RESUMEN
OBJECTIVES: To compare next-generation sequencing (NGS) platforms with mutation-specific analysis platforms in a clinical setting, in terms of sensitivity, mutation specificity, costs, capacity, and ease of use. METHODS: We analyzed 25 formalin-fixed, paraffin-embedded lung cancer samples of different size and tumor percentage for known KRAS and EGFR hotspot mutations with two dedicated genotyping platforms (cobas [Roche Diagnostics, Almere, The Netherlands] and Rotor-Gene [QIAGEN, Venlo, The Netherlands]) and two NGS platforms (454 Genome Sequencer [GS] junior [Roche Diagnostics] and Ion Torrent Personal Genome Machine [Life Technologies, Bleiswijk, The Netherlands]). RESULTS: All platforms, except the 454 GS junior, detected the mutations originally detected by Sanger sequencing and high-resolution melting prescreening and detected an additional KRAS mutation. The dedicated genotyping platforms outperformed the NGS platforms in speed and ease of use. The large sequencing capacity of the NGS platforms enabled them to deliver all mutation information for all samples at once. CONCLUSIONS: Sensitivity for detecting mutations was highly comparable among all platforms. The choice for either a dedicated genotyping platform or an NGS platform is basically a trade-off between speed and genetic information.
Asunto(s)
Carcinoma de Pulmón de Células no Pequeñas/genética , Análisis Mutacional de ADN/métodos , Receptores ErbB/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Neoplasias Pulmonares/genética , Proteínas Proto-Oncogénicas/genética , Proteínas ras/genética , Secuencia de Bases , Carcinoma de Pulmón de Células no Pequeñas/diagnóstico , Costos y Análisis de Costo , Análisis Mutacional de ADN/economía , ADN de Neoplasias/química , ADN de Neoplasias/aislamiento & purificación , Educación Médica Continua , Genotipo , Secuenciación de Nucleótidos de Alto Rendimiento/economía , Humanos , Neoplasias Pulmonares/diagnóstico , Mutación , Adhesión en Parafina , Proteínas Proto-Oncogénicas p21(ras) , Sensibilidad y Especificidad , Análisis de Secuencia de ADN , Factores de TiempoRESUMEN
BACKGROUND: Expression of estrogen receptor alpha (ERα) is predictive for endocrine therapy response and an important prognostic factor in breast cancer. Overexpression of ERα can be caused by estrogen receptor 1 (ESR1) gene amplification and was originally reported to be a frequent event associated with a significantly longer survival for ER-positive women treated with adjuvant tamoxifen monotherapy, which was however questioned by subsequent studies. METHODS: This study aimed to reanalyze the frequency of ESR1 amplification by multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridisation (FISH), and to assess clinicopathologic correlations. MLPA was performed in a group of 135 breast cancer patients, and gains/amplifications were subjected to FISH. RESULTS: True ESR1 amplification by MLPA was rare (2%) and only 6% more patients showed a modest gain of ESR1. All MLPA-detected ESR1 amplifications and nearly all ESR1 gains were also FISH amplified and gained, but not all FISH amplifications/gains were MLPA amplified/gained, leading to an overall concordance of only 60% between both techniques. All 3 MLPA and FISH ESR1 amplified cases had high ERα expression, but there was no obvious correlation between ESR1 gain and ER status by IHC. ESR1 gains/amplifications were not associated with HER2 gain/amplification, but seemed to be associated with older age. Surprisingly, ESR1 gain/amplification was not associated with low grade as reported previously, but correlated with high grade and high proliferation. Furthermore, ESR1 gain/amplification by MLPA was not associated with nodal status or tumor size (pT status). CONCLUSIONS: ESR1 amplification as detected by MLPA is rare in breast cancer, and seems to be associated with high ERα expression, high age, high grade and high proliferation. This study confirms previous studies that showed differences in the ESR1 amplification frequencies detected by different techniques.
RESUMEN
BACKGROUND: Expression of estrogen receptor alpha (ERα) is predictive for endocrine therapy response and an important prognostic factor in breast cancer. Overexpression of ERα can be caused by estrogen receptor 1 (ESR1) gene amplification and was originally reported to be a frequent event associated with a significantly longer survival for ER-positive women treated with adjuvant tamoxifen monotherapy, which was however questioned by subsequent studies. METHODS: This study aimed to reanalyze the frequency of ESR1 amplification by multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridisation (FISH), and to assess clinicopathologic correlations. MLPA was performed in a group of 135 breast cancer patients, and gains/amplifications were subjected to FISH. RESULTS: True ESR1 amplification by MLPA was rare (2%) and only 6% more patients showed a modest gain of ESR1. All MLPA-detected ESR1 amplifications and nearly all ESR1 gains were also FISH amplified and gained, but not all FISH amplifications/gains were MLPA amplified/gained, leading to an overall concordance of only 60% between both techniques. All 3 MLPA and FISH ESR1 amplified cases had high ERα expression, but there was no obvious correlation between ESR1 gain and ER status by IHC. ESR1 gains/amplifications were not associated with HER2 gain/amplification, but seemed to be associated with older age. Surprisingly, ESR1 gain/amplification was not associated with low grade as reported previously, but correlated with high grade and high proliferation. Furthermore, ESR1 gain/amplification by MLPA was not associated with nodal status or tumor size (pT status). CONCLUSIONS: ESR1 amplification as detected by MLPA is rare in breast cancer, and seems to be associated with high ERα expression, high age, high grade and high proliferation. This study confirms previous studies that showed differences in the ESR1 amplification frequencies detected by different techniques.