Utility of targeted next-generation sequencing assay to detect 1p/19q co-deletion in formalin-fixed paraffin-embedded glioma specimens

Pallavajjala, Aparna; Haley, Lisa; Stinnett, Victoria; Adams, Emily; Pallavajjala, Roshni; Huang, Jialing; Morsberger, Laura; Hardy, Melanie; Long, Patty; Gocke, Christopher D.; Eshleman, James R.; Rodríguez, Fausto J.; Zou, Ying

doi:10.1016/j.humpath.2022.05.001

Cited by 8 publications

(7 citation statements)

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“…The target NGS assay was described previously [ 28 , 29 ]. Briefly, DNA was extracted from FFPE specimens with the Siemens tissue preparation automated method (Siemens Healthineers, Munich, Germany).…”

Section: Methodsmentioning

confidence: 99%

“…Library preparation was performed using Kapa Roche HyperPrep reagents (Roche Diagnostics, Inc., Wilmington, MA, USA), and hybrid capture was executed using 40,670 Integrated DNA Technologies probes (Integrated DNA Technologies, Inc., Coralville, IA, USA). Copy number alterations from the NGS data generated using bioinformatics pipelines were described previously [ 28 , 30 ]. NGS coverage-based copy number estimation based on the sequencing coverage depth was used to calculate Log2 fold change for copy number detection [ 28 ].…”

Section: Methodsmentioning

confidence: 99%

“…Copy number alterations from the NGS data generated using bioinformatics pipelines were described previously [ 28 , 30 ]. NGS coverage-based copy number estimation based on the sequencing coverage depth was used to calculate Log2 fold change for copy number detection [ 28 ]. Log2 ratio thresholds were set at ≥ 1.3 as a positive result for HER2 amplification and at < 1.3 as a negative result for HER2 amplification.…”

Section: Methodsmentioning

confidence: 99%

“…Given the advances in biostatic analysis pipelines, NGS methods detect not only somatic mutations, but also have been utilized to evaluate HER2 amplification status. 57 breast carcinoma specimens had NGS data for somatic mutations and HER2 amplification status determined using NGS copy number alteration pipelines [ 28 ]. HER2 amplification status was further compared between HER2 NGS and FISH testing to determine whether HER2 amplification status by NGS could be useful to reveal a subset of HER2 -positive breast carcinomas with a negative IHC and a positive HER2 FISH result.…”

Section: Introductionmentioning

confidence: 99%

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HER2 amplification by next-generation sequencing to identify HER2-positive invasive breast cancer with negative HER2 immunohistochemistry

et al. 2022

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Background Human epidermal growth factor receptor 2 (HER2) positive breast carcinomas due to HER2 amplification are associated with aggressive behavior and a poor prognosis. Anti-HER2-targeted therapies are widely used to treat HER2-positive breast carcinomas with excellent outcomes. Accurate identification of HER2 amplification status in breast carcinomas is of important diagnostic and treatment value. Currently, HER2 amplification status is routinely determined by immunohistochemistry (IHC) and/or fluorescence in situ hybridization (FISH) testing. This study will review our past HER2 data to determine and characterize discordant results between HER2 IHC and FISH. It will also determine a potential impact of HER2 amplification status by next-generation sequencing (NGS) on these patients. Methods We reviewed a total of 4884 breast carcinomas with coexisting HER2 IHC and HER2 FISH performed at our institution from 2010 to 2022. 57 cases also had a Next-Generation-Sequencing-based (NGS) gene panel performed. Given the advances in biostatic analysis pipelines, NGS methods were utilized to provide results on HER2 amplification status along with somatic mutations. Results While the majority (ranging from 98.5% with IHC score of 0 and 93.1% with IHC score of 1 +) of 4884 breast carcinomas had concordant results from HER2 IHC and HER2 FISH testing, a small percentage of patients (ranging from 1.5% in those with IHC score of 0, to 6.9% with IHC score of 1 +) had discordant results, with negative HER2 IHC and positive HER2 FISH results. These patients could be reported as HER2-negative breast carcinomas if only HER2 IHC testing has been performed according to a current cost-effective HER2 test strategy. 57 patients had HER2 amplification status determined by NGS, and all patients had concordant results between HER2 NGS and FISH tests. A HER2-amplified breast carcinoma by NGS had a negative IHC and a positive HER2 FISH result. This case was classified as a HER2-positive breast carcinoma, had anti-HER2-targeted therapy, and achieved a complete clinical response. Conclusions A small percentage of HER2-positive breast carcinomas are unidentified because of a negative HER2 IHC based on our current cost-effective HER2 test strategy. It is not feasible and affordable in routine clinical practice to perform HER2 FISH for the cases with negative HER2 IHC (IHC score 0 and 1 +). Therefore, NGS assays capable of simultaneously detecting both somatic mutations and HER2 amplification could provide a more comprehensive genetic profiling for breast carcinomas in a clinical setting. Identification of HER2 amplification by NGS in HER2-positive breast carcinomas with negative HER2 IHC results is important since these cases are concealed by our current cost-effective HER2 test strategy with IHC first (for all cases) and FISH reflex (only for cases with IHC score of 2 +), and would offer the opportunity for potentially beneficial anti-HER2-targeted therapies for these patients.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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HER2 amplification by next-generation sequencing to identify HER2-positive invasive breast cancer with negative HER2 immunohistochemistry

et al. 2022

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“…En 247 pacientes consecutivos con tumores cerebrales fijados en formalina e incluidos en parafina con varios subtipos, la NGS reveló la codeleción 1p/19q en 26 oligodendrogliomas y un astrocitoma de tipo salvaje IDH. Se encontró también pérdida parcial en los cromosomas 1p y 19q; pérdida de todo el brazo en solo uno de los dos cromosomas, y CN-LOH en 11 tumores no oligodendrogliales 71 .…”

Section: Tema Centralunclassified

Ventajas de la secuenciación de próxima generación sobre la hibridación fluorescente in situ para detectar la codeleción 1p/19q en oligodendrogliomas

Gómez¹,

Pareja²,

Sanchez³

et al. 2023

MedUPB

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El perfil molecular de los gliomas permite garantizar la precisión del diagnóstico, informar el pronóstico e identificar opciones de tratamiento. Esta revisión tiene como objetivo exponer que con la secuenciación de próxima generación (NSG) el diagnóstico de los pacientes con oligodendrogliomas puede ser más exacto. Además, con un dispositivo de diagnóstico in vitro, basado en la NSG (F1CDx), en el que se utilizan los bloques de parafina de gliomas para analizar hasta 395 genes relacionados con cáncer (incluido IDH 1 y 2), se puede también informar la pérdida de la totalidad del brazo corto del cromosoma 1 y del brazo largo del cromosoma 19 (codeleción 1p/19q), a diferencia de la hibridación fluorescente in situ (FISH) que detecta desde la más mínima deleción, lo cual los hace sensibles pero no específicos ya que el FISH es incapaz de distinguir entre la pérdida de la totalidad del brazo del cromosoma y una deleción focal. Esta distinción es importante ya que la sobrevida es inferior en tumores con deleción parcial en relación con los oligodendrogliomas, que tienen por definición la pérdida total de ambos cromosomas. Se hace también alusión a otras plataformas genómicas como GlioSeq y GLIO-DNA panel, que pueden cumplir la misma función. En conclusión, la F1CDx puede determinar con precisión 1p/19q con una concordancia del 96.7% frente a FISH. Los casos en que el FISH dio positivo y no concordaban con F1CDx, era porque no se trataba de oligodendrogliomas. F1CDx también analiza todos los genes que permiten la aproximación más exacta al diagnóstico de oligodendroglioma.

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The development of a custom RNA-sequencing panel for the identification of predictive and diagnostic biomarkers in glioma

Shirai,

Ueno,

Kojima

et al. 2024

J Neurooncol

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Purpose Various molecular profiles are needed to classify malignant brain tumors, including gliomas, based on the latest classification criteria of the World Health Organization, and their poor prognosis necessitates new therapeutic targets. The Todai OncoPanel 2 RNA Panel (TOP2-RNA) is a custom-target RNA-sequencing (RNA-seq) using the junction capture method to maximize the sensitivity of detecting 455 fusion gene transcripts and analyze the expression profiles of 1,390 genes. This study aimed to classify gliomas and identify their molecular targets using TOP2-RNA. Methods A total of 124 frozen samples of malignant gliomas were subjected to TOP2-RNA for classification based on their molecular profiles and the identification of molecular targets. Results Among 55 glioblastoma cases, gene fusions were detected in 11 cases (20%), including novel MET fusions. Seven tyrosine kinase genes were found to be overexpressed in 15 cases (27.3%). In contrast to isocitrate dehydrogenase (IDH) wild-type glioblastoma, IDH-mutant tumors, including astrocytomas and oligodendrogliomas, barely harbor fusion genes or gene overexpression. Of the 34 overexpressed tyrosine kinase genes, MDM2 and CDK4 in glioblastoma, 22 copy number amplifications (64.7%) were observed. When comparing astrocytomas and oligodendrogliomas in gene set enrichment analysis, the gene sets related to 1p36 and 19q were highly enriched in astrocytomas, suggesting that regional genomic DNA copy number alterations can be evaluated by gene expression analysis. Conclusions TOP2-RNA is a highly sensitive assay for detecting fusion genes, exon skipping, and aberrant gene expression. Alterations in targetable driver genes were identified in more than 50% of glioblastoma. Molecular profiling by TOP2-RNA provides ample predictive, prognostic, and diagnostic biomarkers that may not be identified by conventional assays and, therefore, is expected to increase treatment options for individual patients with glioma.

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Utility of targeted next-generation sequencing assay to detect 1p/19q co-deletion in formalin-fixed paraffin-embedded glioma specimens

Cited by 8 publications

References 36 publications

HER2 amplification by next-generation sequencing to identify HER2-positive invasive breast cancer with negative HER2 immunohistochemistry

HER2 amplification by next-generation sequencing to identify HER2-positive invasive breast cancer with negative HER2 immunohistochemistry

Ventajas de la secuenciación de próxima generación sobre la hibridación fluorescente in situ para detectar la codeleción 1p/19q en oligodendrogliomas

The development of a custom RNA-sequencing panel for the identification of predictive and diagnostic biomarkers in glioma

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