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Ladel L, Tan WY, Jeyakanthan T, Sailo B, Sharma A, Ahuja N. The Promise of Epigenetics Research in the Treatment of Appendiceal Neoplasms. Cells 2023; 12:1962. [PMID: 37566041 PMCID: PMC10417136 DOI: 10.3390/cells12151962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
Appendiceal cancers (AC) are a rare and heterogeneous group of malignancies. Historically, appendiceal neoplasms have been grouped with colorectal cancers (CRC), and treatment strategies have been modeled after CRC management guidelines due to their structural similarities and anatomical proximity. However, the two have marked differences in biological behavior and treatment response, and evidence suggests significant discrepancies in their respective genetic profiles. In addition, while the WHO classification for appendiceal cancers is currently based on traditional histopathological criteria, studies have demonstrated that histomorphology does not correlate with survival or treatment response in AC. Due to their rarity, appendiceal cancers have not been studied as extensively as other gastrointestinal cancers. However, their incidence has been increasing steadily over the past decade, making it crucial to identify new and more effective strategies for detection and treatment. Recent efforts to map and understand the molecular landscape of appendiceal cancers have unearthed a wealth of information that has made it evident that appendiceal cancers possess a unique molecular profile, distinct from other gastrointestinal cancers. This review focuses on the epigenetic landscape of epithelial appendiceal cancers and aims to provide a comprehensive overview of the current state of knowledge of epigenetic changes across different appendiceal cancer subtypes, highlighting the challenges as well as the promise of employing epigenetics in the quest for the detection of biomarkers, therapeutic targets, surveillance markers, and predictors of treatment response and survival in epithelial appendiceal neoplasms.
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Affiliation(s)
- Luisa Ladel
- Surgical Oncology Research Laboratories, Division of Surgical Oncology, Department of Surgery, Yale School of Medicine, Yale University, New Haven, CT 06519, USA; (L.L.); (W.Y.T.); (T.J.); (B.S.); (A.S.)
- Affiliated Internal Medicine Residency Program at Norwalk Hospital, Department of Internal Medicine, Norwalk Hospital, Yale University, Norwalk, CT 06850, USA
| | - Wan Ying Tan
- Surgical Oncology Research Laboratories, Division of Surgical Oncology, Department of Surgery, Yale School of Medicine, Yale University, New Haven, CT 06519, USA; (L.L.); (W.Y.T.); (T.J.); (B.S.); (A.S.)
- Affiliated Internal Medicine Residency Program at Norwalk Hospital, Department of Internal Medicine, Norwalk Hospital, Yale University, Norwalk, CT 06850, USA
| | - Thanushiya Jeyakanthan
- Surgical Oncology Research Laboratories, Division of Surgical Oncology, Department of Surgery, Yale School of Medicine, Yale University, New Haven, CT 06519, USA; (L.L.); (W.Y.T.); (T.J.); (B.S.); (A.S.)
- Affiliated Internal Medicine Residency Program at Norwalk Hospital, Department of Internal Medicine, Norwalk Hospital, Yale University, Norwalk, CT 06850, USA
| | - Bethsebie Sailo
- Surgical Oncology Research Laboratories, Division of Surgical Oncology, Department of Surgery, Yale School of Medicine, Yale University, New Haven, CT 06519, USA; (L.L.); (W.Y.T.); (T.J.); (B.S.); (A.S.)
| | - Anup Sharma
- Surgical Oncology Research Laboratories, Division of Surgical Oncology, Department of Surgery, Yale School of Medicine, Yale University, New Haven, CT 06519, USA; (L.L.); (W.Y.T.); (T.J.); (B.S.); (A.S.)
| | - Nita Ahuja
- Surgical Oncology Research Laboratories, Division of Surgical Oncology, Department of Surgery, Yale School of Medicine, Yale University, New Haven, CT 06519, USA; (L.L.); (W.Y.T.); (T.J.); (B.S.); (A.S.)
- Department of Pathology, Yale School of Medicine, New Haven, CT 06519, USA
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2
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Afolabi HA, Salleh SM, Zakaria Z, Ch’ng ES, Mohd Nafi SN, Abdul Aziz AAB, Irekeola AA, Wada Y, Al-Mhanna SB. A GNAS Gene Mutation's Independent Expression in the Growth of Colorectal Cancer: A Systematic Review and Meta-Analysis. Cancers (Basel) 2022; 14:cancers14225480. [PMID: 36428574 PMCID: PMC9688108 DOI: 10.3390/cancers14225480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
Globally, colorectal carcinoma CRC is the third most common cancer and the third most common reason for cancer-associated mortality in both genders. The GNAS mutations are significantly linked with poor prognosis and failed treatment outcomes in CRC. A systematic review and meta-analysis of multiple studies executed following Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) criteria and registered with PROSPERO (registration number: CRD42021256452). The initial search includes a total of 271 publications; however, only 30 studies that merit the eligibility criteria were eventually chosen. Data analysis via OpenMeta Analyst and comprehensive meta-analysis 3.0 (CMA 3.0) software were used to investigate the prevalence of GNAS gene mutation among CRC patients. The meta-analysis consisted of 10,689 participants with most being males 6068/10,689 (56.8%). Overall, prevalence of GNAS mutations was 4.8% (95% CI: 3.1−7.3) with I2 = 94.39% and (p < 0.001). In 11/30 studies, the frequency of GNAS gene mutations was majorly in codons R201C [40.7% (95% CI: 29.2−53.2%)] and in codon R201H [39.7% (95% CI = 27.1−53.8)]. Overall prevalence of GNAS mutations was highest among the male gender: 53.9% (95% CI: 48.2−59.5%: I2 = 94.00%, (p < 0.001), tumour location (colon): 50.5% (95% CI: 33.2−67.6%: I2 = 97.93%, (p < 0.001), tumour grade (Well): 57.5% (95% CI: 32.4−79.2%: I2 = 98.10%, (p < 0.001) and tumour late stage: 67.9% (95% CI: 49.7−84.3%: I2 = 98.%, (p < 0.001). When stratified according to study location, a higher prevalence was observed in Japan (26.8%) while Italy has the lowest (0.4%). Overall prevalence of GNAS gene mutations was 4.8% with codons R201C and R201H being the most mutated, and the results conformed with numerous published studies on GNAS mutation.
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Affiliation(s)
- Hafeez Abiola Afolabi
- Department of General Surgery, School of Medical Sciences, Hospital Universiti Sains Malaysia, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Salzihan Md Salleh
- Department of Pathology, School of Medical Sciences, Hospital Universiti Sains Malaysia (HUSM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia (USM), Health Campus, Kubang Kerian 16150, Malaysia
- Correspondence: or
| | - Zaidi Zakaria
- Department of General Surgery, School of Medical Sciences, Hospital Universiti Sains Malaysia, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Ewe Seng Ch’ng
- Advanced Medical and Dental Institute, Universiti Sains Malaysia USM, Kepala Batas 13200, Malaysia
| | - Siti Norasikin Mohd Nafi
- Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia (USM), Health Campus, Kubang Kerian 16150, Malaysia
| | - Ahmad Aizat Bin Abdul Aziz
- Department of Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Ahmad Adebayo Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Yusuf Wada
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Sameer Badri Al-Mhanna
- Department of Physiology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
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3
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Nazha B, Zhuang TZ, Dada HI, Drusbosky LM, Brown JT, Ravindranathan D, Carthon BC, Kucuk O, Goldman J, Master VA, Bilen MA. Blood-Based Next-Generation Sequencing in Adrenocortical Carcinoma. Oncologist 2022; 27:462-468. [PMID: 35462410 PMCID: PMC9177103 DOI: 10.1093/oncolo/oyac061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/16/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Adrenocortical carcinoma (ACC) is a rare and heterogeneous malignancy with poor prognosis. We aimed to evaluate the feasibility of next-generation sequencing (NGS) testing of circulating cell-free tumor DNA (ctDNA) in patients with ACC, to characterize the genomic landscape of alterations, and to identify potential clinically actionable mutations. METHODS Retrospective analysis of genomic data from 120 patients with ACC who had ctDNA testing between 12/2016 and 10/2021 using Guardant360 (Guardant Health, CA) was performed. ctDNA NGS analysis interrogated single nucleotide variants, fusions, indels, and copy number amplifications of up to 83 genes. The frequency of genomic alterations, landscape of co-occurring mutations, and pathogenic/likely pathogenic alterations with potential targeted therapies was identified. The prevalence of alterations identified in ctDNA was compared to those detected in tissue using a publicly available database (cBioPortal). RESULTS The median age of this cohort was 53 years (range 21-81), and 56% of patients were female. Ninety-six patients (80%) had ≥1 somatic alteration detected. TP53 (52%), EGFR (23%), CTNNB1 (18%), MET (18%), and ATM (14%) were found to be the most frequently altered genes in ACC samples. Pathogenic and/or likely pathogenic mutations in therapeutically relevant genes were observed in 56 patients (47%) and included EGFR, BRAF, MET, CDKN2A, CDK4/6, and ATM. The most frequent co-occurring mutations were EGFR + MET (9%), MET + CDK4 (7%), EGFR + CDK4 (7%), and BRAF + MET (7%). The frequencies of mutations detected in ctDNA were similar to those detected in tissue. CONCLUSIONS Utilizing blood-based NGS to characterize genomic alterations in advanced ACC is feasible in over 80% of patients. Almost half of the patients had actionable mutations with approved therapies in other cancers. This approach might inform the development of personalized treatment options or identify clinical trials available for this aggressive malignancy.
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Affiliation(s)
- Bassel Nazha
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Tony Z Zhuang
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | - Jacqueline T Brown
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Deepak Ravindranathan
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Bradley C Carthon
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Omer Kucuk
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jamie Goldman
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Viraj A Master
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Mehmet Asim Bilen
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
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Diefenbach RJ, Lee JH, Stewart A, Menzies AM, Carlino MS, Saw RPM, Stretch JR, Long GV, Scolyer RA, Rizos H. Anchored Multiplex PCR Custom Melanoma Next Generation Sequencing Panel for Analysis of Circulating Tumor DNA. Front Oncol 2022; 12:820510. [PMID: 35494035 PMCID: PMC9039342 DOI: 10.3389/fonc.2022.820510] [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: 11/23/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Detection of melanoma mutations using circulating tumor DNA (ctDNA) is a potential alternative to using genomic DNA from invasive tissue biopsies. To date, mutations in the GC-rich TERT promoter region, which is commonly mutated in melanoma, have been technically difficult to detect in ctDNA using next-generation sequencing (NGS) panels. In this study, we developed a custom melanoma NGS panel for detection of ctDNA, which encompasses the top 15 gene mutations in melanoma including the TERT promoter. We analyzed 21 stage III and IV melanoma patient samples who were treatment-naïve or on therapy. The overall detection rate of the custom panel, based on BRAF/NRAS/TERT promoter mutations, was 14/21 (67%) patient samples which included a TERT C250T mutation in one BRAF and NRAS mutation negative sample. A BRAF or NRAS mutation was detected in the ctDNA of 13/21 (62%) patients while TERT promoter mutations were detected in 10/21 (48%) patients. Co-occurrence of TERT promoter mutations with BRAF or NRAS mutations was found in 9/10 (90%) patients. The custom ctDNA panel showed a concordance of 16/21 (76%) with tissue based-detection and included 12 BRAF/NRAS mutation positive and 4 BRAF/NRAS mutation negative patients. The ctDNA mutation detection rate for stage IV was 12/16 (75%) and for stage III was 1/5 (20%). Based on BRAF, NRAS and TERT promoter mutations, the custom melanoma panel displayed a limit of detection of ~0.2% mutant allele frequency and showed significant correlation with droplet digital PCR. For one patient, a novel MAP2K1 H119Y mutation was detected in an NRAS/BRAF/TERT promoter mutation negative background. To increase the detection rate to >90% for stage IV melanoma patients, we plan to expand our custom panel to 50 genes. This study represents one of the first to successfully detect TERT promoter mutations in ctDNA from cutaneous melanoma patients using a targeted NGS panel.
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Affiliation(s)
- Russell J Diefenbach
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Jenny H Lee
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,Department of Medical Oncology, Chris O'Brien Lifehouse, Sydney, NSW, Australia
| | - Ashleigh Stewart
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Matteo S Carlino
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, Sydney, NSW, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Jonathan R Stretch
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia
| | - Helen Rizos
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
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5
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Shen JP. Regarding Blood-Based Next-Generation Sequencing Analysis of Appendiceal Cancers. Oncologist 2020; 25:e2019-e2020. [PMID: 33037839 PMCID: PMC8186408 DOI: 10.1002/onco.13559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/27/2020] [Indexed: 11/08/2022] Open
Abstract
This letter to the editor questions whether liquid next‐generation sequencing is a reasonable substitute for tissue next‐generation sequencing for all forms of appendiceal cancer.
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Affiliation(s)
- John Paul Shen
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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6
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Shaib W. In Reply. Oncologist 2020; 25:e2021. [PMID: 33037841 PMCID: PMC8108060 DOI: 10.1002/onco.13558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 08/27/2020] [Indexed: 11/11/2022] Open
Abstract
This letter to the editor responds to questions about the role of blood‐based next‐generation testing for appendiceal cancer, supporting its complementary role with tissue‐based testing.
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Affiliation(s)
- Walid Shaib
- Department of Hematology and Oncology, Winship Cancer Institute, Emory UniversityAtlantaGeorgiaUSA
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Raghav K, Shen JP, Jácome AA, Guerra JL, Scally CP, Taggart MW, Foo WC, Matamoros A, Shaw KR, Fournier K, Overman MJ, Eng C. Integrated clinico-molecular profiling of appendiceal adenocarcinoma reveals a unique grade-driven entity distinct from colorectal cancer. Br J Cancer 2020; 123:1262-1270. [PMID: 32733093 PMCID: PMC7553941 DOI: 10.1038/s41416-020-1015-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/29/2020] [Accepted: 07/16/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Appendiceal adenocarcinoma (AA) is an orphan disease with unique clinical attributes but often treated as colorectal cancer (CRC). Understanding key molecular differences between AA and CRC is critical. METHODS We performed retrospective analyses of AA patients (N = 266) with tumour and/or blood next-generation sequencing (NGS) (2013-2018) with in-depth clinicopathological annotation. Overall survival (OS) was examined. For comparison, CRC cohorts annotated for sidedness, consensus molecular subtypes (CMS) and mutations (N = 3283) were used. RESULTS Blood-NGS identified less RAS/GNAS mutations compared to tissue-NGS (4.2% vs. 60.9%, P < 0.0001) and showed poor concordance with tissue for well-/moderately differentiated tumours. RAS (56.2%), GNAS (28.1%) and TP53 (26.9%) were most frequent mutations. Well/moderately differentiated tumours harboured more RAS (69.2%/64.0% vs. 40.5%) and GNAS (48.7%/32.0% vs. 10.1%) while moderate/poorly differentiated tumours had more TP53 (26.0%/27.8% vs. 7.7%) mutations. Appendiceal adenocarcinoma (compared to CRC) harboured significantly fewer APC (9.1% vs. 55.4%) and TP53 (26.9% vs. 67.5%) and more GNAS mutations (28.1% vs. 2.0%) (P < 0.0001). Appendiceal adenocarcinoma mutation profile did not resemble either right-sided CRC or any of the four CMS in CRC. High grade, but no mutation, was independently predictive of survival. CONCLUSION Integrated clinico-molecular profiling of AA identified key molecular drivers distinct from CRC. Appendiceal adenocarcinoma has a predominantly grade-driven biology that trumps mutations.
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Affiliation(s)
- Kanwal Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - John P Shen
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandre A Jácome
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer L Guerra
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher P Scally
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melissa W Taggart
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wai C Foo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aurelio Matamoros
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kenna R Shaw
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keith Fournier
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael J Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cathy Eng
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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8
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Diefenbach RJ, Lee JH, Menzies AM, Carlino MS, Long GV, Saw RPM, Howle JR, Spillane AJ, Scolyer RA, Kefford RF, Rizos H. Design and Testing of a Custom Melanoma Next Generation Sequencing Panel for Analysis of Circulating Tumor DNA. Cancers (Basel) 2020; 12:E2228. [PMID: 32785074 PMCID: PMC7465941 DOI: 10.3390/cancers12082228] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/27/2020] [Accepted: 08/07/2020] [Indexed: 12/17/2022] Open
Abstract
Detection of melanoma-associated mutations using circulating tumor DNA (ctDNA) from plasma is a potential alternative to using genomic DNA from invasive tissue biopsies. In this study, we developed a custom melanoma next-generation sequencing (NGS) panel which includes 123 amplicons in 30 genes covering driver and targetable mutations and alterations associated with treatment resistance. Analysis of a cohort of 74 stage III and IV treatment-naïve melanoma patients revealed that sensitivity of ctDNA detection was influenced by the amount of circulating-free DNA (cfDNA) input and stage of melanoma. At the recommended cfDNA input quantity of 20 ng (available in 28/74 patients), at least one cancer-associated mutation was detected in the ctDNA of 84% of stage IV patients and 47% of stage III patients with a limit of detection for mutant allele frequency (MAF) of 0.2%. This custom melanoma panel showed significant correlation with droplet digital PCR (ddPCR) and provided a more comprehensive melanoma mutation profile. Our custom panel could be further optimized by replacing amplicons spanning the TERT promoter, which did not perform well due to the high GC content. To increase the detection rate to 90% of stage IV melanoma and decrease the sensitivity to 0.1% MAF, we recommend increasing the volume of plasma to 8 mL to achieve minimal recommended cfDNA input and the refinement of poorly performing amplicons. Our panel can also be expanded to include new targetable and treatment resistance mutations to improve the tracking of treatment response and resistance in melanoma patients treated with systemic drug therapies.
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Affiliation(s)
- Russell J. Diefenbach
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (R.J.D.); (J.H.L.)
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
| | - Jenny H. Lee
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (R.J.D.); (J.H.L.)
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
| | - Alexander M. Menzies
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Matteo S. Carlino
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, Sydney, NSW 2145, Australia
| | - Georgina V. Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW 2065, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Robyn P. M. Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Julie R. Howle
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, Sydney, NSW 2145, Australia
| | - Andrew J. Spillane
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Breast and Melanoma Surgery Department, Division of Surgery, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Richard A. Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and New South Wales Health Pathology, Sydney, NSW 2050, Australia
| | - Richard F. Kefford
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Helen Rizos
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (R.J.D.); (J.H.L.)
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
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