EGFR Point Mutations Research Articles

Abstract A1-43: Targeted amplicon-based next-generation sequencing of routine solid tumor specimens to detect clinically relevant somatic alterations

Abstract Background: Although precision medicine approaches have revolutionized oncology, widespread adoption requires robust, inexpensive approaches enabling the targeted assessment of all relevant alteration classes from routine tissue samples. Methods: Here we interrogated >7,000 cancer exomes and transcriptomes, along with >30,000 array based cancer genomes to identify recurrent somatic alterations (mutations, copy number alterations [CNAs] and gene fusions) across solid tumors. From this analysis, we developed and validated an integrated multiplexed PCR based Ion Torrent next generation sequencing panel (Oncomine Cancer Research Panel [OCP]) targeting the actionable somatic cancer genome optimized for 20ng of formalin-fixed, paraffin-embedded (FFPE) tissue isolated DNA/RNA. Results: We validated the OCP using FFPE cell line mixtures, as well as a prospective cohort of 104 FFPE tumor specimens sent for concurrent clinical molecular testing, with >97% sensitivity and specificity for the presence/absence of KRAS, EGFR, BRAF and ALK point mutations, indels or gene fusions in this molecular testing cohort. We also applied the OCP to 100 lung cancers, identifying known and novel alterations, including ALK and ROS1 gene fusions. Lastly, applying the OCP to 116 prostate cancers, including 50 previously treated samples, we recapitulated known molecular subtypes, observed distinct profiles according to previous treatment and obtained 100% concordance for isoform specific TMPRSS2:ERG gene fusion detection compared to qPCR. Additionally, OCP profiling supports a novel molecular subtype of prostate cancer defined by IDH1 R132 hotspot mutations and informed on resistance mechanisms in a pre- and post-treatment sample pair. Importantly, 44%, 35% and 9% of patients in the molecular testing, lung and prostate cancer cohorts, respectively, harbored additional alterations (beyond routine molecular testing) associated with FDA approved or NCCN guideline referenced therapies. Conclusions: Through analysis of both DNA and RNA to assess the actionable somatic cancer genome, the validated OCP panel may have utility in both clinical and research settings. Citation Format: Daniel H. Hovelson, Andrew S. McDaniel, Bryan Johnson, Andi K. Cani, Kate Rhodes, Paul D. Williams, Chia-Jen Liu, Santhoshi Bandla, Catherine S. Grasso, Michael J. Quist, Seth Sadis, Daniel R. Rhodes, Scott A. Tomlins. Targeted amplicon-based next-generation sequencing of routine solid tumor specimens to detect clinically relevant somatic alterations. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-43.

Lung Cancer Risk, Genetic Variation, and Air Pollution

Large-scale multinational genome-wide association studies (GWAS) of the genetic variation associated with lung cancer initially found that the 5p15.33, 6p21.33, and 15q25 regions were associated with risk of lung cancer among smokers (Amos et al., 2008, Hung et al., 2008). Interestingly, unique regions including 10q25.2, 6q22.2 and 6p21.32 were associated with lung cancer risk in those who had never smoked (Lan et al., 2012), suggesting that the risk variants for non-smoking related lung cancer were distinct from those for smoking related lung cancer. Given that tobacco smoking is the leading risk factor for lung cancer, it stands to reason that lung cancer in those that abstain from tobacco use would have additional novel risk factors which might include genetics or environmental exposures. Some of the main non-tobacco exposures associated with lung cancer are household air pollution, radon, occupational exposures, and outdoor air pollution (Alberg and Samet, 2003). Among the a priori regions identified by Lan et al.'s GWAS of never smokers, significant gene–environment interactions with household air pollution (HLA Class II rs2395185, p = 0.02; TP63 rs4488809 (rs4600802), p = 0.04) were identified, thus suggesting that the risk of lung cancer associated with household air pollution exposure varied with the respective alleles for these regions. This study and other similar genetic studies provide evidence that the relationships between airborne exposures and genetic variation may contribute to lung cancer among non-smoking individuals.

Prevalence, Clinicopathologic Associations, and Molecular Spectrum of ERBB2 (HER2) Tyrosine Kinase Mutations in Lung Adenocarcinomas

Activating mutations in the tyrosine kinase domain of HER2 (ERBB2) have been described in a subset of lung adenocarcinomas (ADCs) and are mutually exclusive with EGFR and KRAS mutations. The prevalence, clinicopathologic characteristics, prognostic implications, and molecular heterogeneity of HER2-mutated lung ADCs are not well established in U.S. patients. Lung ADC samples (N = 1,478) were first screened for mutations in EGFR (exons 19 and 21) and KRAS (exon 2), and negative cases were then assessed for HER2 mutations (exons 19-20) using a sizing assay and mass spectrometry. Testing for additional recurrent point mutations in EGFR, KRAS, BRAF, NRAS, PIK3CA, MEK1, and AKT was conducted by mass spectrometry. ALK rearrangements and HER2 amplification were assessed by FISH. We identified 25 cases with HER2 mutations, representing 6% of EGFR/KRAS/ALK-negative specimens. Small insertions in exon 20 accounted for 96% (24/25) of the cases. Compared with insertions in EGFR exon 20, there was less variability, with 83% (20/24) being a 12 bp insertion causing duplication of amino acids YVMA at codon 775. Morphologically, 92% (23/25) were moderately or poorly differentiated ADC. HER2 mutation was not associated with concurrent HER2 amplification in 11 cases tested for both. HER2 mutations were more frequent among never-smokers (P < 0.0001) but there were no associations with sex, race, or stage. HER2 mutations identify a distinct subset of lung ADCs. Given the high prevalence of lung cancer worldwide and the availability of standard and investigational therapies targeting HER2, routine clinical genotyping of lung ADC should include HER2.

EGFR exon 20 insertion mutations: Incidence and clinicopathologic characteristics in U.S. patients with lung adenocarcinoma.

10560 Background: Activating insertion mutations in exon 20 of EGFR are reported in a small subset of lung adenocarcinomas (ADC). In contrast to the classic EGFR mutations, they appear to confer primary resistance to currently approved EGFR tyrosine kinase inhibitors. Their incidence and clinicopathologic features are not well established. Methods: Lung ADCs (n=1500) were screened for major activating mutations in EGFR (exons 19 and 21) and KRAS (exon 2). Negative cases were tested for EGFR exon 20 insertions by a PCR-based sizing assay. Extended testing for additional recurrent point mutations in EGFR, KRAS, BRAF, NRAS, PIK3CA, MEK1 and AKT was performed in all cases by Sequenom mass spectrometry. A subset of cases was also tested for ALK rearrangements by FISH. Results: We identified 32cases withEGFRexon 20 insertions, accounting for 11% of all EGFR mutations. EGFRexon 20 insertions were mutually exclusive with the other genetic alterations tested except for PIK3CA mutations. The incidence was higher among never-smokers (p&lt;0.0001) but there was no association with sex, ethnic origin or stage at diagnosis. Insertions were 3, 6, 9 or 12bp; 9bp insertions were most common (50%, 16/32). Morphologically, 90% of tumors were moderate to poorly differentiated with a predominant mixed ADC phenotype. Conclusions: EGFR exon 20 testing may identify a unique subset of EGFR mutant lung ADCs which is significantly larger than previously reported, making this the third most common type of EGFR mutation after exon 19 deletions and L858R. This population could potentially benefit from alternate targeted therapies, many of which are currently in clinical development.

Abstract 129: miR-145 reduces tumor growth by regulating EGFR in human lung adenocarcinoma but not in Erlotinib-resistant cells

Abstract OBJECTIVE: Recent studies suggested that lung adenocarcinomas in never-smokers have characteristics distinct from those in smokers. miRNAs are important modulators in cellular pathways. In this study, we investigate the expression profile of miRNAs in lung adenocarcinomas from nonsmokers and identify their target genes. Our in vitro analyses also assess the miRNA expression associated with erlotinib therapy. METHODS: Lung adenocarcinoma and adjacent normal lung parenchyma were obtained from nonsmokers. Microarray analysis was preformed and the profiling results were validated by qRT-PCR. Transfected cell viability assays were applied to determine the effects of candidate miRNAs on lung cancer cells. Systemic bioinformatic analysis was performed to investigate the potential targets of miRNA in lung cancer. The associations of miRNA and its targeted genes’ expressions were analyzed by miRNA and mRNA microarray profiling in tumor specimens from patients with lung adenocarcinoma. Expressions of miRNA and its gene targets in lung cancer cells were determined by qRT-PCR and validated by Western blot analysis. RESULTS: Comparing paired lung adenocarcinoma tissue with corresponding noncancerous tissues, miR-126*, -145, -21, -182, -183, and -210 were found to be the most differentially expressed miRNAs. An obvious inhibition of cell growth was observed in the EGFR mutant lung adenocarcinoma cells after transfection of pre-miR-145. Our study further identified EGFR and NUTD1 as potential targets of miR-145. The mRNA expressions of EGFR and NUDT1 were significantly downregulated by 60% and 50% respectively after miR-145 transfection. The enforced expression of miR-145 in three lung adenocarcinoma cell lines led to a decrease (2.5-, 5-, and 2-fold) of EGFR protein and the abolishing of NUDT1 protein expressions. In vitro analysis showed that miR-145 can gradually inhibit cell proliferation on transfected lung adenocarcinoma cells over three time points (24, 48, and 72 hours). It was also noteworthy that miR-145 expression and EGFR status correlated with sensitivity to erlotinib. The 3 cell lines treated with erlotinib showing increased expression levels of miR-145 were all mutant EGFR, but not in the 4 lung cancer cell lines with wild-type EGFR or T790M point mutation. DISCUSSION: This study has identified several miRNAs that may play a role in carcinogenesis of lung adenocarcinomas in nonsmokers. Our results also show that restoration of miR-145 inhibits cancer cell growth in EGFR mutant lung adenocarcinoma by targeting EGFR and NUDT1. We further reveal that miR-145 may reduce tumor growth by regulating EGFR in human lung adenocarcinoma but not in erlotinib-resistant cells. Our findings provide new insight into the complex regulating pathway comprising miR-145 and EGFR. Understanding this important pathway may lead to new therapeutic strategies for lung adenocarcinoma in nonsmokers. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 129. doi:1538-7445.AM2012-129

Competitive allele specific TaqMan PCR for KRAS, BRAF and EGFR mutation detection in clinical formalin fixed paraffin embedded samples

BackgroundThe development of targeted therapies has created a need for robust molecular characterization of cancer and it has become a challenge to validate methods to ensure accuracy in tumor mutation testing. MethodsThe current study was designed to evaluate KRAS, BRAF and EGFR genotyping by Competitive Allele Specific hydrolysis probes (TaqMan) PCR technology (CAST), on suboptimal formalin fixed paraffin embedded (FFPE) tumor samples. Assays were calibrated on FFPE samples and a minimal quantification cycle (Cq) cut-off was determined to standardize analyses and avoid over-interpretation of degraded material. Sensibility, specificity and blinded clinical sample screenings (n=63) were evaluated. ResultsCAST PCR allowed efficient amplification of FFPE samples, probes were highly specific and all assays had a sensibility inferior to 1% except for the EGFR p.T790M assay. 60/63 samples were correctly typed. The three missed mutations were EGFR exon 19 deletions that were not recognized by the DEL19 assays that were used. ConclusionsThis technology is less laborious and prevent crossover of PCR products as compared to multistep methods. TaqMan® Mutation Detection assay is an important technology to consider in the field of mutation detection for KRAS, BRAF and EGFR point mutation screening. Assay calibration on FFPE samples may prevent erroneous interpretations that will ultimately harm clinical oncology practice.

Stromal micropapillary pattern predominant lung adenocarcinoma - a report of two cases

Generally, adenocarcinomas with micropapillary pattern, featuring small papillary tufts lacking a central fibrovascular core, are thought to have poor prognosis. This pattern has been described in various organs. However, tumor cells with micropapillary pattern of lung adenocarcinoma are more often seen to float within alveolar spaces (aerogenous micropapillary pattern, AMP) than in fibrotic stroma like other organs (stromal micropapillary pattern, SMP) and SMP predominant lung adenocarcinoma (SMPPLA) has not been well described yet. We presented two cases of SMPPLA which were found in the last four years. Both the cases showed more than 50% of SMP in the tumor area. The majority of the stromal micropapillary clusters expressed MUC1 and epithelial membrane antigen along the outer surface of cell membrane. On the other hand, connective tissues surrounding stromal micropapillary clusters showed no reactivity for epithelial markers (thyroid transcription factor-1 and cytokeratin) or endothelial marker (D2-40 and CD34). It means clusters of SMP do not exist within air space or lymphatic or vessel lumens. The tumors with SMP often presented lymphatic permeation and vessel invasion, and intriguingly, one of the two cases showed metastasis to the mediastinal lymph node. Additionally, both the cases showed EGFR point mutations of exon 21. These results suggest that SMPPLA might be associated with poor prognosis and effective for EGFR tyrosine kinase inhibitors.

Erlotinib May be More Effective for Central Nervous Metastasis of Lung Adenocarcinoma Than Gefitinib Because of the Difference in the Clinical Regimes

A 54-year-old woman with lung adenocarcinoma which has EGFR point mutation at exon 21 initially improved by administration of gefitinib. Lung lesions responded to gefitinib at 250 mg, but central nervous system lesions, such as carcinomatous meningitis and brain metastasis occurred. The therapy was changed from gefitinib to erlotinib at 150 mg, resulting in remarkable improvement of carcinomatous meningitis and brain metastasis improved dramatically. We hypothesized that the effective concentration of the clinical dose of erlotinib in the CSF is higher than that of gefitinib. doi:10.4021/jmc253w

TP53 and p16INK4A mutations in adult-T cell leukemia/lymphoma (ATL) in Bahia (Brazil)

ATL is an aggressive malignancy associated with the HTLV-1. The development of ATL is believed to involve a multitude of factors that include the accumulation of genetic alterations. The aim of this study was to analyze the presence of mutations in the TP53, p16INK4A, p15INK4B, K-ras, PI3K and EGFR genes in ATL patients from Bahia (Brazil) with the acute and chronic subtypes. Fourteen patients with acute ATL and five with chronic ATL were included. Exons 4-9 of the TP53 gene, exons 1-3 of the p16INK4A gene, exons 1-2 of the p15INK4B gene, exons 18-21 of the EGFR gene and exons 9 and 21 of the PI3Ka gene were investigated using PCR followed by sequencing. Mutations at codons 12 and 13 of the K-ras gene were analyzed by RFLP following PCR amplification. In 5 of the 19 ATL patients (26%), missense mutations were observed in the TP53 gene. All of these patients had the acute subtype. Alterations were detected in exon 5 (codons 155 and 181), exon 7 (codon 248) and exon 8 (codon 282). Mutations in codons 155, 181 and 282 had not previously been described in ATL. Missense mutation was observed in p16INK4A in only one patient with acute ATL who did not have alterations in the TP53 gene. Point mutations in p15INK4B, K-ras, EGFR and PI3Ka genes were not found. These results are in agreement with the findings of previous studies suggesting that mutations of the TP53 and p16INK4A genes may play a role in aggressive ATL.

Identification of non-small-cell lung cancer with activating EGFR mutations in malignant effusion and cerebrospinal fluid: Rapid and sensitive detection of exon 19 deletion E746-A750 and exon 21 L858R mutation by immunocytochemistry

Background Recently, we have reported that EGFR mutation-specific antibodies performed well in immunohistochemical analysis, with good sensitivity. We investigated whether this method could detect non-small-cell lung cancer (NSCLC) carrying EGFR mutations in malignant effusions and cerebrospinal fluid (CSF), comparable to the peptide nucleic acid–locked nucleic acid (PNA–LNA) PCR clamp assay. Furthermore, we compared activating EGFR mutations between primary and recurrent NSCLC. Patients and methods Twenty-four patients with NSCLC effusions and CSF were examined by immunocytochemistry using antibodies specific for the E746-A750 deletion mutation in exon 19 and the L858R point mutation in exon 21. The PNA–LNA PCR clamp assay was used to detect the E746-A750 deletion at exon 19, L858R mutation at exon 21, and T790M mutation at exon 20. Results We were able to identify EGFR mutations in NSCLC effusion and CSF with a sensitivity of 100% (5/5) using the anti-delE746-A750 antibody and 100% (8/8) using the anti-L858R antibody. Furthermore, in samples without these EGFR mutations, immunocytochemistry with the two specific antibodies identified 91% (10/11) as negative for both the deletion and the point mutations in EGFR. Activating EGFR mutations decreased in recurrent NSCLC compared with primary NSCLC, and the T790M mutation was detected in recurrent NSCLC of patients receiving gefitinib treatment. Conclusions Identification of EGFR mutations is important for patients with primary and recurrent NSCLC. Rapid and sensitive immunocytochemistry using mutation-specific antibodies to detect EGFR mutations will be useful for diagnosing responsiveness to EGFR-targeted drugs.

Erlotinib May be More Effective for Central Nervous Metastasis of Lung Adenocarcinoma Than Gefitinib Because of the Difference in the Clinical Regimes

A 54-year-old woman with lung adenocarcinoma which has EGFR point mutation at exon 21 initially improved by administration of gefitinib. Lung lesions responded to gefitinib at 250 mg, but central nervous system lesions, such as carcinomatous meningitis and brain metastasis occurred. The therapy was changed from gefitinib to erlotinib at 150 mg, resulting in remarkable improvement of carcinomatous meningitis and brain metastasis improved dramatically. We hypothesized that the effective concentration of the clinical dose of erlotinib in the CSF is higher than that of gefitinib. J Med Cases. 2011;2(5):190-193 doi: https://doi.org/10.4021/jmc253w

Activity and tolerance of XL647 in NSCLC patients with acquired resistance to EGFR-TKIs: Preliminary results of a phase II trial

8028 Background: XL647 is an orally bioavailable small molecule inhibitor of RTKs (EGFR, HER2, and VEGFR2) involved in tumor growth, angiogenesis, and metastasis. First-generation EGFR TKIs are active in NSCLC particularly in pts with EGFR mutations and amplification. However, pts who respond to erlotinib or gefitinib relapse, and no standard therapy exists. In ∼50% of cases this is associated with a second EGFR point mutation (T790M). Preclinically, XL647 inhibits growth of cell lines such as H1975 which also harbor T790M. This study examines the activity of XL647 in pts who have relapsed after initial benefit from erlotinib or gefitinib. Methods: Simon two- stage study with primary endpoint of best confirmed response rate. In case of ≥ 1 response in Stage 1 the study will proceed to Stage 2. Eligibility: Adult pts with relapsed or recurrent NSCLC (Stage IIIB or IV) with documented progressive disease (PD) after benefit including stable disease (SD) from single agent erlotinib or gefitinib administered for ≥12 wks OR who have known T790M. Treatment: XL647 as a single daily dose of 300 mg on a 28-day cycle. Assessment: Response is evaluated by RECIST. EGFR and KRAS2 from circulating plasma DNA are being analyzed using Scorpion ARMS technology (DxS, UK) and also from tumor tissue if available. Results: Twenty-three pts (19F/4M) with a median age of 71 yrs (range 27–90) have been enrolled. One pt had a PR and 7 pts had SD at their first assessment; 14 pts are too early to evaluate; 1 pt discontinued before first assessment with unrelated cardiac arrhythmia. Pts have commonly reported improvement in symptoms while on study. Two pts with SD have discontinued with AEs, one had drug-related grade (g) 4 pulmonary emboli, and one drug-related g2 creatinine elevation (pt had one functional kidney). The most common AEs are g1 diarrhea, rash, and nausea, and g1/2 fatigue. Analysis of plasma from a subset of pts did not reveal common mutations in EGFR or KRAS2. A T790M mutation was detected in tumor tissue from 1pt. Conclusions: XL647 has activity and is well-tolerated in this population. Accrual has been brisk and with the observed partial response the trial has proceeded to Stage 2. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Exelixis

Impact of Common Epidermal Growth Factor Receptor and HER2 Variants on Receptor Activity and Inhibition by Lapatinib

The goal of this study was to characterize the effects of non-small cell lung carcinoma (NSCLC)-associated mutations in epidermal growth factor receptor (EGFR/ErbB1) and HER2 (ErbB2) on interactions with the dual tyrosine kinase inhibitor lapatinib. Biochemical studies show that commonly observed variants of EGFR [G719C, G719S, L858R, L861Q, and Delta746-750 (del15)] are enzyme activating, increasing the tyrosine kinase V(max) and increasing the K(m)((app)) for ATP. The point mutations G719C and L861Q had minor effects on lapatinib K(i)s, whereas EGFR mutations L858R and del15 had a higher K(i) for lapatinib than wild-type EGFR. Structural analysis of wild-type EGFR-lapatinib complexes and modeling of the EGFR mutants were consistent with these data, suggesting that loss of structural flexibility and possible stabilization of the active-like conformation could interfere with lapatinib binding, particularly to the EGFR deletion mutants. Furthermore, EGFR deletion mutants were relatively resistant to lapatinib-mediated inhibition of receptor autophosphorylation in recombinant cells expressing the variants, whereas EGFR point mutations had a modest or no effect. Of note, EGFR T790M, a receptor variant found in patients with gefitinib-resistant NSCLC, was also resistant to lapatinib-mediated inhibition of receptor autophosphorylation. Two HER2 insertional variants found in NSCLC were less sensitive to lapatinib inhibition than two HER2 point mutants. The effects of lapatinib on the proliferation of human NSCLC tumor cell lines expressing wild-type or variant EGFR and HER2 cannot be explained solely on the basis of the biochemical activity or receptor autophosphorylation in recombinant cells. These data suggest that cell line genetic heterogeneity and/or multiple determinants modulate the role played by EGFR/HER2 in regulating cell proliferation.

Gemcitabine (G) combined with gefitinib in patients with inoperable or metastatic pancreatic cancer. A phase II trial

15016 Introduction: Pancreatic cancer is one of the most lethal cancers, with a high incidence of overexpression of EGFR and its ligands. Gemcitabine (G) is the treatment of choice in this tumor. Patients and Methods: From June 2004 to May 2006, 54 patients were registered in the study. Median age was 65 years (range 44–80) and median Karnofsky performance status was 80%. G (1000 mg/m2) was administered weekly for 7 cycles. Gefitinib (250 mg) was given orally. EGFR, HER-2 and PTEN were assessed by IHC and FISH. Biopsies containing =70% tumor were evaluated for the presence of somatic mutations in exons 18–21 of EGFR and exon 2 of RAS by bi-directional sequencing. Results: Ten patients (19%) completed treatment, while 36 patients (67%) progressed before the completion of the treatment. Three patients (6%) had a partial response and 11 patients (20%) had stable disease. After a median follow-up of 9 months, median survival time was 7.4 months, while median time to disease progression (TTP) was 3.9 months. The one-year survival rate was 23%. Rash of any grade was reported in 28 patients (52%). Most common severe toxicities were neutropenia (13%) and leucopenia (6%). RAS mutations were identified in 18/34 patients (53%). Two additional patients had an EGFR point mutation in exon 20. EGFR expression was found in 23/30 patients (77%), while EGFR amplification was not observed. HER-2 gain was detected in 4/20 patients and PTEN deletion in 14/20 patients. PTEN expression was noticed in 7/30 patients and was the only marker associated with significantly increased TTP (p=0.008). Conclusions: The results from this small single arm study were similar to those seen with G plus erlotinib with respect to median and one-year survival. These findings, and the selection of patients with better prognosis based on molecular markers, need to be confirmed in a larger study. No significant financial relationships to disclose.

Impact of EGFR point mutations on the sensitivity to gefitinib: Insights from comparative structural analyses and molecular dynamics simulations

Emergence of resistant mutations in drug targets represents a serious problem in the targeted chemotherapy. One challenging issue is to understand the atomic-detailed effect of the mutation on the target. Another intriguing issue is how to predict specific mutations that would show up in the clinical setting, leading to drug resistance. By computational approaches, we have investigated structural, dynamics and energetic effects of a series of EGFR mutations identified from the lung cancer patients. We demonstrated mutation L858R caused gefitinib move closer to the hinge region, whereas T790M caused the ligand escape from the binding pocket. In particular, the T790M decreased the size of the hydrophobic slot formed by L718 and G796. This suggests that, to be effective against the T790M mutant, the inhibitors should avoid interactions with the hydrophobic slot. Mutations T790M, L858R, and their combinations are found to cause different conformational redistribution and to perturb the electrostatic potential at the ATP-binding pocket. Normal mode analysis revealed the mutations resulted in changes in the correlated movements in the protein. In an attempt to develop a computational descriptor for predicting the functional effect of EGFR mutations, we have developed a Plarm algorithm, and the Plarm score was found to be an excellent predictor of the functional impact of six clinical relevant mutations in EGFR tyrosine kinase domains, including T790M, L858R, G719C, L861Q, T790M + L858R double mutant, and delL747-P753insS. The Plarm algorithm could be readily extended to investigate other drug targets.

EGFR point mutation confers resistance to gefitinib in a patient with non-small-cell lung cancer

EGFR point mutation confers resistance to gefitinib in a patient with non-small-cell lung cancer