Assessing standardization of molecular testing for non-small-cell lung cancer: results of a worldwide external quality assessment (EQA) scheme for EGFR mutation testing

BACKGROUND

The external quality assurance (EQA) process aims at establishing laboratory performance levels. Leading European groups in the fields of EQA, Pathology, and Medical and Thoracic Oncology collaborated in a pilot EQA scheme for somatic epidermal growth factor receptor (EGFR) gene mutational analysis in non-small-cell lung cancer (NSCLC).

METHODS

EQA samples generated from cell lines mimicking clinical samples were provided to participating laboratories, each with a mock clinical case. Participating laboratories performed the analysis using their usual method(s). Anonymous results were assessed and made available to all participants. Two subsequent EQA rounds followed the pilot scheme.

RESULTS

One hundred and seventeen labs from 30 countries registered and 91 returned results. Sanger sequencing and a commercial kit were the main methodologies used. The standard of genotyping was suboptimal, with a significant number of genotyping errors made. Only 72 out of 91 (72%) participants passed the EQA. False-negative and -positive results were the main sources of error. The quality of reports submitted was acceptable; most were clear, concise and easy to read. However, some participants reported the genotyping result in the absence of any interpretation and many obscured the interpretation required for clinical care.

CONCLUSIONS

Even in clinical laboratories, the technical performance of genotyping in EGFR mutation testing for NSCLC can be improved, evident from a high level of diagnostic errors. Robust EQA can contribute to global optimisation of EGFR testing for NSCLC patients.

Evidence for the role of EPHX2 gene variants in anorexia nervosa

Anorexia nervosa (AN) and related eating disorders are complex, multifactorial neuropsychiatric conditions with likely rare and common genetic and environmental determinants. To identify genetic variants associated with AN, we pursued a series of sequencing and genotyping studies focusing on the coding regions and upstream sequence of 152 candidate genes in a total of 1205 AN cases and 1948 controls. We identified individual variant associations in the Estrogen Receptor-ß (ESR2) gene, as well as a set of rare and common variants in the Epoxide Hydrolase 2 (EPHX2) gene, in an initial sequencing study of 261 early-onset severe AN cases and 73 controls (P=0.0004). The association of EPHX2 variants was further delineated in: (1) a pooling-based replication study involving an additional 500 AN patients and 500 controls (replication set P=0.00000016); (2) single-locus studies in a cohort of 386 previously genotyped broadly defined AN cases and 295 female population controls from the Bogalusa Heart Study (BHS) and a cohort of 58 individuals with self-reported eating disturbances and 851 controls (combined smallest single locus P<0.01). As EPHX2 is known to influence cholesterol metabolism, and AN is often associated with elevated cholesterol levels, we also investigated the association of EPHX2 variants and longitudinal body mass index (BMI) and cholesterol in BHS female and male subjects (N=229) and found evidence for a modifying effect of a subset of variants on the relationship between cholesterol and BMI (P<0.01). These findings suggest a novel association of gene variants within EPHX2 to susceptibility to AN and provide a foundation for future study of this important yet poorly understood condition.

Schizophrenia-risk variant rs6994992 in the neuregulin-1 gene on brain developmental trajectories in typically developing children

The neuregulin-1 (NRG1) gene is one of the best-validated risk genes for schizophrenia, and psychotic and bipolar disorders. The rs6994992 variant in the NRG1 promoter (SNP8NRG243177) is associated with altered frontal and temporal brain macrostructures and/or altered white matter density and integrity in schizophrenic adults, as well as healthy adults and neonates. However, the ages when these changes begin and whether neuroimaging phenotypes are associated with cognitive performance are not fully understood. Therefore, we investigated the association of the rs6994992 variant on developmental trajectories of brain macro- and microstructures, and their relationship with cognitive performance. A total of 972 healthy children aged 3-20 years had the genotype available for the NRG1-rs6994992 variant, and were evaluated with magnetic resonance imaging (MRI) and neuropsychological tests. Age-by-NRG1-rs6994992 interactions and genotype effects were assessed using a general additive model regression methodology, covaried for scanner type, socioeconomic status, sex and genetic ancestry factors. Compared with the C-carriers, children with the TT-risk-alleles had subtle microscopic and macroscopic changes in brain development that emerge or reverse during adolescence, a period when many psychiatric disorders are manifested. TT-children at late adolescence showed a lower age-dependent forniceal volume and lower fractional anisotropy; however, both measures were associated with better episodic memory performance. To our knowledge, we provide the first multimodal imaging evidence that genetic variation in NRG1 is associated with age-related changes on brain development during typical childhood and adolescence, and delineated the altered patterns of development in multiple brain regions in children with the T-risk allele(s).

Lifelong training preserves some redox-regulated adaptive responses after an acute exercise stimulus in aged human skeletal muscle

Several redox-regulated responses to an acute exercise bout fail in aged animal skeletal muscle, including the ability to upregulate the expression of antioxidant defense enzymes and heat shock proteins (HSPs). These findings are generally derived from studies on sedentary rodent models and thus may be related to reduced physical activity and/or intraspecies differences as opposed to aging per se. This study, therefore, aimed to determine the influence of age and training status on the expression of HSPs, antioxidant enzymes, and NO synthase isoenzymes in quiescent and exercised human skeletal muscle. Muscle biopsy samples were obtained from the vastus lateralis before and 3 days after an acute high-intensity-interval exercise bout in young trained, young untrained, old trained, and old untrained subjects. Levels of HSP72, PRX5, and eNOS were significantly higher in quiescent muscle of older compared with younger subjects, irrespective of training status. 3-NT levels were elevated in muscles of the old untrained but not the old trained state, suggesting that lifelong training may reduce age-related macromolecule damage. SOD1, CAT, and HSP27 levels were not significantly different between groups. HSP27 content was upregulated in all groups studied postexercise. HSP72 content was upregulated to a greater extent in muscle of trained compared with untrained subjects postexercise, irrespective of age. In contrast to every other group, old untrained subjects failed to upregulate CAT postexercise. Aging was associated with a failure to upregulate SOD2 and a downregulation of PRX5 in muscle postexercise, irrespective of training status. In conclusion, lifelong training is unable to fully prevent the progression toward a more stressed muscular state as evidenced by increased HSP72, PRX5, and eNOS protein levels in quiescent muscle. Moreover, lifelong training preserves some (e.g., CAT) but not all (e.g., SOD2, HSP72, PRX5) of the adaptive redox-regulated responses after an acute exercise bout. Collectively, these data support many but not all of the findings from previous animal studies and suggest parallel aging effects in humans and mice at rest and after exercise that are not modulated by training status in human skeletal muscle.

Energy dependence of the transverse momentum distributions of charged particles in pp collisions measured by ALICE

Differential cross sections of charged particles in inelastic pp collisions as a function of p_T have been measured at [Formula: see text] at the LHC. The p_T spectra are compared to NLO-pQCD calculations. Though the differential cross section for an individual [Formula: see text] cannot be described by NLO-pQCD, the relative increase of cross section with [Formula: see text] is in agreement with NLO-pQCD. Based on these measurements and observations, procedures are discussed to construct pp reference spectra at [Formula: see text] up to p_T=50 GeV/c as required for the calculation of the nuclear modification factor in nucleus-nucleus and proton-nucleus collisions.

Directed flow of charged particles at midrapidity relative to the spectator plane in Pb-Pb collisions at √(s(NN))=2.76 TeV

The directed flow of charged particles at midrapidity is measured in Pb-Pb collisions at √(s(NN))=2.76 TeV relative to the collision symmetry plane defined by the spectator nucleons. A negative slope of the rapidity-odd directed flow component with approximately 3 times smaller magnitude than found at the highest RHIC energy is observed. This suggests a smaller longitudinal tilt of the initial system and disfavors the strong fireball rotation predicted for the LHC energies. The rapidity-even directed flow component is measured for the first time with spectators and found to be independent of pseudorapidity with a sign change at transverse momenta p(T) between 1.2 and 1.7  GeV/c. Combined with the observation of a vanishing rapidity-even p(T) shift along the spectator deflection this is strong evidence for dipolelike initial density fluctuations in the overlap zone of the nuclei. Similar trends in the rapidity-even directed flow and the estimate from two-particle correlations at midrapidity, which is larger by about a factor of 40, indicate a weak correlation between fluctuating participant and spectator symmetry planes. These observations open new possibilities for investigation of the initial conditions in heavy-ion collisions with spectator nucleons.

K(S)0 and Λ production in Pb-Pb collisions at √(s(NN))=2.76 TeV

The ALICE measurement of K(S)(0) and Λ production at midrapidity in Pb-Pb collisions at √(s(NN))=2.76 TeV is presented. The transverse momentum (p(T)) spectra are shown for several collision centrality intervals and in the p(T) range from 0.4 GeV/c (0.6 GeV/c for Λ) to 12 GeV/c. The p(T) dependence of the Λ/K(S)(0) ratios exhibits maxima in the vicinity of 3 GeV/c, and the positions of the maxima shift towards higher p(T) with increasing collision centrality. The magnitude of these maxima increases by almost a factor of three between most peripheral and most central Pb-Pb collisions. This baryon excess at intermediate p(T) is not observed in pp interactions at √s=0.9 TeV and at √s=7 TeV. Qualitatively, the baryon enhancement in heavy-ion collisions is expected from radial flow. However, the measured p(T) spectra above 2 GeV/c progressively decouple from hydrodynamical-model calculations. For higher values of p(T), models that incorporate the influence of the medium on the fragmentation and hadronization processes describe qualitatively the p(T) dependence of the Λ/K(S)(0) ratio.

Charmonium and e+e- pair photoproduction at mid-rapidity in ultra-peripheral Pb-Pb collisions at [Formula: see text]

The ALICE Collaboration at the LHC has measured the J/ψ and ψ' photoproduction at mid-rapidity in ultra-peripheral Pb-Pb collisions at [Formula: see text]. The charmonium is identified via its leptonic decay for events where the hadronic activity is required to be minimal. The analysis is based on an event sample corresponding to an integrated luminosity of about 23 μb-1. The cross section for coherent and incoherent J/ψ production in the rapidity interval -0.9 Collapse

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Abstract PL02-04: IDH mutations and tumorigenicity

Mutations in the isocitrate dehydrogenase 1 (IDH1) and 2 (IDH2) genes are present in ∼20% of acute myeloid leukemia, and cause a neomorphic enzyme activity that results in the production of 2-hydroxyglutarate (2HG). Mutational and epigenetic profiling of a large patient cohort of acute myeloid leukemia (AML) has revealed that IDH1/2-mutant AMLs display global DNA hypermethylation and impaired hematopoietic differentiation.

To further investigate the intrinsic effect of 2HG on hematopoietic proliferation and differentiation, we transfected an erythroleukemia cell line (TF-1) with either IDH1 or IDH2 mutant alleles. These cells overexpress the mutant enzyme, have high levels of 2HG, and exhibit GM-CSF independent growth. Consistent with clinical observations, overexpression of the IDH mutant proteins led to hypermethylation of both histones and DNA. These results suggest that mutations in IDH1/2 could lead to epigenetic rewiring of cells that could facilitate the gain of function phenotype. We are currently studying the global and specific effects of IDH1/2 mutant overexpression to gain a broader understanding of the biological consequence of the IDH1/2 gain of function mutations.

We have also generated mutation selective molecules that are capable of inhibiting IDHm enzymes. Upon compound treatment in vitro, we are able to reverse hypermethylation of both histones and DNA and induce cellular differentiation in IDHm cell lines and primary human IDHm AML patient samples(1, 2). These data suggest that an inhibitor of IDH1/2 mutations could correct the altered gene expression patterns seen in IDH1/2 mutant AML tumors leading to a profound effect on hematopoietic differentiation, proliferation and tumor growth.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):PL02-04.

Citation Format: F. Wang, J. Travins, B. DeLaBarre, V. Penard-Lacronique, S. Schalm, E. Hansen, K. Straley, A. Kernytsky, W. Liu, C. Gliser, H. Yang, S. Gross, E. Artin, V Saada, E. Mylonas, C. Quivoron, J. Popovici-Muller, J. O. Saunders, F. G. Salituro, S. Yan, S. Murray, W. Wei, Y. Gao, L. Dang, M. Dorsch, S. Agresta, D. P. Schenkein, S. A. Biller, S. M. Su, S. de Botton, Katharine E. Yen. IDH mutations and tumorigenicity. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr PL02-04.

J/ψ elliptic flow in Pb-Pb collisions at √(s(NN))=2.76 TeV

We report on the first measurement of inclusive J/ψ elliptic flow v2 in heavy-ion collisions at the LHC. The measurement is performed with the ALICE detector in Pb-Pb collisions at √(s(NN))=2.76 TeV in the rapidity range 2.5<y<4.0. The dependence of the J/ψ v2 on the collision centrality and on the J/ψ transverse momentum is studied in the range 0≤p(T)<10 GeV/c. For semicentral Pb-Pb collisions at √(s(NN))=2.76 TeV, an indication of nonzero v2 is observed with a largest measured value of v2=0.116±0.046(stat)±0.029(syst) for J/ψ in the transverse momentum range 2≤p(T)<4 GeV/c. The elliptic flow measurement complements the previously reported ALICE results on the inclusive J/ψ nuclear modification factor and favors the scenario of a significant fraction of J/ψ production from charm quarks in a deconfined partonic phase.

D meson elliptic flow in noncentral Pb-Pb collisions at sqrt[sNN]=2.76 Tev

Azimuthally anisotropic distributions of D0, D+, and D*+ mesons were studied in the central rapidity region (|y|<0.8) in Pb-Pb collisions at a center-of-mass energy sqrt[sNN]=2.76  TeV per nucleon-nucleon collision, with the ALICE detector at the LHC. The second Fourier coefficient v2 (commonly denoted elliptic flow) was measured in the centrality class 30%-50% as a function of the D meson transverse momentum pT, in the range 2-16  GeV/c. The measured v2 of D mesons is comparable in magnitude to that of light-flavor hadrons. It is positive in the range 2<pT<6  GeV/c with 5.7σ significance, based on the combination of statistical and systematic uncertainties.

The association of pre-treatment neutrophil to lymphocyte ratio with overall survival in patients with glioblastoma multiforme

Neutrophil-lymphocyte ratio (NLR) is a marker of systemic inflammatory response and its elevation has recently been shown to be a poor prognostic factor in many malignancies including colon, prostate and bladder cancer. The primary aim of this study was to assess the prognostic impact of NLR in a clinically annotated cohort of patients with glioblastoma multiforme (GBM). We hypothesised that elevated NLR would be associated with worse prognosis. Between 2004 and 2009, 137 patients had surgery for GBM and were assessed for consideration of adjuvant therapy at our institution. Of these, 84 patients with an evaluable pre-corticosteroid full blood count result were identified and included in the final analysis. Median overall survival was 9.3 months (range 0.7-82.1). On univariate analysis, age >65 years, gender, ECOG performance status ≥2, frontal tumour, extent of surgical resection, completion of adjuvant chemoradiation protocol and NLR > 4 were significantly correlated with overall survival. Patients with NLR > 4, had a worse median overall survival at 7.5 months versus 11.2 months in patients with NLR ≤ 4 (hazard ratio 1.6, 95 % CI 1.00-2.52, p = 0.048). On multivariate analysis NLR > 4 remained an independent prognostic indicator for poor outcome. These data are an important reminder of the potential relevance of host immunity in GBM. In our cohort, NLR > 4 conferred a worse prognosis independent of other well established prognostic factors. If validated in other cohorts NLR may prove to be a useful addition in predicting prognosis in GBM patients. The demonstration that host immunity plays a role in GBM biology suggests that investigation of emerging therapies which modulate host immune response are warranted in this disease.

Comparison of the sulfur hexafluoride tracer and respiration chamber techniques for estimating methane emissions and correction for rectum methane output from dairy cows

The objectives of the present study were to compare the sulfur hexafluoride (SF₆) and respiration chamber techniques for measuring methane (CH₄) emissions from dairy cows and to determine the proportion of CH₄ that is released through the rectum. Data used were derived from 20 early lactation dairy cows in a 2 × 2 factorial design study for 4 periods with 6 wk/period. The 4 treatment diets consisted of grass silage and 2 levels of concentrate (30 and 60% dry matter basis), with or without yeast supplement. At the end of each period, CH₄ emissions were measured simultaneously using the SF₆ and respiration chamber techniques when cows were housed in chambers. The SF₆ technique was also used when cows were housed in digestibility units (barn location) before and after respiratory chamber measurements (chamber location). The simultaneous measurements in chamber location revealed that CH₄ emission estimates by the SF₆ technique were similar to those by the respiration chamber technique in the first 3 periods, although the SF₆ estimates were significantly higher in period 4. The regression of all data from the 4 periods demonstrated a linear relationship between the SF₆ and respiration chamber measurements for total CH₄ emissions (g/d, R² = 0.69) and for CH₄ emissions per unit of milk yield (g/kg, R² = 0.88), and a quadratic relationship for CH₄ emissions per unit of dry matter intake (g/kg, R² = 0.64). The CH₄ emissions from the rectum were calculated as the difference between CH₄ estimates from the SF₆ technique when cows were housed in respiratory chambers and barn locations, which was 3% of the total CH₄ emissions from the mouth, nostrils, and rectum. The SF₆ estimates in the chamber location accounted for all sources of emissions, whereas those in the barn location, like that in grazing conditions, did not include CH₄ emission from the rectum. Therefore, the SF₆ measurements for grazing cattle should be adjusted for CH₄ emissions from the rectum (3% of total). We conclude that the SF₆ technique is reasonably accurate for estimating CH₄ emissions.