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Wahl SGF, Dai HY, Emdal EF, Ottestad AL, Dale VG, Richardsen E, Halvorsen TO, Grønberg BH. Prognostic value of absolute quantification of mutated KRAS in circulating tumour DNA in lung adenocarcinoma patients prior to therapy. J Pathol Clin Res 2021; 7:209-219. [PMID: 33502820 PMCID: PMC8073004 DOI: 10.1002/cjp2.200] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
Droplet digital polymerase chain reaction (ddPCR) is a highly sensitive and accurate method for quantification of nucleic acid sequences. We used absolute quantification of mutated v-Ki-ras2 Kirsten rat sarcoma viral oncogene homology gene (KRAS) by ddPCR to investigate the prognostic role of mutated KRAS in patients with KRAS-mutated lung adenocarcinomas. Pre-treatment plasma samples from 60 patients with stages I-IV KRAS-mutated lung adenocarcinomas were analysed for KRAS mutations. The associations between survival, detectable KRAS mutations in plasma, and the plasma concentration of mutated KRAS were assessed. Overall, 23 of 60 (38%) patients had detectable KRAS mutation in plasma. The percentage of patients with detectable mutation was 8% in stage I, 30% in stage II, 71% in stage III, and 73% in stage IV. Estimated overall median progression-free survival (PFS) and overall survival (OS) were 26.2 months [95% confidence interval (CI) 12.5-39.9] and 50.8 months (95% CI 0-107.3), respectively. Patients with detectable mutations in plasma had significantly worse median PFS compared to patients with undetectable mutation (13.1 versus 70.1 months) and shorter median OS (20.7 versus not reached). High circulating tumour DNA (ctDNA) concentrations of mutated KRAS were significantly associated with shorter PFS [hazard ratio (HR) 1.008, 95% CI 1.004-1.012] and OS (HR 1.007, 95% CI 1.003-1.011). All associations remained statistically significant in multivariable analyses. In conclusion, ddPCR is an accurate and easily feasible technique for quantification of KRAS mutations in ctDNA. The presence of detectable KRAS mutation in plasma at baseline was associated with worse PFS and OS. High concentration of mutated KRAS in ctDNA was an independent negative prognostic factor for both PFS and OS.
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Affiliation(s)
- Sissel Gyrid Freim Wahl
- Department of PathologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
- Department of Clinical and Molecular MedicineNTNU, Norwegian University of Technology and ScienceTrondheimNorway
| | - Hong Yan Dai
- Department of PathologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
- Department of Clinical and Molecular MedicineNTNU, Norwegian University of Technology and ScienceTrondheimNorway
| | - Elisabeth F Emdal
- Department of PathologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
| | - Anine L Ottestad
- Department of Clinical and Molecular MedicineNTNU, Norwegian University of Technology and ScienceTrondheimNorway
| | - Vibeke G Dale
- Department of PathologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
| | - Elin Richardsen
- Department of Medical BiologyUiT, The Arctic University of NorwayTromsøNorway
- Department of Clinical PathologyUniversity Hospital of North NorwayTromsøNorway
| | - Tarje O Halvorsen
- Department of Clinical and Molecular MedicineNTNU, Norwegian University of Technology and ScienceTrondheimNorway
- Department of OncologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
| | - Bjørn Henning Grønberg
- Department of Clinical and Molecular MedicineNTNU, Norwegian University of Technology and ScienceTrondheimNorway
- Department of OncologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
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Dunwell TL, Dailey SC, Ottestad AL, Yu J, Becker PW, Scaife S, Richman SD, Wood HM, Slaney H, Bottomley D, Yang X, Xiao H, Wahl SGF, Grønberg BH, Dai H, Fu G. Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA. Sci Rep 2021; 11:3138. [PMID: 33542447 PMCID: PMC7862664 DOI: 10.1038/s41598-021-82737-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 01/22/2021] [Indexed: 11/12/2022] Open
Abstract
Liquid biopsy testing utilising Next Generation Sequencing (NGS) is rapidly moving towards clinical adoption for personalised oncology. However, before NGS can fulfil its potential any novel testing approach must identify ways of reducing errors, allowing separation of true low-frequency mutations from procedural artefacts, and be designed to improve upon current technologies. Popular NGS technologies typically utilise two DNA capture approaches; PCR and ligation, which have known limitations and seem to have reached a development plateau with only small, stepwise improvements being made. To maximise the ultimate utility of liquid biopsy testing we have developed a highly versatile approach to NGS: Adaptor Template Oligo Mediated Sequencing (ATOM-Seq). ATOM-Seq's strengths and versatility avoid the major limitations of both PCR- and ligation-based approaches. This technology is ligation free, simple, efficient, flexible, and streamlined, and it offers novel advantages that make it perfectly suited for use on highly challenging clinical material. Using reference and clinical materials, we demonstrate detection of known SNVs down to allele frequencies of 0.1% using as little as 20–25 ng of cfDNA, as well as the ability to detect fusions from RNA. We illustrate ATOM-Seq’s suitability for clinical testing by showing high concordance rates between paired cfDNA and FFPE clinical samples.
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Affiliation(s)
- Thomas L Dunwell
- GeneFirst Ltd, Building E5, Culham Science Centre, Abingdon, OX14 3DB, UK
| | - Simon C Dailey
- GeneFirst Ltd, Building E5, Culham Science Centre, Abingdon, OX14 3DB, UK
| | - Anine L Ottestad
- Department of Oncology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jihang Yu
- GeneFirst Ltd, Building E5, Culham Science Centre, Abingdon, OX14 3DB, UK
| | - Philipp W Becker
- GeneFirst Ltd, Building E5, Culham Science Centre, Abingdon, OX14 3DB, UK
| | - Sarah Scaife
- GeneFirst Ltd, Building E5, Culham Science Centre, Abingdon, OX14 3DB, UK
| | - Susan D Richman
- Pathology and Data Analytics, Leeds Institute of Medical Research, University of Leeds, St James University Hospital, Leeds, LS9 7TF, UK
| | - Henry M Wood
- Pathology and Data Analytics, Leeds Institute of Medical Research, University of Leeds, St James University Hospital, Leeds, LS9 7TF, UK
| | - Hayley Slaney
- Pathology and Data Analytics, Leeds Institute of Medical Research, University of Leeds, St James University Hospital, Leeds, LS9 7TF, UK
| | - Daniel Bottomley
- Pathology and Data Analytics, Leeds Institute of Medical Research, University of Leeds, St James University Hospital, Leeds, LS9 7TF, UK
| | - Xiangsheng Yang
- Guangzhou Biotron Technology Co., Ltd, Room 204, Zone C, Science and Technology Innovation Base, No. 80, Lanyue Road, Science City, Guangzhou, China
| | - Hui Xiao
- Guangzhou Biotron Technology Co., Ltd, Room 204, Zone C, Science and Technology Innovation Base, No. 80, Lanyue Road, Science City, Guangzhou, China
| | - Sissel G F Wahl
- Department of Oncology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Bjørn H Grønberg
- Department of Oncology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Hongyan Dai
- Department of Oncology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway.,Department of Pathology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Guoliang Fu
- GeneFirst Ltd, Building E5, Culham Science Centre, Abingdon, OX14 3DB, UK.
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