Variant allele frequency: a decision-making tool in precision oncology?

被引：38

作者：

Bielo, Luca Boscolo ^{[1
,2
]}

Trapani, Dario ^{[1
,2
]}

Repetto, Matteo ^{[1
,2
,3
]}

Crimini, Edoardo ^{[1
,2
]}

Valenza, Carmine ^{[1
,2
]}

Belli, Carmen ^{[1
]}

Criscitiello, Carmen ^{[1
,2
]}

Marra, Antonio ^{[1
]}

Subbiah, Vivek ^{[4
]}

Curigliano, Giuseppe ^{[1
,2
]}

机构：

[1] IRCCS, European Inst Oncol, Div New Drugs & Early Drug Dev Innovat Therapies, Milan, Italy

[2] Univ Milan, Dept Oncol & Hemato Oncol, Milan, Italy

[3] Mem Sloan Kettering Canc Ctr, Early Drug Dev Serv, New York, NY USA

[4] Sarah Cannon Res Inst, Drug Dev Unit, Nashville, TN USA

来源：

TRENDS IN CANCER | 2023年 / 9卷 / 12期

关键词：

CIRCULATING TUMOR DNA; CELL-FREE DNA; LUNG ADENOCARCINOMA; MUTATION DETECTION; CLINICAL UTILITY; EGFR-TKI; PLASMA; EFFICACY; HETEROGENEITY; ABUNDANCE;

D O I：

10.1016/j.trecan.2023.08.011

中图分类号：

R73 [肿瘤学];

学科分类号：

100214 ;

摘要：

Precision oncology requires additional predictive biomarkers for targeted therapy selection. Variant allele frequency (VAF), measuring the proportion of variant alleles within a genomic locus, provides insights into tumor clonality in somatic genomic testing, yielding a strong rationale for targeting dominant cancer cell populations. The prognostic and predictive roles of VAF have been evaluated across different studies. Yet, the absence of validated VAF thresholds and a lack of standardization between sequencing assays currently hampers its clinical utility. Therefore, analytical and clinical validation must be further examined. This Review summarizes the evidence regarding the use of VAF as a predictive biomarker and discusses challenges and opportunities for its clinical implementation as a decision-making tool for targeted therapy selection.

引用

页码：1058 / 1068

页数：11

共 78 条

[1]

Avila M, 2019, CLIN ADV HEMATOL ONC, V17, P447

[2] Bead-Based Isolation of Circulating Tumor DNA from Pancreatic Cancer Patients Enables High Fidelity Next Generation Sequencing [J].

Balendran-Braun, Sukirthini ;

Kieler, Markus ;

Liebmann-Reindl, Sandra ;

Unseld, Matthias ;

Bianconi, Daniela ;

Prager, Gerald W. ;

Streubel, Berthold .

CANCER MANAGEMENT AND RESEARCH, 2021, 13 :6249-6261

[3] Independent prognostic value of ultra-sensitive quantification of tumor pretreatment T790M subclones in EGFR mutated non-small cell lung cancer (NSCLC) treated by first/second generation TKI, depends on variant allele frequency (VAF): Results of the French cooperative thoracic intergroup (IFCT) biomarkers France project [J].

Beau-Faller, Michele ;

Pencreach, Erwan ;

Leduc, Charlotte ;

Blons, Helene ;

Merlio, Jean-Philippe ;

Bringuier, Pierre-Paul ;

de Fraipont, Florence ;

Escande, Fabienne ;

Lemoine, Antoinette ;

Ouafik, L'Houcine ;

Denis, Marc ;

Hofman, Paul ;

Lacave, Roger ;

Melaabi, Samia ;

Langlais, Alexandra ;

Missy, Pascale ;

Morin, Franck ;

Moro-Sibilot, Denis ;

Barlesi, Fabrice ;

Cadranel, Jacques ;

Tran, Q. ;

Deroy, A. ;

Dos Santos, S. ;

Audigier-Valette, C. ;

Boyer, J. C. ;

Chiappa, A. M. ;

Debieuvre, D. ;

Fraboulet-Moreau, S. ;

Guichard, F. ;

Le Gac, G. ;

Leotard, B. ;

Morel, A. ;

Mosser, J. ;

Mougin, C. ;

Pedeutour, F. ;

Penault-Llorca, F. .

LUNG CANCER, 2020, 140 :19-26

[4] High BRAF variant allele frequencies are associated with distinct pathological features and responsiveness to target therapy in melanoma patients [J].

Berrino, E. ;

Balsamo, A. ;

Pisacane, A. ;

Gallo, S. ;

Becco, P. ;

Miglio, U. ;

Caravelli, D. ;

Poletto, S. ;

Paruzzo, L. ;

Debernardi, C. ;

Piccinelli, C. ;

Zaccagna, A. ;

Rescigno, P. ;

Aglietta, M. ;

Sapino, A. ;

Carnevale-Schianca, F. ;

Venesio, T. .

ESMO OPEN, 2021, 6 (03)

[5] Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies [J].

Bettegowda, Chetan ;

Sausen, Mark ;

Leary, Rebecca J. ;

Kinde, Isaac ;

Wang, Yuxuan ;

Agrawal, Nishant ;

Bartlett, Bjarne R. ;

Wang, Hao ;

Luber, Brandon ;

Alani, Rhoda M. ;

Antonarakis, Emmanuel S. ;

Azad, Nilofer S. ;

Bardelli, Alberto ;

Brem, Henry ;

Cameron, John L. ;

Lee, Clarence C. ;

Fecher, Leslie A. ;

Gallia, Gary L. ;

Gibbs, Peter ;

Le, Dung ;

Giuntoli, Robert L. ;

Goggins, Michael ;

Hogarty, Michael D. ;

Holdhoff, Matthias ;

Hong, Seung-Mo ;

Jiao, Yuchen ;

Juhl, Hartmut H. ;

Kim, Jenny J. ;

Siravegna, Giulia ;

Laheru, Daniel A. ;

Lauricella, Calogero ;

Lim, Michael ;

Lipson, Evan J. ;

Marie, Suely Kazue Nagahashi ;

Netto, George J. ;

Oliner, Kelly S. ;

Olivi, Alessandro ;

Olsson, Louise ;

Riggins, Gregory J. ;

Sartore-Bianchi, Andrea ;

Schmidt, Kerstin ;

Shih, Ie-Ming ;

Oba-Shinjo, Sueli Mieko ;

Siena, Salvatore ;

Theodorescu, Dan ;

Tie, Jeanne ;

Harkins, Timothy T. ;

Veronese, Silvio ;

Wang, Tian-Li ;

Weingart, Jon D. .

SCIENCE TRANSLATIONAL MEDICINE, 2014, 6 (224)

[6]

Black JRM, 2023, bioRxiv, DOI [10.1101/2023.03.09.531725, 10.1101/2023.03.09.531725, DOI 10.1101/2023.03.09.531725]

[7] Cancer therapy shapes the fitness landscape of clonal hematopoiesis [J].

Bolton, Kelly L. ;

Ptashkin, Ryan N. ;

Gao, Teng ;

Braunstein, Lior ;

Devlin, Sean M. ;

Kelly, Daniel ;

Patel, Minal ;

Berthon, Antonin ;

Syed, Aijazuddin ;

Yabe, Mariko ;

Coombs, Catherine C. ;

Caltabellotta, Nicole M. ;

Walsh, Mike ;

Offit, Kenneth ;

Stadler, Zsofia ;

Mandelker, Diana ;

Schulman, Jessica ;

Patel, Akshar ;

Philip, John ;

Bernard, Elsa ;

Gundem, Gunes ;

Ossa, Juan E. Arango ;

Levine, Max ;

Martinez, Juan S. Medina ;

Farnoud, Noushin ;

Glodzik, Dominik ;

Li, Sonya ;

Robson, Mark E. ;

Lee, Choonsik ;

Pharoah, Paul D. P. ;

Stopsack, Konrad H. ;

Spitzer, Barbara ;

Mantha, Simon ;

Fagin, James ;

Boucai, Laura ;

Gibson, Christopher J. ;

Ebert, Benjamin L. ;

Young, Andrew L. ;

Druley, Todd ;

Takahashi, Koichi ;

Gillis, Nancy ;

Ball, Markus ;

Padron, Eric ;

Hyman, David M. ;

Baselga, Jose ;

Norton, Larry ;

Gardos, Stuart ;

Klimek, Virginia M. ;

Scher, Howard ;

Bajorin, Dean .

NATURE GENETICS, 2020, 52 (11) :1219-+

[8] Dabrafenib in an elderly patient with metastatic melanoma and BRAF V600R mutation: A case report [J].

Casadevall D. ;

Vidal J. ;

Gallardo F. ;

Zuccarino F. ;

Arumí-Uría M. ;

Dalmases A. ;

Bellosillo B. ;

Montagut C. .

Journal of Medical Case Reports, 10 (1)

[9] Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing [J].

Chan, K. C. Allen ;

Jiang, Peiyong ;

Zheng, Yama W. L. ;

Liao, Gary J. W. ;

Sun, Hao ;

Wong, John ;

Siu, Shing Shun N. ;

Chan, Wing C. ;

Chan, Stephen L. ;

Chan, Anthony T. C. ;

Lai, Paul B. S. ;

Chiu, Rossa W. K. ;

Lo, Y. M. D. .

CLINICAL CHEMISTRY, 2013, 59 (01) :211-224

[10] Allele-specific copy number profiling by next-generation DNA sequencing [J].

Chen, Hao ;

Bell, John M. ;

Zavala, Nicolas A. ;

Ji, Hanlee P. ;

Zhang, Nancy R. .

NUCLEIC ACIDS RESEARCH, 2015, 43 (04)

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