Lung cancer mutation testing: a clinical retesting study of agreement between a real-time PCR and a mass spectrometry test

Shepherd, Phillip; Sheath, Karen; Tin, Sandar Tin; Khwaounjoo, Prashannata; Aye, Phyu Sin; Li, Angie; Laking, George; Kingston, Nicola; Elwood, J. Mark; Love, Donald R.; McKeage, Mark J.

doi:10.18632/oncotarget.21023

Cited by 13 publications

(11 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The study was approved by the Northern Health and Disability Ethics committee (No: 13/NTB/165/AM02) and registered (ACTRN12615000998549). More details about the study design and setting are described elsewhere …”

Section: Methodsmentioning

confidence: 99%

Screening for anaplastic lymphoma kinase (ALK) gene rearrangements in non‐small‐cell lung cancer in New Zealand

McKeage

Tin

Khwaounjoo

et al. 2020

Internal Medicine Journal

Self Cite

View full text Add to dashboard Cite

Background Lung cancer is a major cause of death in New Zealand. In recent years, targeted therapies have improved outcomes. Aim To determine the uptake of anaplastic lymphoma kinase (ALK) testing, and the prevalence, demographic profile and outcomes of ALK‐positive non‐small‐cell lung cancer (NSCLC), in New Zealand, where no national ALK‐testing guidelines or subsidised ALK tyrosine kinase inhibitor (TKI) therapies are available. Methods A population‐based observational study reviewed databases to identify patients presenting with non‐squamous NSCLC over 6.5 years in northern New Zealand. We report the proportion tested for ALK gene rearrangements and the results. NSCLC samples tested by fluorescence in situ hybridisation were retested by next generation sequencing and ALK immunohistochemistry. A survival analysis compared ALK‐positive patients treated or not treated with ALK TKI therapy. Results From a total of 3130 patients diagnosed with non‐squamous NSCLC, 407 (13%) were tested for ALK gene rearrangements, and patient selection was variable and inequitable. Among those tested, 34 (8.4%) had ALK‐positive NSCLC. ALK‐positive disease was more prevalent in younger versus older patients, non‐smokers versus smokers and in Māori, Pacific or Asian ethnic groups than in New Zealand Europeans. Fluorescence in situ hybridisation, ALK immunohistochemistry and next generation sequencing showed broad concordance for detecting ALK–positive disease under local testing conditions. Among patients with ALK‐positive metastatic NSCLC, those treated with ALK TKI survived markedly longer than those not treated with ALK TKI (median overall survival 5.12 vs 0.55 years). Conclusion Lung cancer outcomes in New Zealand may be improved by providing national guidelines and funding policy for ALK testing and access to subsidised ALK TKI therapy.

show abstract

Section: Methodsmentioning

confidence: 99%

Screening for anaplastic lymphoma kinase (ALK) gene rearrangements in non‐small‐cell lung cancer in New Zealand

McKeage

Tin

Khwaounjoo

et al. 2020

Internal Medicine Journal

Self Cite

View full text Add to dashboard Cite

show abstract

“…TestSafe is a clinical information sharing service, which compiles the laboratory and radiology reports from DHB facilities, community laboratories, and pharmacists [36]. EGFR mutations were tested by the Roche Cobas® real-time PCR that detects 41 variant sequences in the tyrosine kinase domain (exons 18-21) of the EGFR gene [37] or Agena MassARRAY OncoFOCUS™ [38] test that detects 128 EGFR gene mutations and 63 KRAS, NRAS and BRAF gene mutations, which we previously validated [21]. The positive EGFR mutation in this study refers to EGFR-TKI-sensitive mutations (i.e.…”

Section: Patient Datamentioning

confidence: 99%

“…Soon after testing had commenced in New Zealand, we began a population-based cohort study of non-squamous NSCLC patients presenting in northern New Zealand, which is on-going. Previously we reported on the uptake and impact of EGFR mutation testing in 1857 cohort patients diagnosed up until April 2014 [ 20 ]; EGFR mutation retesting of a subgroup of 532 cohort patients [ 21 ]; the impact of incomplete uptake of testing on estimates of mutation prevalence in 2701 cohort patients diagnosed up until December 2015 [ 22 ], and screening for ALK gene rearrangements in 3130 cohort patients diagnosed up until July 2016 [ 23 ]. In this large population-based study, in northern New Zealand, only 3.7% of non-squamous NSCLC patients were tested in 2010; this increased to 64.6% in 2014 and remained stable afterwards [ 20 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

Development and validation of a predictive model for estimating EGFR mutation probabilities in patients with non-squamous non-small cell lung cancer in New Zealand

et al. 2020

Self Cite

View full text Add to dashboard Cite

Background: Targeted treatment with Epidermal Growth Factor Receptor (EGFR) tyrosine kinase inhibitors (TKIs) is superior to systemic chemotherapy in non-small cell lung cancer (NSCLC) patients with EGFR gene mutations. Detection of EGFR mutations is a challenge in many patients due to the lack of suitable tumour specimens for molecular testing or for other reasons. EGFR mutations are more common in female, Asian and never smoking NSCLC patients. Methods: Patients were from a population-based retrospective cohort of 3556 patients diagnosed with non-squamous non-small cell lung cancer in northern New Zealand between 1 Feb 2010 and 31 July 2017. A total of 1694 patients were tested for EGFR mutations, of which information on 1665 patients was available for model development and validation. A multivariable logistic regression model was developed based on 1176 tested patients, and validated in 489 tested patients. Among 1862 patients not tested for EGFR mutations, 129 patients were treated with EGFR-TKIs. Their EGFR mutation probabilities were calculated using the model, and their duration of benefit and overall survival from the start of EGFR-TKI were compared among the three predicted probability groups: < 0.2, 0.2-0.6, and > 0.6. Results: The model has three predictors: sex, ethnicity and smoking status, and is presented as a nomogram to calculate EGFR mutation probabilities. The model performed well in the validation group (AUC = 0.75). The probability cut-point of 0.2 corresponds 68% sensitivity and 78% specificity. The model predictions were related to outcome in a group of TKItreated patients with no biopsy testing available (n = 129); in subgroups with predicted probabilities of < 0.2, 0.2-0.6, and > 0.6, median overall survival times from starting EGFR-TKI were 4.0, 5.5 and 18.3 months (p = 0.02); and median times remaining on EGFR-TKI treatment were 2.0, 4.2, and 14.0 months, respectively (p < 0.001). Conclusion: Our model may assist clinical decision making for patients in whom tissue-based mutation testing is difficult or as a supplement to mutation testing.

show abstract

“…This technology is based on PCR amplification and allele‐specific single‐based primer extension. Each nucleotide or base added to the primer has a defined mass and is analysed using MALDI‐TOF where the time of flight is proportional to the mass and is linked to specific genotype calls . The actionable mutations BRAF, EGFR, KRAS, NRAS and c‐Kit genes are covered by the OncoCarta Panel.…”

Section: Maldi‐tof Mass Spectrometrymentioning

confidence: 99%

“…Each nucleotide or base added to the primer has a defined mass and is analysed using MALDI-TOF where the time of flight is proportional to the mass and is linked to specific genotype calls. 71 The actionable mutations BRAF, EGFR, KRAS, NRAS and c-Kit genes are covered by the OncoCarta Panel. Other panels include Lung-Carta, OncoFOCUS and the UltraSEEK.…”

Section: Maldi-tof Mass Spectrometrymentioning

confidence: 99%

Somatic mutations and immune checkpoint biomarkers

et al. 2019

View full text Add to dashboard Cite

The development of molecular testing for identifying somatic mutations and immune checkpoint biomarkers has directed treatment towards personalized medicine for patients with non‐small cell lung cancer. The choice of molecular testing in a clinical setting is influenced by cost, expertise in the technology, instrumentation setup and sample type availability. The molecular techniques described in this review include immunohistochemistry (IHC), fluorescent in situ hybridization, direct sequencing, real‐time polymerase chain reaction (PCR), denaturing high‐performance liquid chromatography, matrix‐assisted laser desorption/ionization time of flight mass spectrometry and next‐generation sequencing (NGS). IHC is routinely used in clinical practice for the classification, differentiation, histology and identification of targetable alterations of epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK) and programmed death ligand‐1 (PD‐L1). Recently, the PD‐L1 pathway was identified as being exploited by tumour cells, allowing immune resistance and tumour evasion. The development of immune checkpoint inhibitors as treatment for tumours expressing checkpoints has highlighted the need for standardized IHC assays to inform treatment decisions for patients. Direct sequencing was historically the gold standard for mutation testing for EGFR, KRAS (Kirsten rat sarcoma viral oncogene homologue) and BRAF (v‐Raf murine sarcoma viral oncogene homologue B1) requiring a high ratio of tumour to normal cells, but this has been superseded by more sensitive methods. NGS is a new emerging technique, which allows high‐throughput coverage of frequently mutated genes, including less common BRAF and MET mutations and alterations in tumour suppressor genes. When an NGS platform is unavailable, PCR‐based technologies offer an efficient and cost‐effective single gene test to guide patient treatment. This article will review these techniques and discuss the future of molecular platforms underpinning clinical management decisions.

show abstract

Lung cancer mutation testing: a clinical retesting study of agreement between a real-time PCR and a mass spectrometry test

Cited by 13 publications

References 29 publications

Screening for anaplastic lymphoma kinase (ALK) gene rearrangements in non‐small‐cell lung cancer in New Zealand

Screening for anaplastic lymphoma kinase (ALK) gene rearrangements in non‐small‐cell lung cancer in New Zealand

Development and validation of a predictive model for estimating EGFR mutation probabilities in patients with non-squamous non-small cell lung cancer in New Zealand

Somatic mutations and immune checkpoint biomarkers

Contact Info

Product

Resources

About