Idylla EGFR assay on extracted DNA: advantages, limits and place in molecular screening according to the latest guidelines for non-small-cell lung cancer (NSCLC) patients

AIMS

Idylla epidermal growth factor receptor (EGFR) is a fast and fully automated mutation assay that is easy to implement. However, under the Biocartis-recommended technical conditions, tissue sections are directly introduced into the cartridge, at the risk of exhausting the tumour sample. In this study, we evaluate the performance of Idylla EGFR on extracted DNA and discuss its place within the global non-small-cell lung cancer (NSCLC) screening strategy.

METHODS

577 comparative tests between Idylla EGFR on extracted DNA and next-generation sequencing (NGS) were performed across two centres.

RESULTS

Preanalytical thresholds were established (20% tumour cell content, 50 ng DNA input) and challenged prospectively in routine practice. 16.8% of samples referred for screening were considered non eligible for Idylla EGFR testing. Due to discordant by design cases, Idylla EGFR sensitivity was 86.9% for currently actionable EGFR mutations. Idylla EGFR specificity was 100% in first-line screening. NGS was always feasible on the same DNA.

CONCLUSION

Idylla EGFR on extracted DNA is feasible and enables tumour material to be saved compared with tissue section use. It is not necessary to replace the analytical thresholds of the Biocartis algorithm. Due to both the limits of the mutational repertoire and the high increase of targetable genes in NSCLC, the use of Idylla EGFR should be restricted to clinical emergency situations accompanied by NGS.

An array CGH based genomic instability index (G2I) is predictive of clinical outcome in breast cancer and reveals a subset of tumors without lymph node involvement but with poor prognosis

Background

Despite entering complete remission after primary treatment, a substantial proportion of patients with early stage breast cancer will develop metastases. Prediction of such an outcome remains challenging despite the clinical use of several prognostic parameters. Several reports indicate that genomic instability, as reflected in specific chromosomal aneuploidies and variations in DNA content, influences clinical outcome but no precise definition of this parameter has yet been clearly established.

Methods

To explore the prognostic value of genomic alterations present in primary tumors, we performed a comparative genomic hybridization study on BAC arrays with a panel of breast carcinomas from 45 patients with metastatic relapse and 95 others, matched for age and axillary node involvement, without any recurrence after at least 11 years of follow-up. Array-CGH data was used to establish a two-parameter index representative of the global level of aneusomy by chromosomal arm, and of the number of breakpoints throughout the genome.

Results

Application of appropriate thresholds allowed us to distinguish three classes of tumors highly associated with metastatic relapse. This index used with the same thresholds on a published set of tumors confirms its prognostic significance with a hazard ratio of 3.24 [95CI: 1.76-5.96] p = 6.7x10^-5 for the bad prognostic group with respect to the intermediate group. The high prognostic value of this genomic index is related to its ability to individualize a specific group of breast cancers, mainly luminal type and axillary node negative, showing very high genetic instability and poor outcome. Indirect transcriptomic validation was obtained on independent data sets.

Conclusion

Accurate evaluation of genetic instability in breast cancers by a genomic instability index (G2I) helps individualizing specific tumors with previously unexpected very poor prognosis.

BRAF mutation status in gastrointestinal stromal tumors

Gastrointestinal stromal tumors (GISTs) are mesenchymal tumors characterized by mutations of KIT or PDGFRA. The objectives of this study were to evaluate BRAF mutations in GISTs and then to correlate BRAF mutational status in the tumor with clinical parameters, with B-raf expression, and with activation of some cellular pathways. BRAF mutation was screened in 321 GISTs with 70 wild-type GISTs. BRAF V600E was detected in 9 (13%) of 70 wild-type GISTs. No mutations were detected in GISTs bearing KIT or PDGFRA mutations. BRAF V600E detection in the tumor does not induce a higher expression of the B-raf protein or the preferential activation of the p42/44 mitogen-activated protein kinase (MAPK) signaling pathway compared with GISTs without the BRAF mutation. In comparison with the GIST group with KIT or PDGFRA mutation or the wild-type GIST group without BRAF mutation, the wild-type GIST group with a BRAF mutation is not different in terms of B-raf expression or the p44/42 MAPK- or AKT-activated signaling pathway.

Genomic score predictive of metastatic evolution in breast cancer

Abstract #5069

Background: Despite of the existence of clinical and pathological prognostic factors, the metastatic evolution in breast cancer remains uncertain in a substantial proportion of cases. Previous studies have suggested that genome profiling could address this question. In this context we developed a genomic score to evaluate the total level of copy number aberrations in a given tumor, based on data from array-CGH analysis.
 Material and Methods:We performed array-CGH analysis in a series of 135 sporadic, operable breast cancers treated at our institution between 1989 and 1992 (more than 10 years follow-up). These cases included 45 invasive ductal carcinomas with metastatic evolution (M+) and 90 cases that did not relapse at 11 years (M- ). Cases were paired on patients age and initial axillary lymph node status (pN +/pN0), and were equally distributed between the two groups of evolution: 25 pN0/M+, 20 pN+/M+, 50 pN0/M- and 40 pN+/M-. Tumoral DNA was co-hybridized with pooled normal germline DNA from 20 individuals on a 4407 BAC-array (CIT-V6) provided by the CIT program and manufactured by Integragen. Gain, normal and loss status (GNL) were generated from the CapWeb pipeline developped by the bioinformatics plateforme from Institut Curie (Paris). Clinical, pathological and genomic data were retrieved through Annotator, the CIT cancer database and the analysis has been driven by using the R statistical software along with the CIT R packages.
 Results:The proposed score of genomic instability is based on two items: (i) the proportion of alteration and (ii) the number of altered genomic regions. By applying a set of appropriate thresholds on these two items we were able to define three highly different prognostic subgroups, 95 % (18/19), 74 % (65/88) and 25 % (7/28) 11 years metastatic-free survival respectively (p-value = 4.04e−10) while univariate analysis of histological parameters such as tumor size and SBR grade showed weaker associations (p-values of 0.006 and 0.065 respectively). The predictive properties of the genomic score have been assessed by cross-validation but also on other independent large data sets. A signature of genome instability inferred from genomic and gene expression profiles will also be proposed.
 Conclusion: Genomic profiling in breast carcinoma is a strong tool for prognostication in breast cancer. We developed a computational method to characterize genome instability of that predict clinical outcome in breast cancer and could be useful for more accurate therapeutic choice but also for identifying new therapeutical targets.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 5069.

Contribution of PTEN large rearrangements in Cowden disease: a multiplex amplifiable probe hybridisation (MAPH) screening approach

BACKGROUND

Cowden disease is an autosomal dominant syndrome predisposing to cancer and characterised by the occurrence throughout life of hyperplastic, hamartomatous and tumoural lesions affecting various organs. In 60-80% of patients a germline intragenic point mutation of the PTEN tumour suppressor gene is identified, but at least 20% of patients with a well characterised phenotype remain without any identified mutation.

METHODS

To evaluate the impact of large rearrangement involving the PTEN locus in Cowden disease, we analysed by a multiplex amplifiable probe hybridisation (MAPH) technique 80 unrelated patients referred for diagnosed or suspected Cowden disease, and in whom no PTEN point mutation was detected by a denaturing gradient gel electrophoresis (DGGE) screening.

RESULTS

Four heterozygous genomic deletions involving the PTEN gene were identified. These deletions ranged from 13.6-662 kb and are restricted to the PTEN locus in two cases. In the two other cases, the deletion encompassed PTEN and either two or three contiguous genes without any obvious phenotypic effect, except a possible consequence of PAPSS2 haploinsufficiency on bone growth. Sequence analysis of the four deleted alleles did not reveal identity or sequence homology at the two breakpoints of a same allele, suggesting that a mechanism such as non-homologous recombination of the breakage and reunion type could lead to the occurrence of these deletions.

CONCLUSION

Large rearrangements of the PTEN gene can be involved as causing mutation in Cowden disease and MAPH is an efficient screening methodology to detect such a genetic alteration.