A platform for rapid detection of multiple oncogenic mutations with relevance to targeted therapy in non-small-cell lung cancer.

Su, Zengliu; Dias-Santagata, Dora; Duke, MarKeesa; Hutchinson, Katherine; Lin, Ya-Lun; Borger, Darrell R.; Chung, Christine H.; Massion, Pierre P.; Vnencak-Jones, Cindy L.; Iafrate, A. John; Pao, William

doi:10.1016/j.jmoldx.2010.11.010

Cited by 176Lung Cancer Treatments and MutationsCancer Genomics and DiagnosticsLung Cancer Diagnosis and Treatment

A platform for rapid detection of multiple oncogenic mutations with relevance to targeted therapy in non-small-cell lung cancer.

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Su, Zengliu, Dias-Santagata, Dora, Duke, MarKeesa, Hutchinson, Katherine, Lin, Ya-Lun, Borger, Darrell R., Chung, Christine H., Massion, Pierre P. +3 more·2011·The Journal of Molecular Diagnostics

DOI 10.1016/j.jmoldx.2010.11.010PMC PMC3070558

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Abstract

The identification of somatically acquired tumor mutations is increasingly important in the clinical management of cancer because the sensitivity of targeted drugs is related to the genetic makeup of individual tumors. Thus, mutational profiles of tumors can help prioritize anticancer therapy. We report herein the development and validation of two multiplexed assays designed to detect in DNA from FFPE tissue more than 40 recurrent mutations in nine genes relevant to existing and emerging targeted therapies in lung cancer. The platform involves two methods: a screen (SNaPshot) based on multiplex PCR, primer extension, and capillary electrophoresis that was designed to assess for 38 somatic mutations in eight genes (AKT1, BRAF, EGFR, KRAS, MEK1, NRAS, PIK3CA, and PTEN) and a PCR-based sizing assay that assesses for EGFR exon 19 deletions, EGFR exon 20 insertions, and HER2 exon 20 insertions. Both the SNaPshot and sizing assays can be performed rapidly, with minimal amounts of genetic material. Compared with direct sequencing, in which mutant DNA needs to compose 25% or more of the total DNA to easily detect a mutation, the SNaPshot and sizing assays can detect mutations in samples in which mutant DNA composes 1.56% to 12.5% and 1.56% to 6.25% of the total DNA, respectively. These robust, reliable, and relatively inexpensive assays should help accelerate adoption of a genotype-driven approach in the treatment of lung cancer.

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Pre-clinical reports suggest that third-generation agents can induce switching to multiple signaling mechanisms that bypass EGFR dependency, including ERK and AKT pathways.
“Indeed, pre-clinical reports have suggested that “third generation” agents can induce switching to multiple signaling mechanisms that bypass EGFR dependency such as ERK and AKT pathways (35, 61, 62).”
From AZD9291, an Irreversible EGFR TKI, Overcomes T790M-Mediated Resistance to EGFR Inhibitors in Lung Cancer (2014) · cites this paper as [61]

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De Greve JL, Teugels E, De Mey J, Geers C, Galdermans D, Decoster L, In 't Veld P, Schallier D, Taton M, Shahidi M: Clinical activity of BIBW 2992, an irreversible inhibitor of EGFR and HER2 in adenocarcinoma of the lung with mutations in the kinase domain of HER2neu (ab- stract). J Thorac Oncol 2009, 4:s307
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Background
Oncogene status predicts patterns of metastatic spread in treatment‐naive nonsmall cell lung cancer
Doebele, R. C., Lu, X. J. D., Sumey, C. J., Maxson, D. A., Weickhardt, A. J., Oton, A. B., Bunn, P. A., Barón, A. E., Franklin, W. A., Aisner, D. L., et al. (2012) · Cancer · doi:10.1002/cncr.27409 · Cited by 279 · see citing works
“No imaging 8 (20) 12 (31) 8 (16) 27 (34) 55 (27)”
Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement in Clinical Cancer Specimens
Pritchard, C. C., Salipante, S. J., Koehler, K. M., Smith, C., Scroggins, S. M., Wood, B. L., Wu, D., Lee, M. K., Dintzis, S. M., Adey, A., et al. (2013) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2013.08.004 · Cited by 271 · see citing works
“Most currently available multiplexed clinical assays examine only a limited number of specific sites in a relatively small number of genes.(13,14) More recently, next-generation sequencing assays have been developed for detecting cancer-associated mutations in clinical specimens in a more comprehensive manner, but the…”
Background
Rationale for co-targeting IGF-1R and ALK in ALK fusion-positive lung cancer
Lovly, C. M., McDonald, N. T., Chen, H., Ortiz-Cuaran, S., Heukamp, L. C., Yan, Y., Florin, A., Ozretić, L., Lim, D., Wang, L., et al. (2014) · Nature Medicine · doi:10.1038/nm.3667 · Cited by 268 · see citing works
Molecular Biology of Lung Cancer
Nana-Sinkam, S. P., & Powell, C. A. (2013) · CHEST Journal · doi:10.1378/chest.12-2346 · Cited by 248 · see citing works
The IGNITE network: a model for genomic medicine implementation and research
on behalf of the IGNITE Network, Weitzel, K. W., Alexander, M., Bernhardt, B. A., Calman, N., Carey, D. J., Cavallari, L. H., Field, J. R., Hauser, D., Junkins, H., et al. (2015) · BMC Medical Genomics · doi:10.1186/s12920-015-0162-5 · Cited by 251 · see citing works
“The Personalized Cancer Medicine Initiative (PCMI) provides routine, multiplexed tumor gene mutation testing for patients with various cancer diagnoses, including non-small cell lung cancer (NSCLC) and melanoma.[12, 13] The Pharmacogenomic Resource for Enhanced Decisions In Care and Treatment (PREDICT) program provide…”
Method
Clinical cancer genomic profiling
Chakravarty, D., & Solit, D. B. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00338-8 · Cited by 227 · see citing works
The challenge of NSCLC diagnosis and predictive analysis on small samples. Practical approach of a working group
Thunnissen, E., Kerr, K. M., Herth, F. J. F., Lantuéjoul, S., Papotti, M. G., Rintoul, R. C., Rossi, G., Skov, B. G., Weynand, B., Bubendorf, L., et al. (2011) · Lung Cancer · doi:10.1016/j.lungcan.2011.10.017 · Cited by 228 · see citing works
Epidermal growth factor receptor exon 20 insertions in advanced lung adenocarcinomas: Clinical outcomes and response to erlotinib
Naidoo, J., Sima, C. S., Rodriguez, K., Busby, N., Nafa, K., Ladanyi, M., Riely, G. J., Kris, M. G., Arcila, M. E., & Yu, H. A. (2015) · Cancer · doi:10.1002/cncr.29493 · Cited by 211 · see citing works
“Positive cases were characterized via Sanger sequencing with the primers FW1:50-CATTCA TGCGTCTTCACCTG-30 and REV1:50-GTATA GGGGTACCGTTTGAG-30.”
Method
Routine Multiplex Mutational Profiling of Melanomas Enables Enrollment in Genotype-Driven Therapeutic Trials
Lovly, C. M., Dahlman, K. B., Fohn, L. E., Su, Z., Dias-Santagata, D. C., Hicks, D. J., Hucks, D., Berry, E., Terry, C. R., Duke, M., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035309 · Cited by 203 · see citing works
“Here, we present development, validation, and clinical implementation of a disease-specific SNaPshot-based screen [23,24] to assess melanoma tumor samples simultaneously for 43 somatic recurrent point mutations in 6 genes with relevance to targeted therapy.”
Influential
The Incidence of Brain Metastases in Stage IV ROS1-Rearranged Non–Small Cell Lung Cancer and Rate of Central Nervous System Progression on Crizotinib
Patil, T., Smith, D. E., Bunn, P. A., Aisner, D. L., Le, A. T., Hancock, M., Purcell, W. T., Bowles, D. W., Camidge, D. R., & Doebele, R. C. (2018) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2018.07.001 · Cited by 205 · see citing works
Identification of KIF5B-RET and GOPC-ROS1 Fusions in Lung Adenocarcinomas through a Comprehensive mRNA-Based Screen for Tyrosine Kinase Fusions
Suehara, Y., Arcila, M. E., Wang, L., Hasanovic, A., Ang, D. C., Ito, T., Kimura, Y., Drilon, A. E. D. C., Guha, U., Rusch, V. W., et al. (2012) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-12-0838 · Cited by 181 · see citing works
“[7] Su Z, Dias-Santagata D, Duke M, Hutchinson K, Lin YL, Borger DR, et al.”
BackgroundMethod
Prioritizing targets for precision cancer medicine
André, F., Mardis, E. R., Salm, M. P., Soria, J., Siu, L. L., & Swanton, C. (2014) · Annals of Oncology · doi:10.1093/annonc/mdu478 · Cited by 163 · see citing works
“Early examples of hot spot focused multigene diagnostic assays were devised on mass-spectrometry platforms such as the Sequenom MassArray genotyping instrument [8] or on capillary sequencers [9].”
Method
MAP2K1 ( MEK1 ) Mutations Define a Distinct Subset of Lung Adenocarcinoma Associated with Smoking
Arcila, M. E., Drilon, A. E. D. C., Sylvester, B. E., Lovly, C. M., Borsu, L. A., Reva, B. A., Kris, M. G., Solit, D. B., & Ladanyi, M. (2014) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-14-2124 · Cited by 141 · see citing works
Existing and Emerging Technologies for Tumor Genomic Profiling
MacConaill, L. E. (2013) · Journal of Clinical Oncology · doi:10.1200/jco.2012.46.5948 · Cited by 138 · see citing works
“Indeed, multiple cancer centers worldwide have instituted such technologies to anchor their initial precision cancer medicine initiatives.(5,26-32) Several of these programs have implemented enterprise-wide projects to systematically profile patient tumor samples for mutations in potentially actionable or informative…”
Background
Characteristics of Lung Cancers Harboring NRAS Mutations
Ohashi, K., Sequist, L. V. D., Arcila, M. E., Lovly, C. M., Chen, X., Rudin, C. M., Morán, T., Camidge, D. R., Vnencak‐Jones, C. L., Berry, L. D., et al. (2013) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-12-3173 · Cited by 142 · see citing works
“5 Range 30–91 Race N 1⁄4 30 Caucasian 13 (64) Asian 5 (27) African American 3 (9) Unknown 8 Smoking history N 1⁄4 30 Never 1 (5) Former 7 (33) Current 11 (52) Yes 2 (10) Unknown 9 Pack-years N 1⁄4 19 Median 34 Range 0–163”
Oncogenic KRAS and BRAF Drive Metabolic Reprogramming in Colorectal Cancer
Hutton, J. E., Wang, X., Zimmerman, L. J., Slebos, R. J. C., Trenary, I. A., Young, J. D., Li, M., & Liebler, D. C. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m116.058925 · Cited by 133 · see citing works
EGFR-mutated oncogene-addicted non-small cell lung cancer: Current trends and future prospects
Soria, J., Mok, T. S. K., Cappuzzo, F., & Janne, P. A. (2011) · Cancer Treatment Reviews · doi:10.1016/j.ctrv.2011.10.003 · Cited by 129 · see citing works
Clinical Analysis and Interpretation of Cancer Genome Data
Allen, E. M. V., Wagle, N., & Levy, M. A. (2013) · Journal of Clinical Oncology · doi:10.1200/jco.2013.48.7215 · Cited by 126 · see citing works
Clinicopathologic features and outcomes of patients with lung adenocarcinomas harboring BRAF mutations in the L ung C ancer M utation C onsortium
Villaruz, L. C., Socinski, M. A., Abberbock, S. R., Berry, L. D., Johnson, B. E., Kwiatkowski, D. J., Iafrate, A. J., Varella‐Garcia, M., Franklin, W. A., Camidge, D. R., et al. (2014) · Cancer · doi:10.1002/cncr.29042 · Cited by 127 · see citing works
“median (range) 65 (42-80) 63 (31-86) 65 (26-86) 54 (23-76) 60 (28-84) 64 (18-93) 62 (41-78)”
A Personalized Treatment for Lung Cancer: Molecular Pathways, Targeted Therapies, and Genomic Characterization
Hensing, T. A., Chawla, A., Batra, R., & Salgia, R. (2013) · Advances in experimental medicine and biology · doi:10.1007/978-1-4614-8778-4_5 · Cited by 125 · see citing works
State of the art in medical applications using non-thermal atmospheric pressure plasma
Tanaka, H., Ishikawa, K., Mizuno, M., Toyokuni, S., Kajiyama, H., Kikkawa, F., Metelmann, H., & Hori, M. (2017) · Reviews of Modern Plasma Physics · doi:10.1007/s41614-017-0004-3 · Cited by 123 · see citing works
“…can cause cancer, and these mutations include those to the TP53 (tumor suppressor protein p53), PTEN (phosphatase and tensin homolog), and EGFR (epidermal growth factor receptor) genes in cancerous cells (Loeb et al. 2003; Su et al. 2011; Carneiro et al. 2014; Arena et al. 2015; Zhang et al. 2016).”
Background
Epidermal growth factor receptor tyrosine kinase inhibitors as initial therapy for non-small cell lung cancer: Focus on epidermal growth factor receptor mutation testing and mutation-positive patients
Roengvoraphoj, M., Tsongalis, G. J., Dragnev, K. H., & Rigas, J. R. (2013) · Cancer Treatment Reviews · doi:10.1016/j.ctrv.2013.05.001 · Cited by 120 · see citing works
Combining Highly Multiplexed PCR with Semiconductor-Based Sequencing for Rapid Cancer Genotyping
Beadling, C., Neff, T. L., Heinrich, M. C., Rhodes, K., Thornton, M., Leamon, J. H., Andersen, M., & Corless, C. L. (2012) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2012.09.003 · Cited by 119 · see citing works
The potential of exploiting DNA-repair defects for optimizing lung cancer treatment
Postel-Vinay, S. C., Vanhecke, E., Olaussen, K. A., Lord, C. J., Ashworth, A., & Soria, J. (2012) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2012.3 · Cited by 113 · see citing works
“In addition to IHC assays, high-throughput DNA sequencing platforms, multiplexed assays designed for NSCLC (such as the SNaPshot/PCR-based platform described by Su et al”
Method
Uncommon Epidermal Growth Factor Receptor mutations in non-small cell lung cancer and their mechanisms of EGFR tyrosine kinase inhibitors sensitivity and resistance
Massarelli, E., Johnson, F. M., Erickson, H. S., Wistuba, I. I., & Papadimitrakopoulou, V. (2013) · Lung Cancer · doi:10.1016/j.lungcan.2013.01.018 · Cited by 110 · see citing works
The evolving genomic classification of lung cancer
Shames, D. S., & Wistuba, I. I. (2013) · The Journal of Pathology · doi:10.1002/path.4275 · Cited by 98 · see citing works
“A number of multiplexed PCR-based assays are available, including SNaPshot (Applied Biosystems, Foster City, CA, USA), which detects hotspot mutation sites in key cancer genes using fluorescentlylabelled primer extension products [96], and Sequenom MassARRAY (Sequenom Inc, San Diego, CA, USA), which analyses primer…”
Method
Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing
Harismendy, O., Schwab, R. B., Bao, L., Olson, J., Rozenzhak, S., Kotsopoulos, S. K., Pond, S. J. K., Crain, B., Chee, M. S., Messer, K. S., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-12-r124 · Cited by 98 · see citing works
“While most available clinical assays interrogate one or only a few commonly mutated loci in cancers, two published clinical assays, SNaPShot [3] and OncoMap [4], respectively target 38 mutations in 8 genes by single base extension assays and approximately 400 mutations in 33 genes by mass spectrometry.”
Background
Translating genomic information into clinical medicine: Lung cancer as a paradigmPreprint
Levy, M. A., Lovly, C. M., & Pao, W. J. (2012) · Genome Research · doi:10.1101/gr.131128.111 · Cited by 90 · see citing works
“…directed cancer treatment at Vanderbilt The Vanderbilt-Ingram Cancer Center was faced with the challenges discussed above when we implemented ‘‘first-generation’’ (SNaPshot-based) tumor gene mutation testing for NSCLC in our CLIA-certified molecular diagnostics lab in July 2010 (Su et al. 2011).”
BackgroundMethod
Patient-derived xenografts faithfully replicated clinical outcome in a phase II co-clinical trial of arsenic trioxide in relapsed small cell lung cancer
Owonikoko, T. K., Zhang, G., Kim, H. S., Stinson, R., Bechara, R. I., Zhang, C., Chen, Z., Saba, N. F., Pakkala, S., Pillai, R. N., et al. (2016) · Journal of Translational Medicine · doi:10.1186/s12967-016-0861-5 · Cited by 89 · see citing works
“Sample preparation and genetic mutation identification followed previously described methodologies [16].”
Method
Frequency and outcomes of brain metastases in patients with HER2‐mutant lung cancers
Offin, M. D., Feldman, D., Ni, A., Myers, M. L., Lai, W. V., Pentsova, E. I., Boire, A. A., Daras, M., Jordan, E., Solit, D. B., et al. (2019) · Cancer · doi:10.1002/cncr.32461 · Cited by 89 · see citing works
“Age, median (range), y 65 (24-90) 63 (34-85) 67 (35-90) 63 (24-89)”
A phase II study of temsirolimus and erlotinib in patients with recurrent and/or metastatic, platinum-refractory head and neck squamous cell carcinoma
Bauman, J. E., Arias‐Pulido, H., Lee, S. J., Fekrazad, M. H., Ozawa, H., Fertig, E. J., Howard, J. D., Bishop, J. A., Wang, H., Olson, G. T., et al. (2013) · Oral Oncology · doi:10.1016/j.oraloncology.2012.12.016 · Cited by 87 · see citing works
“PIK3CA and HRAS mutations were analyzed using DNA isolated from paraffin-embedded tissues as previously described.(29,30) The association of each mutation with RECIST was quantified with a Fisher’s exact test that defined groups as (1) wildtype vs.”
Prospective Enterprise-Level Molecular Genotyping of a Cohort of Cancer Patients
MacConaill, L. E., Garcia, E., Shivdasani, P., Ducar, M. D., Adusumilli, R., Breneiser, M., Byrne, M. N., Chung, L. P., Conneely, J., Crosby, L., et al. (2014) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2014.06.004 · Cited by 87 · see citing works
The Tissue Is the Issue: Personalized Medicine for Non-Small Cell Lung Cancer
Hirsch, F. R., Wynes, M. W., Gandara, D. R., & Bunn, P. A. (2010) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-10-2005 · Cited by 81 · see citing works
Integrating cancer genomic data into electronic health records
Warner, J. L., Jain, S. K., & Levy, M. A. (2016) · Genome Medicine · doi:10.1186/s13073-016-0371-3 · Cited by 82 · see citing works
“Although the turnaround is relatively fast, PCR can only be scaled to “ hotspot ” testing of 40 – 50 variants, such as the SNaPshot test [42].”
Method
Direct inhibition of PI3K in combination with dual HER2 inhibitors is required for optimal antitumor activity in HER2+ breast cancer cells
Rexer, B. N., Chanthaphaychith, S., Dahlman, K. B., & Arteaga, C. L. (2014) · Breast Cancer Research · doi:10.1186/bcr3601 · Cited by 80 · see citing works
“This assay involves multiplexed polymerase chain reaction (PCR) and multiplexed single-base primer extension, followed by capillary electrophoresis [27-29]; Vandana G Abramson et al.”
Method
ReCAP: Feasibility and Accuracy of Extracting Cancer Stage Information From Narrative Electronic Health Record Data
Warner, J. L., Levy, M. A., & Neuss, M. N. (2016) · Journal of Oncology Practice · doi:10.1200/jop.2015.004622 · Cited by 79 · see citing works
The role of cytology specimens in molecular testing of solid tumors: Techniques, limitations, and opportunities
Aisner, D. L., & Sams, S. B. (2012) · Diagnostic Cytopathology · doi:10.1002/dc.22820 · Cited by 76 · see citing works
Assessment of mutational profile of Japanese lung adenocarcinoma patients by multitarget assays: A prospective, single‐institute study
Serizawa, M., Koh, Y., Kenmotsu, H., Isaka, M., Murakami, H., Akamatsu, H., Mori, K. P., Abe, M., Hayashi, I., Taira, T., et al. (2014) · Cancer · doi:10.1002/cncr.28604 · Cited by 74 · see citing works
“We developed a tumor genotyping panel to screen patients with lung cancer for genetic alterations relevant to novel molecular-targeted therapeutics in ongoing clinical trials.(1-3,15) (Supporting Table 1; see online supporting information).”
Method
Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non-Small Cell Lung, Melanoma, and Gastrointestinal Malignancies
Fisher, K. E., Zhang, L., Wang, J., Smith, G. H., Newman, S., Schneider, T. M., Pillai, R. N., Kudchadkar, R. R., Owonikoko, T. K., Ramalingam, S. S., et al. (2016) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2015.11.006 · Cited by 71 · see citing works
“Forty NSCLC and two GI samples underwent multiplex PCR, primer extension, and capillary electrophoresis to detect 44 somatic hotspot mutations in 10 genes (AKT1, BRAF, EGFR, IDH1, IDH2, KRAS, MAP2K1, NRAS, PIK3CA, and PTEN), as described.(13) IDH1 exon 4 and IDH2 exon 4 were amplified using the following primers: 50-G…”
Method
Genetically informed lung cancer medicine
Pao, W. J., Iafrate, A. J., & Su, Z. (2010) · The Journal of Pathology · doi:10.1002/path.2788 · Cited by 67 · see citing works
Beyond Histology: Translating Tumor Genotypes into Clinically Effective Targeted Therapies
Meador, C. B., Micheel, C., Levy, M. A., Lovly, C. M., Horn, L., Warner, J. L., Johnson, D. B., Zhao, Z., Anderson, I. A., Sosman, J. A., et al. (2014) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-13-1591 · Cited by 67 · see citing works
“We implemented SNaPshot analysis at the Vanderbilt-Ingram Cancer Center (Nashville, TN) in July, 2010, for routine stratification of NSCLCs and melanomas into clinically relevant molecular subtypes (15, 20).”
Method
Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView
Kudo, T., Meireles, A. M., Moncada, R., Chen, Y., Wu, P., Gould, J., Hu, X., Kornfeld, O., Jesudason, R., Foo, C., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-024-02391-0 · Cited by 74 · see citing works
“…each spot identified in the first step using an ad hoc quality score per sequencing call, based on the highest and second-highest intensity channels 83,84 , calculated as A table containing barcode information and associated quality scores was then used to assign the most common barcode reads to…”
From targets to targeted therapies and molecular profiling in non-small cell lung carcinoma
Thomas, A., Rajan, A., López-Chávez, A., Wang, Y., & Giaccone, G. (2012) · Annals of Oncology · doi:10.1093/annonc/mds478 · Cited by 63 · see citing works
SMART precision cancer medicine: a FHIR-based app to provide genomic information at the point of care
Warner, J. L., Rioth, M. J., Mandl, K. D., Mandel, J. C., Kreda, D., Kohane, I. S., Carbone, D., Oreto, R., Wang, L. L., Zhu, S., et al. (2016) · Journal of the American Medical Informatics Association · doi:10.1093/jamia/ocw015 · Cited by 63 · see citing works
“Solid tumor oncology patients with certain histologies (eg, lung cancer, melanoma) seen at VUMC have, since July 2010, routinely undergone molecular profiling with SNaPshot, a fast, high-throughput, multiplex mutational profiling method based on the Applied Biosystems SNaPshot platform.(5,7) SNaPshot assays for common…”
Method
RAF265 Inhibits the Growth of Advanced Human Melanoma Tumors
Su, Y., Vilgelm, A. E., Kelley, M. C., Hawkins, O. E., Liu, Y., Boyd, K. L., Kantrow, S. M., Splittgerber, R. C., Short, S. P., Sobolik, T., et al. (2012) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-11-1122 · Cited by 62 · see citing works
Trametinib with or without Vemurafenib in BRAF Mutated Non-Small Cell Lung Cancer
Joshi, M., Rice, S. J., Liu, X., Miller, B., & Belani, C. P. (2015) · PLoS ONE · doi:10.1371/journal.pone.0118210 · Cited by 61 · see citing works
“) [21].”
High-Throughput Detection of Clinically Relevant Mutations in Archived Tumor Samples by Multiplexed PCR and Next-Generation Sequencing
Bourgon, R., Lu, S., Yan, Y., Lackner, M. R., Wang, W., Weigman, V., Wang, D., Guan, Y., Ryner, L. C., Koeppen, H., et al. (2014) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-13-3114 · Cited by 61 · see citing works
“primer extension assays, mass spectrometry and allele-specific PCR (asPCR) – have been successfully used in archived clinical samples(1-3), these technologies are limited to assaying well-characterized loci.”
Method
Current concepts on the molecular pathology of non-small cell lung carcinoma
Fujimoto, J., & Wistuba, I. I. (2014) · Seminars in Diagnostic Pathology · doi:10.1053/j.semdp.2014.06.008 · Cited by 57 · see citing works
Clinical Implementation of Comprehensive Strategies to Characterize Cancer Genomes: Opportunities and Challenges
MacConaill, L. E., Hummelen, P. V., Meyerson, M. M., & Hahn, W. C. (2011) · Cancer Discovery · doi:10.1158/2159-8290.cd-11-0110 · Cited by 53 · see citing works
Somatic Mutation Spectrum of Non–Small-Cell Lung Cancer in African Americans: A Pooled Analysis
Araujo, L. H., Lammers, P. E., Matthews-Smith, V., Eisenberg, R., González, A., Schwartz, A. G., Timmers, C. D., Shilo, K., Zhao, W., Natarajan, T. G., et al. (2015) · Journal of Thoracic Oncology · doi:10.1097/jto.0000000000000650 · Cited by 49 · see citing works
“SNaPshot/sizing assays were performed in a Clinical Laboratory Improvement Amendments-certified laboratory (Vanderbilt-Ingram Cancer Center) and followed standard protocols for sample selection and genotyping.(20) SNaPshot technique involved multiplex polymerase chain reaction, single-base extension, and analysis by c…”
Achievements and Challenges of Molecular Targeted Therapy in Melanoma
Sullivan, R. J., LoRusso, P. M., Boerner, S. A., & Dummer, R. (2015) · American Society of Clinical Oncology Educational Book · doi:10.14694/edbook_am.2015.35.177 · Cited by 46 · see citing works
Afatinib plus Cetuximab Delays Resistance Compared to Single-Agent Erlotinib or Afatinib in Mouse Models of TKI-Naïve EGFR L858R-Induced Lung Adenocarcinoma
Pirazzoli, V., Ayeni, D. O., Meador, C. B., Sanganahalli, B. G., Hyder, F., de Stanchina, E., Goldberg, S. B., Pao, W. J., & Politi, K. A. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-0620 · Cited by 45 · see citing works
“Genomic DNA was extracted using the DNeasy kit (Qiagen #69504) and was subjected to SNaPshot sequencing for T790M (16).”
Method
PIK3CA mutations as prognostic factor in squamous cell lung carcinoma
McGowan, M., Silye, A., Lund‐Iversen, M., Solberg, S. K., Helland, Å., Hirsch, F. R., & Brustugun, O. T. (2016) · Lung Cancer · doi:10.1016/j.lungcan.2016.11.018 · Cited by 46 · see citing works
BEAMing Up Personalized Medicine: Mutation Detection in Blood
Richardson, A. L., & Iglehart, J. D. (2012) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-12-0871 · Cited by 44 · see citing works
“Many cancer centers are developing gene mutation screening approaches that can be applied to archived FFPE tumor samples (8,9).”
Background
Intertumor heterogeneity of non-small-cell lung carcinomas revealed by multiplexed mutation profiling and integrative genomics
Tan, D. S. W., Camilleri‐Broët, S., Tan, E. H., Alifano, M., Lim, W., Bobbio, A., Zhang, S., Ng, Q., Ang, M., Iyer, N. G., et al. (2014) · International Journal of Cancer · doi:10.1002/ijc.28750 · Cited by 43 · see citing works
“MET 16 (3,13) 2 (1,1) 2 (0,2) 2 (1,1) 0 1 (0,1) 0 0 0 0 7 (43.”
Multiplex Detection of DNA Mutations by the Fluorescence Fingerprint Spectrum Technique
Song, J., Zhang, J., Lv, F., Cheng, Y., Wang, B., Feng, L., Liu, L., & Wang, S. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201305461 · Cited by 42 · see citing works
The Determinants of Head and Neck Cancer: Unmasking the PI3K Pathway Mutations
Squarize, F. S. G. C. H. (2013) · Journal of Carcinogenesis & Mutagenesis · doi:10.4172/2157-2518.s5-003 · Cited by 42 · see citing works
“Potential effects of HNSCC mutations are suggested by where PIK3CB PIK3C1 P42338 PIK3CB p110β, PI3Kβ Synonymous p.P422P [2] PIK3CD O00329 PIK3CD p110δ, PI3Kδ Missense p.T423S [5] Missense p.T458S [2] PIK3CG P48736 PIK3CG p110γ, PI3Kγ Missense p.A156V [2] Missense p.G491E [2] Missense p.L843H [2] Missense p.P526S [2] M…”
Influential
Next‐generation sequencing and clinical outcomes of patients with lung adenocarcinoma treated with stereotactic body radiotherapy
Cassidy, R. J., Zhang, X., Patel, P. R., Shelton, J. W., Escott, C., Sica, G., Rossi, M. R., Hill, C. E., Steuer, C. E., Pillai, R. N., et al. (2017) · Cancer · doi:10.1002/cncr.30794 · Cited by 42 · see citing works
“SNaPshot is a multiplex polymerase chain reaction assay followed by single base primer excision, whose methods have been described previously.(33) TruSight Tumor 26 is a next-generation sequencing platform that allows for highly accurate variant analysis, and the methods for which previously have been detailed.”
Method
Driver mutations among never smoking female lung cancer tissues in China identify unique EGFR and KRAS mutation pattern associated with household coal burning
Hosgood, H. D., Pao, W. J., Rothman, N., Hu, W., Pan, Y., Kuchinsky, K., Jones, K. D., Xu, J., Vermeulen, R. C. H., Simko, J. P., et al. (2013) · Respiratory Medicine · doi:10.1016/j.rmed.2013.08.018 · Cited by 41 · see citing works
“Of note, PCR carryover of the EGFR exon 18 mutation is unlikely to explain our results, as no template controls are used throughout our assay [20].”
Prospective genetic profiling of squamous cell lung cancer and adenosquamous carcinoma in Japanese patients by multitarget assays
Kenmotsu, H., Serizawa, M., Koh, Y., Isaka, M., Takahashi, T., Taira, T., Ono, A., Maniwa, T., Takahashi, S., Mori, K. P., et al. (2014) · BMC Cancer · doi:10.1186/1471-2407-14-786 · Cited by 37 · see citing works
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Method
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Result
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Method
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BackgroundMethod
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Authors: Su, Z., Dias-Santagata, D., Duke, M., Hutchinson, K., Lin, Y.-L., Borger, D. R., Chung, C. H., Massion, P. P., Vnencak-Jones, C. L., Iafrate, A. J., & Pao, W.
Affiliations: Vanderbilt University (US)
Massachusetts General Hospital (US)
Corresponding author: Pao, William
ORCID: Dias-Santagata, Dora
Hutchinson, Katherine
Chung, Christine H.
Massion, Pierre P.
Iafrate, A. John
Pao, William
Venue: The Journal of Molecular Diagnostics
Publisher: Elsevier BV
Published: 2011-01
Volume: 13
Issue: 1
Pages: 74-84
ISSN: 1525-1578 (ISSN-L)
DOI: 10.1016/j.jmoldx.2010.11.010
PMC: PMC3070558
OpenAlex: W2033780390
Cited by: 176
References: 36
Citations by year: 2026: 1 · 2025: 5 · 2024: 4 · 2022: 1 · 2021: 3 · 2020: 4 · 2019: 3 · 2018: 5 · 2017: 10 · 2016: 21 · 2015: 29 · 2014: 32 · 2013: 25 · 2012: 23
FWCI: 23.94
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 3268 d)
Locations: Journal of Molecular Diagnostics (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: NIH/National Cancer Institute (R01 CA121210, P01 CA129243, U54 CA143798, CA102353, RC2-CA148394-01)
VICC Specialized Program of Research Excellence in Lung Cancer (CA90949)
Vanderbilt-Ingram Cancer Center Core (CA68485)
V Foundation
TJ Martell Foundation
Kleberg Foundation
Topics: Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Lung Cancer Treatments and Mutations
Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Lung Cancer Diagnosis and Treatment
Keywords: non-small cell lung cancer, somatic mutations, targeted therapy, snapshots, EGFR exon 19 deletion, EGFR exon 20 insertion, HER2 exon 20 insertion, AKT1, BRAF, KRAS, MEK1, NRAS, PIK3CA, PTEN, formalin-fixed paraffin-embedded tissue
MeSH terms: Carcinoma, Non-Small-Cell Lung, DNA, Neoplasm, Genetic Testing, Humans, Lung Neoplasms, Mutation, Reproducibility of Results, Cell Line, Tumor, High-Throughput Nucleotide Sequencing

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A platform for rapid detection of multiple oncogenic mutations with relevance to targeted therapy in non-small-cell lung cancer.

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