scholarly journals GENE-52. ANALYSIS OF RECURRENT MUTATIONS WITHIN CANCERS REVEALS PATTERNS OF DIRECTIONAL EVOLUTION IN BRAIN TUMORS

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi109-vi109
Author(s):  
Asli Küçükosmanoglu ◽  
Carolien L Van Der Borden ◽  
David Noske ◽  
Tom Wurdinger ◽  
Bart Westerman

Abstract INTRODUCTION Intratumor genetic heterogeneity is commonly caused by a stochastic evolution, but can also show remarkable selectivity resulting in directional evolution. We hypothesized that directional evolution is driven by its genetic onset-stage. This process could enforce already existing traits resulting in an enhancement of linear pathways rather than the complementary/parallel evolution. METHODS We generated a prediction model for directional evolution based on its genetic onset-stage. We performed a comprehensive analysis of 16 different tumor types of ~10,000 patients of whole-exome sequencing and copy number variation, obtained from The Cancer Genome Atlas. RESULTS We found in 5% of the patients that directional evolution occurs on a fixed genetic onset stage. There is a strong relationship between the frequencies of directional evolution and the frequencies of commonly co-occurring mutations in the onset stage. These co-occurring mutations are frequently observed in the same chromosomal region and occasionally in the same pathway. Brain tumors show a frequent directional evolution towards EGFR mutations and to a lesser extent PIK3CA mutations. CONCLUSION Given these strong correlations and since directional evolution is apparently a highly selective process, our prediction model could predict more effective therapies by choosing therapies targeting both the mutated gene that is affected by directional evolution as well as the commonly occurring co-mutated genes.

Cancers ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2389
Author(s):  
Yun Mi Choi ◽  
Jinyeong Lim ◽  
Min Ji Jeon ◽  
Yu-Mi Lee ◽  
Tae-Yon Sung ◽  
...  

In pheochromocytoma and paraganglioma (PPGL), germline or somatic mutations in one of the known susceptibility genes are identified in up to 60% patients. However, the peculiar genetic events that drive the aggressive behavior including metastasis in PPGL are poorly understood. We performed targeted next-generation sequencing analysis to characterize the mutation profile in fifteen aggressive PPGL patients and compared accessible data of aggressive PPGLs from The Cancer Genome Atlas (TCGA) with findings of our cohort. A total of 115 germline and 34 somatic variants were identified with a median 0.58 per megabase tumor mutation burden in our cohort. The most frequent mutation was SDHB germline mutation (27%) and the second frequent mutations were somatic mutations for SETD2, NF1, and HRAS (13%, respectively). Patients were subtyped into three categories based on the kind of mutated genes: pseudohypoxia (n = 5), kinase (n = 5), and unknown (n = 5) group. In copy number variation analysis, deletion of chromosome arm 1p harboring SDHB gene was the most frequently observed. In our cohort, SDHB mutation and pseudohypoxia subtype were significantly associated with poor overall survival. In conclusion, subtyping of mutation profile can be helpful in aggressive PPGL patients with heterogeneous prognosis to make relevant follow-up plan and achieve proper treatment.


2010 ◽  
Vol 28 (30) ◽  
pp. 4616-4620 ◽  
Author(s):  
Yihua Sun ◽  
Yan Ren ◽  
Zhaoyuan Fang ◽  
Chenguang Li ◽  
Rong Fang ◽  
...  

Purpose To determine the proportion of lung adenocarcinomas from East Asian never-smokers who harbor known oncogenic driver mutations. Patients and Methods In this surgical series, 52 resected lung adenocarcinomas from never-smokers (< 100 cigarettes in a lifetime) at a single institution (Fudan University, Shanghai, China) were analyzed concurrently for mutations in EGFR, KRAS, NRAS, HRAS, HER2, BRAF, ALK, PIK3CA, TP53 and LKB1. Results Forty-one tumors harbored EGFR mutations, three harbored EML4-ALK fusions, two harbored HER2 insertions, and one harbored a KRAS mutation. All mutations were mutually exclusive. Thus, 90% (47 of 52; 95% CI, 0.7896 to 0.9625) of lung adenocarcinomas from never-smokers were found to harbor well-known oncogenic mutations in just four genes. No BRAF, NRAS, HRAS, or LKB1 mutations were detected, while 15 had TP53 mutations. Four tumors contained PIK3CA mutations, always together with EGFR mutations. Conclusion To our knowledge, this study represents the first comprehensive and concurrent analysis of major recurrent oncogenic mutations found in a large cohort of lung adenocarcinomas from East Asian never-smokers. Since drugs are now available that target mutant EGFR, HER2, and ALK, respectively, this result indicates that prospective mutation testing in these patients should successfully assign a targeted therapy in the majority of cases.


Author(s):  
Chakkrit Tantithamthavorn ◽  
Shane McIntosh ◽  
Ahmed E Hassan ◽  
Kenichi Matsumoto

Shepperd et al. (2014) find that the reported performance of a defect prediction model shares a strong relationship with the group of researchers who construct the models. In this paper, we perform an alternative investigation of Shepperd et al. (2014)’s data. We observe that (a) researcher group shares a strong association with the dataset and metric families that are used to build a model; (b) the strong association among the explanatory variables introduces a large amount of interference when interpreting the impact of the researcher group on model performance; and (c) after mitigating the interference, we find that the researcher group has a smaller impact than the metric family. These observations lead us to conclude that the relationship between the researcher group and the performance of a defect prediction model may have more to do with the tendency of researchers to reuse experimental components (e.g., datasets and metrics). We recommend that researchers experiment with a broader selection of datasets and metrics to combat potential bias in their results.


The basis of any analysis is done by the elements that are processed in an information system: data, information, knowledge, wisdom, highlighting the characteristics and differences between them. A higher level of organization and information processing involve analysis of information systems and management information system. There is a strong relationship between business architecture and software architecture, taking into account their interdependence and their parallel evolution in the business. SCADA, as technology for supervising and controlling industrial processes is presented through its characteristics and how it has contributed to the reorganization of the electricity system. The main objective of the chapter is to understand that the information processed in the REB cannot be treated chaotically, but should be treated properly, within a management information system, that allows processing of a huge volume of data in real time.


2019 ◽  
Vol 2019 ◽  
pp. 1-7
Author(s):  
Qian Gao ◽  
Yan Cui ◽  
Yanan Shen ◽  
Yanyan Li ◽  
Xue Gao ◽  
...  

The pathogenesis and prognosis of glioblastoma (GBM) remain poorly understood. Mutual exclusivity analysis can distinguish driver genes and pathways from passenger ones. The purpose of this study was to identify mutually exclusive gene sets (MEGSs) that have prognostic value and to detect novel driver genes in GBM. The genomic alteration profile and clinical information were derived from The Cancer Genome Atlas, and the MEGSA method was used to identify the MEGS. Next, we performed survival analysis and constructed a risk prediction model for prognostic stratification. Leave-one-out cross-validation and permutation test were used to evaluate its performance. Finally, we identified 21 statistically significant MEGSs. We found that the MEGS in the RB pathway was significantly associated with poor prognosis, after adjusting for age and gender (HR = 1.837, 95% CI: 1.192–2.831). Based on the risk prediction model, 208 (80.9%) and 49 (19.1%) patients were assigned to high- and low-risk groups, respectively (log-rank: p<0.001, adjusted p=0.001). Additionally, we found that SPTA1, a novel gene involved in the MEGS, was mutually exclusive with members of cell cycle, P53, and RB pathways. In conclusion, the MEGS in the RB pathway had considerable clinical value for GBM prognostic stratification. Mutated SPTA1 may be involved in GBM development.


2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kanggeun Lee ◽  
Hyoung-oh Jeong ◽  
Semin Lee ◽  
Won-Ki Jeong

AbstractWith recent advances in DNA sequencing technologies, fast acquisition of large-scale genomic data has become commonplace. For cancer studies, in particular, there is an increasing need for the classification of cancer type based on somatic alterations detected from sequencing analyses. However, the ever-increasing size and complexity of the data make the classification task extremely challenging. In this study, we evaluate the contributions of various input features, such as mutation profiles, mutation rates, mutation spectra and signatures, and somatic copy number alterations that can be derived from genomic data, and further utilize them for accurate cancer type classification. We introduce a novel ensemble of machine learning classifiers, called CPEM (Cancer Predictor using an Ensemble Model), which is tested on 7,002 samples representing over 31 different cancer types collected from The Cancer Genome Atlas (TCGA) database. We first systematically examined the impact of the input features. Features known to be associated with specific cancers had relatively high importance in our initial prediction model. We further investigated various machine learning classifiers and feature selection methods to derive the ensemble-based cancer type prediction model achieving up to 84% classification accuracy in the nested 10-fold cross-validation. Finally, we narrowed down the target cancers to the six most common types and achieved up to 94% accuracy.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1685-1685 ◽  
Author(s):  
Malgorzata Zajac ◽  
Joanna Zaleska ◽  
Anna Dolnik ◽  
Anna Siwiec ◽  
Olga Jankowska-Lecka ◽  
...  

Abstract Background One of the potential mechanisms responsible for leukemic cells evading cytotoxic T lymphocytes might be the pathway of programmed death-1 receptor (PD-1). PD-1 and its ligand PD-L1 play a key role in tumor immune escape and the formation of tumor microenvironment, promoting tumor development. Aims As PD-L1 expression was broadly described in many types of human cancer cells including AML, we were focused on PD-1 expression, which until now was mostly characterized for T cells, where it inhibits proliferation and cytotoxic capabilities. Recently, Wang et al. described PD-L1 expression regulation through miR-34a molecules in AML patients. Overexpression of miR-34a blocked PD-L1 and reduced its surface expression. Moreover, Cortez et al. for the first time identified novel, complete mechanism of PD-L1 regulation by p53 via miR-34a in non-small cell lung cancer (NSCLC). In this study, our comprehensive analyses of PD-1, PD-L1, TP53and miR-34a expression in AML patients shed new light on the complex regulation of PD-1/PD-L1 axis during development of this disease. Methods We performed analysis of TP53, PD-1, PD-L1 and miR-34a expression in 197 AML patients available from The Cancer Genome Atlas (TCGA) database. Moreover, we assessed mRNA expression of TP53 and PD-1 in independent cohort of 54 primary AML patient samples using qRT-PCR method. We also characterized several SNPs for PD-1that demonstrate relevant associations with a higher risk of developing autoimmune diseases: PD-1.1 (rs36084323), PD-1.3 (rs11568821), PD-1.5 (rs2227981), PD-1.6 (rs10204525), PD -1.7 (rs41386349), PD-1.9 (rs2227982) in 54 AML, 64 MDS and 100 HVs samples. Results TCGA data analysis showed higher expression of PD-L1 in the AML group with low expression of TP53 (p=0.008). In contrast, PD-L1 expression was elevated in the group with TP53 mutations compared to unmutated TP53 (p<0.001).We also found a negative correlation of miR-34a and PD-L1 expression (r=-0.2; p=0.005), while there were no differences in PD-L1 expression between groups with or without following mutations: IDH1, TET2, RUNX1, NRAS, CEBPA, PTPN11, KIT, KRAS, FLT3, DNMT3, NPM1 and IDH2. The highest expression of PD-L1 was found in the poor prognosis group according to cytogenetic risk and molecular risk markers. We also observed an association between the expression level of PD-L1 and the number of recurrent mutations present in an AML case. Patients with more than 4 recurrent mutations were characterized with higher expression of PD-L1 compared to the group of patients with 0-3 recurrent mutations (p=0.01). Next, we observed significant differences in PD-1 expression in the group of 54 AML patients compared to HVs (p<0.001), and there were differences in the PD-1expression level regarding the PD-1. 5 polymorphism (p=0.07). Moreover, analysis of the PD-1. 3 polymorphism in HVs and MDS revealed that genotype GG was associated with nearly fivefold lower risk of disease (OR=4.93, p=0.009). We observed significant differences in OS in AML patients in case of presence of certain genotypes of PD-1. 6. Genotype AA was significant associated with higher risk of shorter OS compared to the rest of the genotypes (58 vs 333 days, HR=35; p=0.02). Conclusions Our analyses indicate that p53 might specifically modulate the tumor immune response by regulating PD-L1 via miR-34a which directly binds to the PD-L13'-UTR and blocks its expression. Moreover, we found that high PD-L1 expression is associated with the higher numbers of recurrent mutations as well as poor cytogenetic and molecular risk groups. We found significant differences in PD-1expression in AML patients compared to HVs that further support a deregulation of a signal transduction through the PD-1/PD-1L axis in AML. While our SNP analysis in AML patients suggested a prognostic impact of PD-1. 6 polymorphism, further studies are warranted to evaluate the impact of the PD-1/PD-L1 axis in AML. This work was supported by National Centre for Science Grant HARMONIA (UMO-2013/10/M/NZ5/00313). Disclosures Grzasko: Janssen: Honoraria; Munipharma: Honoraria; Celgene: Honoraria.


2013 ◽  
Vol 31 (4_suppl) ◽  
pp. 389-389
Author(s):  
Zhi-Qin Jiang ◽  
Laurel Deaton ◽  
Nastaran Neishaboori ◽  
Jean-Nicolas Vauthey ◽  
Michael J. Overman ◽  
...  

389 Background: Loss of expression of phosphatase and tensin homolog (PTEN) is associated with activation of the PI3K/AKT pathway, and has been identified as a potential modulator of response to targeted therapies in metastatic colorectal cancer (mCRC). The association of PTEN loss with other molecular characteristics and outcomes has not been described for mCRC. Methods: Tumor from 229 mCRC patients (pts) were included for analysis of PTEN staining by IHC from whole-mounts, across two cohorts of unresectable mCRC or resectable liver-limited disease. PTEN loss was defined as complete loss of staining with preservation of expression of stromal components. Mutation status was defined using mass-spectroscopy or next-generation sequencing platforms. CpG island methylation (CIMP) status was determined using a previously defined 6-marker panel, with methylation of ≥3 markers denoting CIMP-High. Methylation findings where confirmed in 193 pts from the Cancer Genome Atlas (TCGA) database, using previously defined classifications. Results: The overall frequency of complete PTEN loss was 12% in the primary tumor and 15% when assayed from metastatic sites (P=NS). There was no difference in clinical characteristics in patients with PTEN-loss tumors. Complete PTEN loss and PIK3CA mutations were not mutually exclusive, with PIK3CA mutation rate of 24% and 14% in PTEN loss and intact, respectively (p=0.3). There was no association of PTEN loss with KRAS mutations (p=0.3), although there were non-significant trends toward higher rates of CIMP-High, BRAF mutations, and R-sided tumors (OR 3.2, 2.7, and 1.6, respectively; p<0.2), consistent with an association with the serrated adenoma pathway and epigenetic inactivation. In the TCGA, PTEN protein loss (defined by the lowest 12% of expression) was associated with increased AKT signaling (77% increase in pAKT/AKT, p<0.01) and a similar trend with CIMP-H tumors (OR 3.1, p=0.13). Conclusions: In patient samples, PTEN loss is independent of KRAS and PIK3CA mutations, associated with robust AKT pathway activation, and may be more prominent in tumors with hypermethylation and BRAF mutations.


2016 ◽  
Vol 34 (2_suppl) ◽  
pp. 484-484 ◽  
Author(s):  
Gurudatta Naik ◽  
Dongquan Chen ◽  
Michael Crowley ◽  
David Crossman ◽  
Katherine C. Sexton ◽  
...  

484 Background: Molecular alterations and drivers of PSCC, an orphan malignancy, remain unclear. The Cancer Genome Atlas is not studying PSCC and the Catalogue of Somatic Mutations in Cancer has performed targeted analyses only. We report WES of PSCC tumors from a group of patients (pts). Methods: Freshfrozen macrodissected PSCC tumor tissue and adjacent normal tissue samples were procured from the Cooperative Human Tissue Network. DNA was isolated from tissue sections by phenol chloroform extraction. Exome capture was performed with the Agilent SureSelect clinical research exome kit and whole exome-seq was done on the Illumina HiSeq2500 with paired end 100bp chemistry. Raw sequence data in Fastq format were aligned to human reference genome and quantified, and compared by using a local instance of Galaxy (galaxy.uabgrid.uab.edu). These data were analyzed for mutations (SNPs) analysis, by Partek Genomic Suite/Flow(PGS, Partek, St. Louis, MO) for variance calling against human reference genome (hg19) as referenced to dbSNP; and copy number variants (cnv) by FishingCNV tool together with picard tools/samtools/GATK). We focused on missense mutations and amplifications among ≥ 2 tumor samples but not in normal samples as they may cause upregulation of gene/protein function, which may be therapeutically actionable. Results: PSCC tumors were available from 11 patients and adjacent normal tissue from 3 patients. The 10 most common genes with > 4 missense mutations among ≥ 2 tumor samples overall were the following in decreasing order of frequency: MUC4, HLA-DPA1, MUC16, XIRP2, SSPO, TTN, FCGBP, PABPC3, ALPK2 and MKI67. The top upstream transcriptional regulators were PIH1D3, PRDM5, PTK2, Coup-Tf and NBEAL2. When examining candidate actionable genes, recurrent missense alterations were seen in PIK3C2A and PIK3C2G. Additional analysis will study alterations in functional domains and cnv. Conclusions: WES identified a relatively high mutation burden in PSCC withrecurrent missense mutations in multiple genes, notably including the PI3K gene among potentially actionable genes. Validation of these findings and further study of downstream effects is required.


2021 ◽  
Vol 11 ◽  
Author(s):  
Gang Guo ◽  
Gaofeng Li ◽  
Yinqiang Liu ◽  
Heng Li ◽  
Qi Guo ◽  
...  

Xuanwei County in Southwest China shows the highest incidence and mortality rate of lung cancer in China. Although studies have reported distinct clinical characteristics of patients from Xuanwei, the molecular features of these patients with non-small cell lung cancer (NSCLC) remain unclear. Here, we comprehensively characterised such cases using next-generation sequencing (NGS). Formalin-fixed, paraffin-embedded tumour samples from 146 patients from Xuanwei with NSCLC were collected for an NGS-based target panel assay; their features were compared with those of reference Chinese and The Cancer Genome Atlas (TCGA) cohorts. Uncommon EGFR mutations, defined as mutations other than L858R, exon 19del, exon 20ins, and T790M, were the predominant type of EGFR mutations in the Xuanwei cohort. Patients harbouring uncommon EGFR mutations were more likely to have a family history of cancer (p = 0.048). A higher frequency of KRAS mutations and lower frequency of rearrangement alterations were observed in the Xuanwei cohort (p &lt; 0.001). Patients from Xuanwei showed a significantly higher tumour mutation burden than the reference Chinese and TCGA cohorts (p &lt; 0.001). Our data indicates that patients from Xuanwei with NSCLC harbouring G719X/S768I co-mutations may benefit from treatment with EGFR-tyrosine kinase inhibitors. Our comprehensive molecular profiling revealed unique genomic features of patients from Xuanwei with NSCLC, highlighting the potential for improvement in targeted therapy and immunotherapy.


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