• Communications for Statistical Applications and Methods
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• v.26 no.3
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• pp.315-323
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• 2019

Panel data sets have recently been developed in various areas, and many recent studies have analyzed panel, or longitudinal data sets. Often a dichotomous dependent variable occur in survival analysis, biomedical and epidemiological studies that is analyzed by a generalized linear mixed effects model (GLMM). The most common estimation method for the binary panel data may be the maximum likelihood (ML). Many statistical packages provide ML estimates; however, the estimates are computed from numerically approximated likelihood function. For instance, R packages, pglm (Croissant, 2017) approximate the likelihood function by the Gauss-Hermite quadratures, while Rchoice (Sarrias, Journal of Statistical Software, 74, 1-31, 2016) use a Monte Carlo integration method for the approximation. As a result, it can be observed that different packages give different results because of different numerical computation methods. In this note, we discuss the pros and cons of numerical methods compared with the exact computation method.

• Genomics & Informatics
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• v.16 no.4
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• pp.32.1-32.7
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• 2018

Ovarian cancer is one of the leading causes of cancer-related deaths in gynecological malignancies. Over 70% of ovarian cancer cases are high-grade serous ovarian cancers and have high death rates due to their resistance to chemotherapy. Despite advances in surgical and pharmaceutical therapies, overall survival rates are not good, and making an accurate prediction of the prognosis is not easy because of the highly heterogeneous nature of ovarian cancer. To improve the patient's prognosis through proper treatment, we present a prognostic prediction model by integrating high-dimensional RNA sequencing data with their clinical data through the following steps: gene filtration, pre-screening, gene marker selection, integrated study of selected gene markers and prediction model building. These steps of the prognostic prediction model can be applied to other types of cancer besides ovarian cancer.

• Radiation Oncology Journal
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• v.27 no.2
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• pp.55-63
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• 2009

Purpose: This study was performed to objectively evaluate the rate of tumor response to hypofractionated radiotherapy for advanced squamous cell carcinomas of the head and neck. Materials and Methods: Thirty-one patients with advanced squamous cell carcinoma of the head and neck, who were treated by hypofractionated radiotherapy with 3 Gy per fraction for palliative purpose between 1998 and 2008, were reviewed retrospectively. Every tumor-volume was measured and evaluated from CT (computed tomography) images obtained before and 2~3 months after radiotherapy. The radiation toxicity was assessed during and after radiotherapy. A statistical analysis was performed to investigate overall survival, progressionfree survival, and the prognostic factors for survival and response. Results: The median age of the study patients was 70 years. In addition, 85% of the patients were in stage 4 cancer and 66.7% had an ECOG performance status of 1~2. The mean tumor-volume was 128.4 cc. Radiotherapy was administered with a total dose of 24~45 Gy (median: 36 Gy) over 10~25 days. Twenty-nine patients were treated with 30 Gy or more. The observed complete response rate was 12.9% and the partial response rate was 61.3%. Median survival time was 8.9 months and the 1-year progression-free survival rate was 12.9%. The treatment response rate was confirmed as a prognostic factor in the rate of survival. The primary site, stage, tumor-volume, radiotherapy field and overall radiation-dose showed a significant relationship with survival and treatment response. No grade 4 toxicity was observed during and after radiotherapy. Conclusion: There was an objective tumor-regression in about 74% of patients treated by hypofractionated radiotherapy. Further evaluation is needed to select the appropriate fraction-size and patient who may require the additional radiotherapy.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.16
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• pp.7237-7242
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• 2015

Background: Epithelial ovarian cancer (EOC) is the commonest malignancy involving the ovaries. Maximum surgical cytoreduction (MCR) followed by adjuvant taxane-platinum chemotherapy are the standard of care treatments. Aims: To study treatment outcomes of EOC patients that were maximally cyto-reduced and received adjuvant paclitaxel-carboplatin (PC) chemotherapy. Materials and Methods: This retrospective cohort study included 174 patients with EOC treated at the Egyptian National Cancer Institute between 2006 and 2010. For inclusion, they should have had undergone MCR with no-gross residual followed by adjuvant PC chemotherapy. MCR was total abdominal hysterectomy/bilateral salpingo-oophorectomy [TAH/BSO] or unilateral salpingo-oophorectomy [USO] plus comprehensive staging. Results: The median age was 50 years. Most patients were married (97.1%), had offspring (92.5%), were postmenopausal (53.4%), presented with abdominal/pelvic pain and swelling (93.7%), had tumors involving both ovaries (45.4%) without extra-ovarian extension i.e. stage I (55.2%) of serous histology (79.9%) and grade II (87.4%). TAH/BSO was performed in 97.7% of cases. A total of 1,014 PC chemotherapy cycles were administered and were generally tolerable with 93.7% completing 6 cycles. Alopecia and numbness were the commonest adverse events. The median follow up period was 42 months. The 2-year rates for disease free survival (DFS) and overall survival (OS) were 70.7% and 94.8%, respectively. The respective 5-year rates were 52.6% and 81.3%. Advanced stage and high-grade were significantly associated with poor DFS and OS (p<0.001). Age >65 years was associated with poor OS (p =0.008). Using Cox-regression, stage was independent predictor of poor DFS and OS. Age was an independent predictor of poor OS.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.2
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• pp.479-482
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• 2012

Aim: Soy foods are the major source of isoflavones, which are believed to play important roles in genesis of breast cancer and its progression. We here conducted a prospective study to evaluate the association of soy isoflavone food consumption with breast cancer prognosis. Methods: A prospective study was performed from January 2004 and January 2006 in China. Trained interviewers conducted face-to-face interviews using a structured questionnaire to collect information on dietary habits and potential confounding factors. The relative risk [hazard ratio (HR)] and 95% CI were calculated from the Cox regression model for all significant predictors from cancer diagnosis to the endpoint of the study (event). Results: After a median follow up of 52.1 months (range, 9-60 months), a total of 79 breast cancer related deaths were recorded in our study, risk being inversely associated with a high intake of soy isoflavone. With an average intake of soy isoflavone above 17.3 mg/day, the mortality of breast cancer can be reduced by about 38-36%. We also found the decreased breast cancer death with high soy protein intake, with a HR (95% CI) of 0.71 (0.52-0.98). Stratified analysis with reference to the ER status, further demonstrated a better prognosis of ER positive breast cancer with a high intake of soy isoflavone (HR 0.59, 0.40-0.93). Conclusion: Our study shows the soy food intake is associated with longer survival and low recurrence among breast cancer patients. A cohort study with a larger sample size and long term follow-up is now needed.

• Molecular & Cellular Toxicology
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• v.3 no.4
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• pp.320-325
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• 2007

Promoter hypermethylation of the $p16^{INK4a}$ gene was investigated in 52 sets of samples of tumor tissue and adjacent normal tissue from Korean patients with colorectal cancer, using the proposed modified the Real-time PCR/SYBR Green detection method presented in this study. In normal tissue, 29 of 52 patients (56%) were methylated and in tumor tissue, 23 of 52 patients (44%) were methylated. The 34 cases (65.4%) showed a concordant DNA methylation pattern in both normal tissue and tumor tissue. Analyzing the association between the clinicopathologic features and DNA methylation status of the $p16^{INK4a}$ gene, the DNA methylation status according to by Duke's stage was different while other clinicopathological characteristics, including the age, sex, tumor stage, and histologic type of the patient were not found to be correlated with $p16^{INK4a}$ methylation. With multivariate logistic regression, it was observed that the DNA methylation status of $p16^{INK4a}$ gene in normal tissue was correlated with the DNA methylation status of the $p16^{INK4a}$ gene in tumor tissue (P=0.026). According to a Kaplan-Meier survival analysis, a difference in the survival rate by DNA methylation status was found, but it was not significant.

• Genomics & Informatics
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• v.14 no.4
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• pp.205-210
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• 2016

Interleukin-10 (IL10) plays an important role in initiating and maintaining an appropriate immune response to non-Hodgkin lymphoma (NHL). Previous studies have revealed that the transcription of IL10 mRNA and its protein expression may be infl uenced by several single-nucleotide polymorphisms in the promoter and intron regions, including rs1800896, rs1800871, and rs1800872. However, the impact of polymorphisms of the IL10 gene on NHL prognosis has not been fully elucidated. Here, we investigated the association between IL10 polymorphisms and NHL prognosis. This study involved 112 NHL patients treated at the National Cancer Center, Korea. The median age was 57 years, and 70 patients (62.5%) were men. Clinical characteristics, including age, performance status, stage, and extra-nodal involvement, as well as cell lineage and International Prognostic Index (IPI), were evaluated. A total of four polymorphisms in IL10 with heterozygous alleles were analyzed for hazard ratios of overall survival (OS) and progression-free survival (PFS) using Cox proportional hazards regression analysis. Diffuse large B-cell lymphoma was the most common histologic type (n = 83), followed by T-cell lymphoma (n = 18), mantle cell lymphoma (n = 6), and others (n = 5). Cell lineage, IPI, and extra-nodal involvement were predictors of prognosis. In the additive genetic model results for each IL10 polymorphism, the rs1800871 and rs1800872 polymorphisms represented a marginal association with OS (p = 0.09 and p = 0.06) and PFS (p = 0.05 and p = 0.08) in B-cell lymphoma patients treated with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). These findings suggest that IL10 polymorphisms might be prognostic indicators for patients with B-cell NHL treated with R-CHOP.

• Journal of the Korean Society of Fisheries and Ocean Technology
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• v.36 no.3
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• pp.234-243
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• 2000

This paper is to study population ecological characteristics, including growth parameters, survival rate, instantaneous coefficients of natural and fishing mortalities, and age at first capture of the soft-shelled clam, Mya japonioa in the intertidal zone of South Sea in Korea. For describing growth of the clam a von Bertalanffy growth model was adopted, The von Bertalanffy growth curve had an additive error structure and the growth parameters estimated from a non-linear regression were SH/sub ∞/=79.83mm, K=0.26, and t/sub 0/= -0.01. Survival rate (S) of the soft-shelled clam was 0.26 (SD=0.02). The instantaneous coefficients of natural mortality (M) was estimated to be 0.78/year and fishing mortality (F) 0.57/year for the soft-shelled clam. The age at first capture (t/sub c/) was estimated as 2.69 year. The mean densities of the soft-shelled clam by bottom type were 3.40 inds./m²(SE=0.18) in the sand, 63.4 inds./m²(SE= 0.53) in the muddy sand, and 0 inds./m2 (SE=0) in the gravelly sand. The mean densities of the soft-shelled clam by 3 different areas were 4.88 inds./m²(SE=0.09), 2.61 inds./m²(SE=0.13), 7.20 inds./m²(SE=0.18), respectively and the biomass of the clam were estimated as 131mt, 121mt, 665mt, respectively. An yield-per-recruit analysis showed that the current yield-per-recruit of about 8.30g with F=0.57/year and the age at first capture (t/sub c/) 2.69 year, was lower than the maximum possible yield-per-recruit of 9.60g. Fixing to at the current level and increased fishing intensity (F) could produce an increase in the predicted yield-per-recruit from 8.30g to about 9.40. However, estimated yield-per-recruit increased to 1.30g by decreasing to from the current age (2.69 year) to age two with F fixed at the current level. Yield-per-recruit was estimated under harvest strategies based on F/sub max/ and F/sub 0.1/.

• Journal of Preventive Medicine and Public Health
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• v.32 no.4
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• pp.538-545
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• 1999

Objective : To compare the predictive power of International Classification of Diseases 10th Edition(ICD-10) based International Classification of Diseases based Injury Severity Score(ICISS) with Trauma and Injury Severity Score(TRISS) and International Classification of Diseases 9th Edition Clinical Modification(ICD-9CM) based ICISS in the injury severity measure. Methods : ICD-10 version of Survival Risk Ratios(SRRs) was derived from 47,750 trauma patients from 35 Emergency Centers for 1 year. The predictive power of TRISS, the ICD-9CM based ICISS and ICD-10 based ICISS were compared in a group of 367 severely injured patients admitted to two university hospitals. The predictive power was compared by using the measures of discrimination(disparity, sensitivity, specificity, misclassification rates, and ROC curve analysis) and calibration(Hosmer-Lemeshow goodness-of-fit statistics), all calculated by logistic regression procedure. Results : ICD-10 based ICISS showed a lower performance than TRISS and ICD-9CM based ICISS. When age and Revised Trauma Score(RTS) were incorporated into the survival probability model, however, ICD-10 based ICISS full model showed a similar predictive power compared with TRISS and ICD-9CM based ICISS full model. ICD-10 based ICISS had some disadvantages in predicting outcomes among patients with intracranial injuries. However, such weakness was largely compensated by incorporating age and RTS in the model. Conclusions : The ICISS methodology can be extended to ICD-10 horizon as a standard injury severity measure in the place of TRISS, especially when age and RTS were incorporated in the model. In patients with intracranial injuries, the predictive power of ICD-10 based ICISS was relatively low because of differences in the classifying system between ICD-10 and ICD-9CM.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.6
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• pp.2777-2783
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• 2014

The purpose of this study was to explore the expression of ATAD2 in ovarian tumor tissue as well as its relationship with degree of malignancy. Tumor tissue from 110 cases of ovarian cancer was collected in accordance with the Declaration of Helsinki for evaluation of ATAD2 expression iimmunohistochemistry, quantitative PCR (qPCR) and Western blotting. The correlation between the ATAD2 expression and and the prognosis of ovarian cancer was evaluated by Cox regression model. In addition, HO-8910 and OVCAR-3 cells were transfected with two siRNAs targeting ATAD2. Cell viability was evaluated with MTT assay, and cell migration by transwell migration assay. ATAD2 was shown to be highly expressed in 65.5% (72/110) of ovarian cancer cases, both at transcriptional and protein levels. Moreover, highly expression was positively correlated with degree of malignancy. Knock-down of ATAD2 in HO-8910 and OVCAR-3 cells was found to reduce cell migration. In addition, follow-up visits of the patients demonstrated that the 5-year survival rate was lower in patients with high expression of ATAD2. Our study suggested that ovarian tumor tissue may have highly expressed ATAD2, which is associated with tumor stage, omentum-metastasis, ascites and CA-125. Increased ATAD2 may play important roles in tumor proliferation and migration. ATAD2 could serve in particular as a prognostic marker and a therapeutic target for ovarian cancer.