• Asian Pacific Journal of Cancer Prevention
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• v.14 no.11
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• pp.6619-6623
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• 2013

Background:The aim of the research was to explore a cost effective, fast, easy to perform, and sensitive method for epidermal growth factor receptor (EGFR) mutation testing. Methods: High resolution melting analysis (HRM) was introduced to evaluate the efficacy of the analysis for dectecting EGFR mutations in exons 18 to 21 using formalin-fixed paraffin-embedded (FFPE) tissues and plasma free DNA from 120 patients. Results: The total EGFR mutation rate was 37.5% (45/120) detected by direct sequencing. There were 48 mutations in 120 FFPE tissues assessed by HRM. For plasma free DNA, the EGFR mutation rate was 25.8% (31/120). The sensitivity of HRM assays in FFPE samples was 100% by HRM. There was a low false-positive mutation rate but a high false-negative rate in plasma free DNA detected by HRM. Conclusions: Our results show that HRM analysis has the advantage of small tumor sample need. HRM applied with plasma free DNA showed a high false-negative rate but a low false-positive rate. Further research into appropriate methods and analysis needs to be performed before HRM for plasma free DNA could be accepted as an option in diagnostic or screening settings.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.6
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• pp.3641-3645
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• 2013

Background: Assessment of the nursing staff knowledge, attitude and practices about cervical cancer screening in a tertiary care teaching institute of rural India. Materials and Methods: A cross sectional, descriptive, interview-based survey was conducted with a pretested questionnaire among 262 staff nurses of a tertiary care teaching and research institute. Results: In this study 77% respondents knew that Pap smear is used for detection of cervical cancer, but less than half knew that Pap smear can detect even precancerous lesions of cervix. Only 23.4% knew human papilloma virus infection as a risk factor. Only 26.7% of the respondents were judged as having adequate knowledge based on scores allotted for questions evaluating knowledge about cervical cancer and screening. Only 17 (7%) of the staff nurses had themselves been screened by Pap smear, while 85% had never taken a Pap smear of a patient. Adequate knowledge of cervical cancer and screening, higher parity and age >30 years were significantly associated with self screening for cervical cancer. Most nurese held a view that Pap test is a doctor procedure, and nearly 90% of nurses had never referred a patient for Pap testing. Conclusions: The majority of nursing staff in rural India may have inadequate knowledge about cervical cancer screening, and their attitude and practices towards cervical cancer screening could not be termed positive.

• Journal of Digestive Cancer Research
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• v.1 no.2
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• pp.82-88
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• 2013

Cancer is the first leading cause of death in Korea and the second leading cause of death in the USA. There is extensive research into prevention of cancer and the support of oncology patients with diet or dietary supplements. In vitro and in vivo animal studies have indicated that antioxidants, including beta-carotene, alpha-tocopherol, and ascorbic acid, can yield anti-cancer effects in addition to providing protection against oxidative damage. Although many observational studies have shown that consuming fruits and vegetables can reduce the risk of some cancers, the results of several large-scale human intervention trials testing the benefits of a single or combined higher-dose of individual micronutrients have been inconsistent. Cancer can cause profound metabolic and physiological changes which may affect patients' nutrient requirements. Although the optimal route of nutrient delivery is through diet, cancer patients often suffer symptoms that disrupt their food intake, including anorexia, premature satiety, altered taste and smell, and changes in bowel mobility. In particular, micronutrient deficits can slow postoperative healing, contribute to depression symptoms, and decrease immune competence. Cancer patients are generally motivated to take dietary supplements to improve responses to treatment and quality of life. The Physician's Health Study II (PHS II) randomized controlled trial reported recently that daily multivitamin supplementation significantly, albeit modestly, reduced the risk of total cancer. Although evidence of multivitamin use benefits is limited in cancer patients, taking dietary supplements with constituents in the range of the recommended daily allowance according to the Dietary Reference Intake (DRI) recommendation is generally considered to be safe.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.9
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• pp.4221-4227
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• 2012

Cancer of the uterine cervix is a worldwide menace taking innumerable womens' lives. The literature is vast and a large number of studies have been conducted in this field. Analyses have shown significant differences exist in terms of screening and HPV testing facilities among high income and low to middle income countries. In addition, acute lack of awareness and knowledge among the concerned population is particularly noted in rural areas of the low income countries. A detailed review of Indian case studies revealed that early age of marriage and childbirth, multiparity, poor personal hygiene and low socio-economic status among others are the principal risk factors for this disease. This review concludes that a two pronged strategy involving strong government and NGO action is necessary to minimize the occurrence of cervical cancer especially in low and medium income countries.

• BMB Reports
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• v.40 no.2
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• pp.135-141
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• 2007

Conjugation of the methyl group at the fifth carbon of cytosines within the palindromic dinucleotide 5'-CpG-3' sequence (DNA methylation) is the best studied epigenetic mechanism, which acts together with other epigenetic entities: histone modification, chromatin remodeling and microRNAs to shape the chromatin structure of DNA according to its functional state. The cancer genome is frequently characterized by hypermethylation of specific genes concurrently with an overall decrease in the level of 5-methyl cytosine, the pathological implication of which to the cancerous state has been well established. While the latest genome-wide technologies have been applied to classify and interpret the epigenetic layer of gene regulation in the physiological and disease states, the epigenetic testing has also been seriously explored in clinical practice for early detection, refining tumor staging and predicting disease recurrence. This critique reviews the latest research findings on the use of DNA methylation in cancer diagnosis, prognosis and staging/classification.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.1
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• pp.329-337
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• 2012

Considerable attention has been given to the accuracy of HER-2 testing and the correlation between the results of different testing methods. This interest reflects the growing importance of HER-2 status in the management of patients with breast cancer. In this study the detection of HER-2 gene and centromere 17 status was evaluated using dual-colour primed in situ labelling (PRINS) in comparison with fluorescence in situ hybridization (FISH). These two methods were evaluated on a series of 27 formalin fixed paraffin embedded breast carcinoma tumours, previously tested for protein overexpression by HercepTest (grouped into Hercep 1+/0, 2+ and 3+). HER-2 gene amplification (ratio${\geq}2.2$) by PRINS was found in 3:3, 6:21 and 0:3 in IHC 3+, 2+ and 1+/0 cases, respectively. Comparing FISH and IHC (immunohistochemistry), showed the same results as for PRINS and IHC. Chromosome 17 aneusomy was found in 10 of 21 IHC 2+ cases (47.6%), of which 1 (10%) showed hypodisomy (chromosome 17 copy number per cell${\leq}1.75$), 7 (70%) showed low polysomy (chromosome 17 copy number per cell=2.26 - 3.75) and 2 (20%) showed high polysomy (chromosome 17 copy number per cell ${\geq}3.76$). The overall concordance of detection of HER-2 gene amplification by FISH and PRINS was 100% (27:27). Furthermore, both the level of HER-2 amplification and copy number of CEN17 analysis results correlated well between the two methods. In conclusion, PRINS is a reliable, reproducible technique and in our opinion can be used as an additional test to determine HER-2 status in breast tumours.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.17
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• pp.7935-7941
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• 2015

The aim of this study was to implement massive parallel sequencing (MPS) technology in clinical genetics testing. We developed and tested an amplicon-based method for resequencing the BRCA1 and BRCA2 genes on an Illumina MiSeq to identify disease-causing mutations in patients with hereditary breast or ovarian cancer (HBOC). The coding regions of BRCA1 and BRCA2 were resequenced in 96 HBOC patient DNA samples obtained from different sample types: peripheral blood leukocytes, whole blood drops dried on paper, and buccal wash epithelia. A total of 16 random DNA samples were characterized using standard Sanger sequencing and applied to optimize the variant calling process and evaluate the accuracy of the MPS-method. The best bioinformatics workflow included the filtration of variants using GATK with the following cut-offs: variant frequency >14%, coverage ($>25{\times}$) and presence in both the forward and reverse reads. The MPS method had 100% sensitivity and 94.4% specificity. Similar accuracy levels were achieved for DNA obtained from the different sample types. The workflow presented herein requires low amounts of DNA samples (170 ng) and is cost-effective due to the elimination of DNA and PCR product normalization steps.

• Genomics & Informatics
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• v.14 no.4
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• pp.187-195
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• 2016

In genetic association studies with high-dimensional genomic data, multiple group testing procedures are often required in order to identify disease/trait-related genes or genetic regions, where multiple genetic sites or variants are located within the same gene or genetic region. However, statistical testing procedures based on an individual test suffer from multiple testing issues such as the control of family-wise error rate and dependent tests. Moreover, detecting only a few of genes associated with a phenotype outcome among tens of thousands of genes is of main interest in genetic association studies. In this reason regularization procedures, where a phenotype outcome regresses on all genomic markers and then regression coefficients are estimated based on a penalized likelihood, have been considered as a good alternative approach to analysis of high-dimensional genomic data. But, selection performance of regularization procedures has been rarely compared with that of statistical group testing procedures. In this article, we performed extensive simulation studies where commonly used group testing procedures such as principal component analysis, Hotelling's $T^2$ test, and permutation test are compared with group lasso (least absolute selection and shrinkage operator) in terms of true positive selection. Also, we applied all methods considered in simulation studies to identify genes associated with ovarian cancer from over 20,000 genetic sites generated from Illumina Infinium HumanMethylation27K Beadchip. We found a big discrepancy of selected genes between multiple group testing procedures and group lasso.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.12
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• pp.7355-7358
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• 2013

Several lines of evidence support the notion that MUC1 is often aberrantly expressed in gastric cancer, and it is a ligand for Helicobacter pylori. Genetic variation in MUC1 gene may confer susceptibility to H. pylori infection and gastric cancer. We assessed the association of common polymorphisms in MUC1 gene with H. pylori infection and non-cardia gastric cancer using an LD-based tag SNP approach in north-western Chinese Han population. A total of four SNPs were successfully genotyped among 288 patients with non-cardia gastric cancer and 281 age- and sex-matched controls. None of the tested SNPs was associated with H. pylori infection. SNP rs9426886 was associated with a decreased risk of non-cardia gastric cancer, but lost significance after adjustment for multiple testing. Overall, our data indicated that common genetic variations in MUC1 gene might not make a major contribution to the risk of H. pylori infection and non-cardia gastric cancer in our studied population.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.18
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• pp.8187-8190
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• 2016

Human papillomaviruses (HPVs) are small, non-enveloped, double-stranded DNA viruses that infect epithelial tissues. Specific genotypes of human papillomavirus are the single most common etiological agents of cervical intraepithelial lesions and cervical cancer. Cervical cancer usually arises at squamous metaplastic epithelium of transformation zone (TZ) of the cervix featuring infection with one or more oncogenic or high-risk HPV (HR-HPV) types. A hospital-based study in a rural set up was carried out to understand the association of HR-HPV with squamous intraepithelial lesions (SILs) and cervical cancer. In the present study, HR-HPV was detected in 65.7% of low-grade squamous intraepithelial lesions (LSILs), 84.6% of high-grade squamous intraepithelial lesions (HSILs) and 94% of cervical cancer as compared to 10.7% of controls. The association of HPV infection with SIL and cervical cancer was analyzed with Chi square test (p<0.001). The significant association found confirmed that detection of HR-HPV is a suitable candidate for early identification of cervical precancerous lesions and in the prevention of cervical cancer in India.