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Ottestad AL, Johansen H, Halvorsen TO, Dai HY, Wahl SGF, Emdal EF, Grønberg BH. Correction: Associations between detectable circulating tumor DNA and tumor glucose uptake measured by 18F-FDG PET/CT in early-stage non-small cell lung cancer. BMC Cancer 2023; 23:685. [PMID: 37474938 DOI: 10.1186/s12885-023-11173-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023] Open
Affiliation(s)
- Anine Larsen Ottestad
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, 7030, Norway.
- Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway.
| | - Håkon Johansen
- Department of Radiology and Nuclear Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
| | - Tarje Onsøien Halvorsen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, 7030, Norway
- Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
| | - Hong Yan Dai
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, 7030, Norway
- Department of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
| | - Sissel Gyrid Freim Wahl
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, 7030, Norway
- Department of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
| | - Elisabeth Fritzke Emdal
- Department of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
| | - Bjørn Henning Grønberg
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, 7030, Norway
- Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
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Ottestad AL, Johansen H, Halvorsen TO, Dai HY, Wahl SGF, Emdal EF, Grønberg BH. Associations between detectable circulating tumor DNA and tumor glucose uptake measured by 18F-FDG PET/CT in early-stage non-small cell lung cancer. BMC Cancer 2023; 23:646. [PMID: 37434111 PMCID: PMC10334612 DOI: 10.1186/s12885-023-11147-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND The low level of circulating tumor DNA (ctDNA) in the blood is a well-known challenge for the application of liquid biopsies in early-stage non-small cell lung cancer (NSCLC) management. Studies of metastatic NSCLC indicate that ctDNA levels are associated with tumor metabolic activity as measured by 18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET/CT). This study investigated this association in NSCLC patients considered for potentially curative treatment and explored whether the two methods provide independent prognostic information. METHOD Patients with stage I-III NSCLC who had routinely undergone an 18F-FDG PET/CT scan and exploratory ctDNA analyses were included. Tumor glucose uptake was measured by maximum standardized uptake value (SUVmax), metabolic tumor volume (MTV), and total lesion glycolysis (TLG) from the 18F-FDG PET/CT scans. ctDNA detectability and quantity, using variant allele frequency, were estimated by tumor-informed ctDNA analyses. RESULTS In total, 63 patients (median age 70 years, 60% women, and 90% adenocarcinoma) were included. The tumor glucose uptake (SUVmax, MTV, and TLG) was significantly higher in patients with detectable ctDNA (n = 19, p < 0.001). The ctDNA quantity correlated with MTV (Spearman's ρ = 0.53, p = 0.021) and TLG (Spearman's ρ = 0.56, p = 0.013) but not with SUVmax (Spearman's ρ = 0.034, p = 0.15). ctDNA detection was associated with shorter OS independent of MTV (HR: 2.70, 95% CI: 1.07-6.82, p = 0.035) and TLG (HR: 2.63, 95% CI: 1.06-6.51, p = 0.036). Patients with high tumor glucose uptake and detectable ctDNA had shorter overall survival and progression-free survival than those without detectable ctDNA, though these associations were not statistically significant (p > 0.05). CONCLUSION There was a positive correlation between plasma ctDNA quantity and MTV and TLG in early-stage NSCLC patients. Despite the correlation, the results indicated that ctDNA detection was a negative prognostic factor independent of MTV and TLG.
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Affiliation(s)
- Anine Larsen Ottestad
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, 7030, Norway.
- Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway.
| | - Håkon Johansen
- Department of Radiology and Nuclear Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
| | - Tarje Onsøien Halvorsen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, 7030, Norway
- Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
| | - Hong Yan Dai
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, 7030, Norway
- Department of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
| | - Sissel Gyrid Freim Wahl
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, 7030, Norway
- Department of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
| | - Elisabeth Fritzke Emdal
- Department of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
| | - Bjørn Henning Grønberg
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, 7030, Norway
- Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
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Ottestad AL, Huang M, Emdal EF, Mjelle R, Skarpeteig V, Dai HY. Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment. J Pers Med 2022; 13:jpm13010042. [PMID: 36675703 PMCID: PMC9863125 DOI: 10.3390/jpm13010042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
(1) Background: Analysis of tumor DNA by next-generation sequencing (NGS) plays various roles in the classification and management of cancer. This study aimed to assess the performance of two similar and large, comprehensive gene panels with a focus on clinically relevant variant detection and tumor mutation burden (TMB) assessment; (2) Methods: DNA from 19 diagnostic small cell lung cancer biopsies and an AcroMetrix™ assessment sample with >500 mutations were sequenced using Oncomine™ Comprehensive Assay Plus (OCAP) on the Ion Torrent platform and TruSight Oncology 500 Assay (TSO500) on the Illumina platform; (3) Results: OCAP and TSO500 achieved comparable NGS quality, such as mean read coverage and mean coverage uniformity. A total of 100% of the variants in the diagnostic samples and 80% of the variants in the AcroMetrix™ assessment sample were detected by both panels, and the panels reported highly similar variant allele frequency. A proportion of 14/19 (74%) samples were classified in the same TMB category; (4) Conclusions: Comparable results were obtained using OCAP and TSO500, suggesting that both panels could be applied to screen patients for enrolment in personalized cancer treatment trials.
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Affiliation(s)
- Anine Larsen Ottestad
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7030 Trondheim, Norway
- Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
- Correspondence:
| | - Mo Huang
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7030 Trondheim, Norway
- Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
- Department of Biosciences and Nutrition, Karolinska Institute, 17177 Stockholm, Sweden
| | - Elisabeth Fritzke Emdal
- Department of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
| | - Robin Mjelle
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7030 Trondheim, Norway
- Department of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
| | - Veronica Skarpeteig
- Department of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
| | - Hong Yan Dai
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7030 Trondheim, Norway
- Department of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
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Ottestad AL, Emdal EF, Grønberg BH, Halvorsen TO, Dai HY. Fragmentation assessment of FFPE DNA helps in evaluating NGS library complexity and interpretation of NGS results. Exp Mol Pathol 2022; 126:104771. [DOI: 10.1016/j.yexmp.2022.104771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 03/13/2022] [Accepted: 04/09/2022] [Indexed: 11/04/2022]
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Ottestad AL, Dai HY, Halvorsen TO, Emdal EF, Wahl SGF, Grønberg BH. Associations between tumor mutations in cfDNA and survival in non-small cell lung cancer. Cancer Treat Res Commun 2021; 29:100471. [PMID: 34607221 DOI: 10.1016/j.ctarc.2021.100471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Studies have indicated that detection of mutated KRAS or EGFR in circulating tumor DNA (ctDNA) from pre-treatment plasma samples is a negative prognostic factor for non-small cell lung cancer (NSCLC) patients. This study aims to investigate whether this is the case also for NSCLC patients with other tumor mutations. METHODS Tumor tissue DNA from 107 NSCLC patients was sequenced and corresponding pre-treatment plasma samples were analyzed using a limited target next-generation sequencing approach validated in this study. Patients without detected mutations in tumor samples were excluded from further analyses. RESULTS Mutations were detected in tumor samples from 71 patients. Median age was 68 years, 51% were female, and 88% were current/former smokers, 91% had adenocarcinoma, 4% had squamous cell carcinoma and 6% had other NSCLC. The distribution between stage I, II, III and IV was 33%, 8%, 30%, and 29%, respectively. Between one and three tumor mutation(s) were detected in ctDNA from corresponding plasma samples. Patients with detected ctDNA had shorter PFS (9.6 vs. 41.3 months, HR: 2.9, 95% CI: 1.6-5.2, p = 0.0003) and OS (13.6 vs. 115.0 months, HR: 4.0, 95% CI: 2.1-7.6, p = 0.00002) than patients without detected ctDNA. ctDNA remained a significant negative prognostic factor for OS (HR: 2.5, 95% CI: 1.1-5.7, p=0.0327), but not PFS, in the multivariable analyses adjusting for baseline patient and disease characteristics including stage of disease. CONCLUSIONS This study adds further evidence supporting that detectable tumor mutations in cfDNA is associated with a worse prognosis in NSCLC harboring a variety of tumor mutations.
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Affiliation(s)
- Anine Larsen Ottestad
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Department of Oncology, Cancer Clinic, St. Olav's Hospital, Trondheim University Hospital, 7006, Trondheim, Norway
| | - Hong Yan Dai
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Department of Pathology, Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim University Hospital, 7006 Trondheim, Norway
| | - Tarje Onsøien Halvorsen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Department of Oncology, Cancer Clinic, St. Olav's Hospital, Trondheim University Hospital, 7006, Trondheim, Norway
| | - Elisabeth Fritzke Emdal
- Department of Pathology, Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim University Hospital, 7006 Trondheim, Norway
| | - Sissel Gyrid Freim Wahl
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Department of Pathology, Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim University Hospital, 7006 Trondheim, Norway
| | - Bjørn Henning Grønberg
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Department of Oncology, Cancer Clinic, St. Olav's Hospital, Trondheim University Hospital, 7006, Trondheim, Norway.
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Wahl SGF, Dai HY, Emdal EF, Berg T, Halvorsen TO, Ottestad AL, Lund-Iversen M, Brustugun OT, Førde D, Paulsen EE, Donnem T, Andersen S, Grønberg BH, Richardsen E. The Prognostic Effect of KRAS Mutations in Non-Small Cell Lung Carcinoma Revisited: A Norwegian Multicentre Study. Cancers (Basel) 2021; 13:4294. [PMID: 34503114 PMCID: PMC8428342 DOI: 10.3390/cancers13174294] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND due to emerging therapeutics targeting KRAS G12C and previous reports with conflicting results regarding the prognostic impact of KRAS and KRAS G12C in non-small cell lung cancer (NSCLC), we aimed to investigate the frequency of KRAS mutations and their associations with clinical characteristics and outcome. Since mutation subtypes have different preferences for downstream pathways, we also aimed to investigate whether there were differences in outcome according to mutation preference for the Raf, PI3K/Akt, or RalGDS/Ral pathways. METHODS retrospectively, clinicopathological data from 1233 stage I-IV non-squamous NSCLC patients with known KRAS status were reviewed. KRAS' associations with clinical characteristics were analysed. Progression free survival (PFS) and overall survival (OS) were assessed for the following groups: KRAS wild type (wt) versus mutated, KRAS wt versus KRAS G12C versus KRAS non-G12C, among KRAS mutation subtypes and among mutation subtypes grouped according to preference for downstream pathways. RESULTS a total of 1117 patients were included; 38% had KRAS mutated tumours, 17% had G12C. Among KRAS mutated, G12C was the most frequent mutation in former/current smokers (45%) and G12D in never smokers (46%). There were no significant differences in survival according to KRAS status, G12C status, among KRAS mutation subtypes or mutation preference for downstream pathways. CONCLUSION KRAS status or KRAS mutation subtype did not have any significant influence on PFS or OS.
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Affiliation(s)
- Sissel Gyrid Freim Wahl
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Technology and Science, N-7491 Trondheim, Norway; (H.Y.D.); (T.O.H.); (A.L.O.); (B.H.G.)
- Department of Pathology, St. Olav’s Hospital, Trondheim University Hospital, N-7006 Trondheim, Norway;
| | - Hong Yan Dai
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Technology and Science, N-7491 Trondheim, Norway; (H.Y.D.); (T.O.H.); (A.L.O.); (B.H.G.)
- Department of Pathology, St. Olav’s Hospital, Trondheim University Hospital, N-7006 Trondheim, Norway;
| | - Elisabeth Fritzke Emdal
- Department of Pathology, St. Olav’s Hospital, Trondheim University Hospital, N-7006 Trondheim, Norway;
| | - Thomas Berg
- Department of Clinical Pathology, University Hospital of North Norway, N-9038 Tromsø, Norway; (T.B.); (E.R.)
- Department of Medical Biology, UiT, The Arctic University of Norway, N-9011 Tromsø, Norway
| | - Tarje Onsøien Halvorsen
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Technology and Science, N-7491 Trondheim, Norway; (H.Y.D.); (T.O.H.); (A.L.O.); (B.H.G.)
- Department of Oncology, St. Olav’s Hospital, Trondheim University Hospital, N-7030 Trondheim, Norway
| | - Anine Larsen Ottestad
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Technology and Science, N-7491 Trondheim, Norway; (H.Y.D.); (T.O.H.); (A.L.O.); (B.H.G.)
- Department of Oncology, St. Olav’s Hospital, Trondheim University Hospital, N-7030 Trondheim, Norway
| | - Marius Lund-Iversen
- Department of Pathology, Oslo University Hospital, The Norwegian Radium Hospital, N-0310 Oslo, Norway;
| | - Odd Terje Brustugun
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, N-0450 Oslo, Norway;
- Section of Oncology, Drammen Hospital, Vestre Viken Hospital Trust, N-3004 Drammen, Norway
| | - Dagny Førde
- Department of Clinical Medicine, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway; (D.F.); (T.D.); (S.A.)
| | - Erna-Elise Paulsen
- Department of Pulmonary Medicine, University Hospital of North Norway, N-9028 Tromsø, Norway;
| | - Tom Donnem
- Department of Clinical Medicine, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway; (D.F.); (T.D.); (S.A.)
- Department of Oncology, University Hospital of North Norway, N-9038 Tromsø, Norway
| | - Sigve Andersen
- Department of Clinical Medicine, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway; (D.F.); (T.D.); (S.A.)
- Department of Oncology, University Hospital of North Norway, N-9038 Tromsø, Norway
| | - Bjørn Henning Grønberg
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Technology and Science, N-7491 Trondheim, Norway; (H.Y.D.); (T.O.H.); (A.L.O.); (B.H.G.)
- Department of Oncology, St. Olav’s Hospital, Trondheim University Hospital, N-7030 Trondheim, Norway
| | - Elin Richardsen
- Department of Clinical Pathology, University Hospital of North Norway, N-9038 Tromsø, Norway; (T.B.); (E.R.)
- Department of Medical Biology, UiT, The Arctic University of Norway, N-9011 Tromsø, Norway
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Ottestad AL, Emdal EF, Wahl SG, Grønberg BH, Dai HY. Abstract 3099: Ultra-deep next-generation sequencing of selected single genes for detecting circulating tumor DNA in lung cancer patients. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3099] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose
Circulating tumor DNA (ctDNA) can potentially be used to monitor cancer treatment response. In this study, we developed and used a sensitive and selective ultra-deep next-generation sequencing (NGS) approach for detection of ctDNA in lung cancer patients.
Method
Most studies use fixed gene panels for detection of ctDNA by NGS. Deep sequencing of large target regions is expensive and generates a myriad of variants, which are difficult to interpret. For the purpose of using ctDNA for monitoring, we try to overcome these challenges by sequencing only selected regions where mutations were previously found in the tumor. This method is more sensitive and cost-efficient.
In this study, we included about 80 lung cancer patients. Tumor DNA was sequenced with a large gene panel and somatic mutations were identified in each tumor. We then defined the target region according to the tumor mutations and selected primers for constructing NGS libraries. Since the coverage region is small it enables ultra-deep sequencing of several samples simultaneously.
We evaluated the lower limit of detection for this method by sequencing a series of artificially constructed samples with known mutant allele frequencies (MAFs). DNA from peripheral blood leucocytes was sequenced in parallel with plasma DNA to exclude variants from clonal hematopoiesis.
Preliminary results
Using 40 ng as input DNA, which contains approximately 12,000 haploid genomes, we detected mutations down to 0.02% MAF. This corresponds to about 6 mutated copies per mL plasma. Currently, we are applying this method on patient plasma DNA samples.
Conclusion
We have developed a sensitive method for ctDNA detection, and we will present the results of the lung cancer patient samples.
Citation Format: Anine Larsen Ottestad, Elisabeth F. Emdal, Sissel G. Wahl, Bjørn Henning Grønberg, Hong Yan Dai. Ultra-deep next-generation sequencing of selected single genes for detecting circulating tumor DNA in lung cancer patients [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3099.
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Affiliation(s)
| | | | - Sissel G. Wahl
- 1Norwegian University of Science and Technology, Trondheim, Norway
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Ottestad AL, Wahl SGF, Grønberg BH, Skorpen F, Dai HY. The relevance of tumor mutation profiling in interpretation of NGS data from cell-free DNA in non-small cell lung cancer patients. Exp Mol Pathol 2019; 112:104347. [PMID: 31759951 DOI: 10.1016/j.yexmp.2019.104347] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/11/2019] [Accepted: 11/19/2019] [Indexed: 11/26/2022]
Abstract
Studies have indicated that detection of circulating tumor DNA (ctDNA) prior to treatment is a negative prognostic marker in non-small cell lung cancer (NSCLC). ctDNA is currently identified by detection of tumor mutations. Commercial next-generation sequencing (NGS) assays for mutation analysis of ctDNA for routine practice usually include small gene panels and are not suitable for general mutation analysis. In this study, we investigated whether mutation analysis of cfDNA could be performed using a commercially available comprehensive NGS gene panel and bioinformatics workflow. Tumor DNA, plasma DNA and peripheral blood leukocyte DNA from 30 NSCLC patients were sequenced. In two patients (7%), tumor mutations in cfDNA were immediately called by the bioinformatic workflow. In 13 patients (43%), tumor mutations were not called, but were present in ctDNA and were identified based on the known tumor mutation profile. In the remaining 15 patients (50%), no concordant mutations were detected. In conclusion, we were able to identify tumor mutations in ctDNA from 57% of NSCLC patients using a comprehensive gene panel. We demonstrated that sequencing paired tumor DNA was helpful to interpret data and confirm ctDNA, and thus increased the ratio of patients with detectable ctDNA. This approach might be feasible for mutation analysis of ctDNA in routine diagnostic practice, especially in case of suboptimal plasma quality and quantity.
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Affiliation(s)
- Anine Larsen Ottestad
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Cancer Clinic, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway.
| | - Sissel G F Wahl
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Department of Pathology, Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Bjørn Henning Grønberg
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Cancer Clinic, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Frank Skorpen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Cancer Clinic, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Hong Yan Dai
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Department of Pathology, Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
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