Zdenek Pavelka; Simon Bailey; Natacha Entz-Werle; Jacques Grill; Gilles Vassal; Daniel Rodriguez; Paul S Morgan; Tim Jaspan; Angela Mastronuzzi; Mara Vinci; Michael Hubank; Chris Jones Journal: Neurooncol Adv Date: 2021-01-27