• Asian Pacific Journal of Cancer Prevention
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• v.17 no.4
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• pp.2199-2203
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• 2016

One of the most common cancer types faced by the women around the world is breast cancer. Among the several low, moderate and high penetrance genes conferring susceptibility to breast cancer, PTEN is one which is known to be mutated in many tumor types. In this study, we predicted and analyzed the impact of three deleterious coding non-synonymous single nucleotide polymorphisms rs121909218 (G129E), rs121909229 (R130Q) and rs57374291 (D107N) in the PTEN gene on the phenotype of breast tumors using computational tools SIFT, Polyphen-2, PROVEAN, MUPro, POPMusic and the GETAREA server.

• International Journal of Computer Science & Network Security
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• v.22 no.9
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• pp.258-270
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• 2022

Cancer has become a common disease for the past two decades throughout the globe and there is significant increase of cancer among women. Breast cancer and ovarian cancers are more prevalent among women. Majority of the patients approach the physicians only during their final stage of the disease. Early diagnosis of cancer remains a great challenge for the researchers. Although several drugs are being synthesized very often, their multi-benefits are less investigated. With millions of drugs synthesized and their data are accessible through open repositories. Drug repurposing can be done using machine learning techniques. We propose a feature selection technique in this paper, which is novel that generates multiple populations for the grey wolf algorithm and classifies breast cancer drugs efficiently. Leukemia drug dataset is also investigated and Multilayer perceptron achieved 96% prediction accuracy. Three supervised machine learning algorithms namely Random Forest classifier, Multilayer Perceptron and Support Vector Machine models were applied and Multilayer perceptron had higher accuracy rate of 97.7% for breast cancer drug classification.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.6
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• pp.2639-2642
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• 2012

Background: The patterns of gastric cancer recurrence vary across societies. We designed the current study in an attempt to evaluate and reveal the outbreak of the recurrence patterns of gastric cancer and also prediction of time to recurrence and its effected factors in Iran. Materials and Methods: This research was performed from March 2003 to February 2007. Demographic characteristics, clinical and pathological diagnosis and classification including pathologic stage, tumor grade, tumor site and tumor size in of patients with GC recurrent were collected from patients' data files. To evaluate of factors affected on the relapse of the GC patients, gender, age at diagnosis, treatment type and Hgb were included in the research. Data were analyzed using Kaplan-Meier and logistic regression models. Results: After treatment, 82 patients suffered recurrence, 42, 33 and 17 by the ends of first, second and third years. The mean ( SD) and median ( IQR) time to recurrence in patients with GC were 25.5 (20.6-30.1) and 21.5 (15.6-27.1) months, respectively. The results of multivariate analysis logistic regression showed that only pathologic stage, tumor grade and tumor site significantly affected the recurrence. Conclusions: We found that pathologic stage, tumor grade and tumor site significantly affect on the recurrence of GC which has a high positive prognostic value and might be functional for better follow-up and selecting the patients at risk. We also showed time to recurrence to be an important factor for follow-up of patients.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.3
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• pp.1481-1488
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• 2014

Background: To avoid performing axillary lymph node dissection (ALND) for non-sentinel lymph node (SLN)-negative patients with-SLN positive axilla, nomograms for predicting the status have been developed in many centers. We created a new nomogram predicting non-SLN metastasis in SLN-positive patients with invasive breast cancer and evaluated 14 existing breast cancer models in our patient group. Materials and Methods: Two hundred and thirty seven invasive breast cancer patients with SLN metastases who underwent ALND were included in the study. Based on independent predictive factors for non-SLN metastasis identified by logistic regression analysis, we developed a new nomogram. Receiver operating characteristics (ROC) curves for the models were created and the areas under the curves (AUC) were computed. Results: In a multivariate analysis, tumor size, presence of lymphovascular invasion, extranodal extension of SLN, large size of metastatic SLN, the number of negative SLNs, and multifocality were found to be independent predictive factors for non-SLN metastasis. The AUC was found to be 0.87, and calibration was good for the present Ondokuz Mayis nomogram. Among the 14 validated models, the MSKCC, Stanford, Turkish, MD Anderson, MOU (Masaryk), Ljubljana, and DEU models yielded excellent AUC values of > 0.80. Conclusions: We present a new model to predict the likelihood of non-SLN metastasis. Each clinic should determine and use the most suitable nomogram or should create their own nomograms for the prediction of non- SLN metastasis.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.8
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• pp.4847-4851
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• 2013

Objectives: To evaluate accuracy of FDG-PET CT in prediction of persistent disease in head and neck cancer cases and to determine prognostic value of metabolic tumor response. Materials and Methods: Between 2009 and 2011, 46 patients with squamous cell carcinoma of head and neck receiving PET-CT were treated with definitive radiotherapy, with or without chemotherapy. There were 29 nasopharyngeal, 11 hypopharyngeal, 3 oropharyngeal and 3 laryngeal cancer patients, with a median age of 50.5 years (range 16-84), 32 males and 14 females. All patients were evaluated with PET-CT median 3-5 months (2.4-9.4) after completion of radiotherapy. Results: After a median 20 months of follow up, complete metabolic response was observed in 63% of patients. Suspicious residual uptake was present in 10.9% and residual metabolic uptake in 26.0% of patients. The overall sensitivity, specificity, positive predictive value and negative predictive value of FDG-PET-CT for detection of residual disease was 91% and 81%, 64% and 96% respectively. Two year LRC was 95% in complete responders while it was 34% in non-complete responders. Conclusions: FDG PET CT is a valuable tool for assessment of treatment response, especially in patients at high risk of local recurrence, and also as an indicator of prognosis. Definitely more precise criteria are required for assessment of response, there being no clear cut uptake value indicating residual disease. Futhermore, repair processes of normal tissue may consume glucose which appear as increased uptake in control FDG PET CT.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.2
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• pp.937-943
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• 2014

Polymorphisms in miRNA binding sites have been shown to affect miRNA binding to target genes, resulting in differential mRNA and protein expression and susceptibility to common diseases. Our purpose was to predict SNPs (single nucleotide polymorphisms) within miRNA binding sites of inflammatory genes in relation to gastric cancer. A complete list of SNPs in the 3'UTR regions of all inflammatory genes associated with gastric cancer was obtained from Pubmed. miRNA target prediction databases (MirSNP, Targetscan Human 6.2, PolymiRTS 3.0, miRNASNP 2.0, and Patrocles) were used to predict miRNA target sites. There were 99 SNPs with MAF>0.05 within the miRNA binding sites of 41 genes among 72 inflammation-related genes associated with gastric cancer. NF-${\kappa}B$ and JAK-STAT are the two most important signaling pathways. 47 SNPs of 25 genes with 95 miRNAs were predicted. CCL2 and IL1F5 were found to be the shared target genes of hsa-miRNA-624-3p. Bioinformatic methods could identify a set of SNPs within miRNA binding sites of inflammatory genes, and provide data and direction for subsequent functional verification research.

• Experimental and Molecular Medicine
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• v.50 no.11
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• pp.7.1-7.12
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• 2018

Recent findings from The Cancer Genome Atlas project have provided a comprehensive map of genomic alterations that occur in hepatocellular carcinoma (HCC), including unexpected mutations in apolipoprotein B (APOB). We aimed to determine the clinical significance of this non-oncogenetic mutation in HCC. An Apob gene signature was derived from genes that differed between control mice and mice treated with siRNA specific for Apob (1.5-fold difference; P < 0.005). Human gene expression data were collected from four independent HCC cohorts (n = 941). A prediction model was constructed using Bayesian compound covariate prediction, and the robustness of the APOB gene signature was validated in HCC cohorts. The correlation of the APOB signature with previously validated gene signatures was performed, and network analysis was conducted using ingenuity pathway analysis. APOB inactivation was associated with poor prognosis when the APOB gene signature was applied in all human HCC cohorts. Poor prognosis with APOB inactivation was consistently observed through cross-validation with previously reported gene signatures (NCIP A, HS, high-recurrence SNUR, and high RS subtypes). Knowledge-based gene network analysis using genes that differed between low-APOB and high-APOB groups in all four cohorts revealed that low-APOB activity was associated with upregulation of oncogenic and metastatic regulators, such as HGF, MTIF, ERBB2, FOXM1, and CD44, and inhibition of tumor suppressors, such as TP53 and PTEN. In conclusion, APOB inactivation is associated with poor outcome in patients with HCC, and APOB may play a role in regulating multiple genes involved in HCC development.

• Genomics & Informatics
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• v.19 no.1
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• pp.10.1-10.7
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• 2021

Although many models have been proposed to accurately predict the response of drugs in cell lines recent years, understanding the genome related to drug response is also the key for completing oncology precision medicine. In this paper, based on the cancer cell line gene expression and the drug response data, we established a reliable and accurate drug response prediction model and found predictor genes for some drugs of interest. To this end, we first performed pre-selection of genes based on the Pearson correlation coefficient and then used ElasticNet regression model for drug response prediction and fine gene selection. To find more reliable set of predictor genes, we performed regression twice for each drug, one with IC₅₀ and the other with area under the curve (AUC) (or activity area). For the 12 drugs we tested, the predictive performance in terms of Pearson correlation coefficient exceeded 0.6 and the highest one was 17-AAG for which Pearson correlation coefficient was 0.811 for IC₅₀ and 0.81 for AUC. We identify common predictor genes for IC₅₀ and AUC, with which the performance was similar to those with genes separately found for IC₅₀ and AUC, but with much smaller number of predictor genes. By using only common predictor genes, the highest performance was AZD6244 (0.8016 for IC₅₀, 0.7945 for AUC) with 321 predictor genes.

• Journal of Gastric Cancer
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• v.11 no.2
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• pp.109-115
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• 2011

Purpose: As the proportion of early gastric cancer (EGC) has recently been increased, minimally invasive treatment is currently accepted as main therapy for EGC. Accurate preoperative staging is very important in determining treatment options. To know the accuracy of endoscopic ultrasonography (EUS), we compared the depth of invasion of the tumor with preoperative EUS and postoperative pathologic findings. Materials and Methods: We retrospectively analyzed 152 patients who underwent EUS before laparoscopic gastrectomy. The preoperative EUS results were compared with the pathological findings. Results: The overall proportion of coincidence for depth of invasion between EUS and pathologic results was 41.4%. Univariate analysis showed that the rate of corrected prediction of EUS for tumor depth significantly decreased for the lesions more than 3cm in diameter (P=0.033), and those with a depressed morphology (P=0.035). In multivariate analysis, the depressed type (P=0.029, OR=2.873) and upper lesion (P=0.035, OR=2.151) was the significantly independent factors influencing the inaccurate prediction of EUS for tumor depth. Conclusions: When we decide the treatment modality considering the clinical depth of invasion by EUS, the possibility of discordance with pathologic results should be considered for the lesions located in the upper third of the stomach and with a depressed morphology.

• Journal of the Korea Society of Computer and Information
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• v.20 no.2
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• pp.137-147
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• 2015

This study proposes an algorithm for predicting breast cancer prognosis based on genetic network. We identify prognosis-specific network using gene expression data and PPI(protein-protein interaction) data. To acquire the network, we calculate Pearson's correlation coefficient(PCC) between genes in all PPI pairs using gene expression data. We develop a prediction model for breast cancer patients with estrogen-receptor-negative using the network as a classifier. We compare classification performance of our algorithm with existing algorithms on independent data and shows our algorithm is improved. In addition, we make an functionality analysis on the genes in the prognosis-specific network using GO(Gene Ontology) enrichment validation.