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All Journal HAYATI Journal of Biosciences Makara Journal of Health Research
Kaderi, Mohd. Arifin
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Agriculture, Biological Sciences & Forestry Earth & Planetary Sciences

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Detectability of circulating microRNAs in microRNA extracts with low purity and yield using quantitative real-time polymerase chain reaction: Supporting evidence Ahmad, Azmir; Kaderi, Mohd. Arifin; Tumian, Afidalina; Sivanesan, Vijaya Mohan; Abdullah, Kahairi; Leman, Wan Ishlah; Mohamad, Irfan; Wan Zainon, Wan Mohd. Nazri; Mohd. Shiyuti, Muhammad Izani; Mohamed Awang, Kamariah; Rosla, Luqman; Paul, Mark; Syed Yussof, Sharifah Nor Ezura; Ramli, Rosdi
Makara Journal of Health Research Vol. 24, No. 3
Publisher : UI Scholars Hub

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Abstract

Background: Circulating microRNAs (miRNAs) are a group of noncoding RNAs with promising potential as minimal invasive biomarkers for noncommunicable diseases. However, challenges exist in the preparation of these miRNAs from peripheral blood samples for quantification purposes. The low quality of miRNA extracts presents an obstacle. Acknowledging the superior performance of quantitative real-time polymerase chain reaction (qPCR) as gold standard for gene expression analysis, we conducted this study to observe the capabilities of qPCR using the Taqman® protocol in amplifying circulating miRNAs from miRNA extracts with low purity and yield. Methods: miRNAs were extracted from thirty-six plasma samples that were obtained from public subjects. Four selected miRNAs were quantified using the Taqman® protocol in an integrated fluidic circuit chip that was optimized from a previous study. The amplification graph and Cq values were obtained to observe any abnormal amplification signs and expression levels, respectively. Results: The qualitative observation of the amplification of the four miRNAs showed no sign of abnormality, thereby indicating the successful amplification of the miRNAs without enzymatic inhibition. Furthermore, the miRNAs were quantified in high expression levels. Conclusion: The circulating miRNA extracts with low purity and yield were practical for the study of circulating miRNA expression based on the Taqman® protocol as the method of detection.
Identification of Risk Factors Associated with Nasopharyngeal Carcinoma (NPC) in the Pahang State of Malaysia Hospitals Ahmad, Azmir; Basha, Muzaitul Akma Mustapa Kamal; Yassin, Wardah Mohd.; Rahman, Nor Azlina A.; Leman, Wan Ishlah; Rosla, Luqman; Yussof, Sharifah Nor Ezura Syed; Paul, Mark; Awang, Kamariah Mohamed; Abdullah, Kahari; Kaderi, Mohd. Arifin
Makara Journal of Health Research Vol. 26, No. 1
Publisher : UI Scholars Hub

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Background: Nasopharyngeal carcinoma (NPC) is the fifth most common cancer reported in Malaysia. Although several studies on NPC have been carried out, the risk factors associated with NPC in Malaysia are unknown. Therefore, this study was designed to investigate the risk factors associated with NPC cases in Pahang state. Methods: NPC cases that were diagnosed between 2012 and 2017 were recruited from two referral hospitals in Pahang. An interview was conducted using adapted questionnaires, which included demographic data, family history of cancer, and lifestyle. The data were analyzed statistically to identify the associations between the selected variables and NPC. Results: A total of 71 NPC cases and 81 control subjects were recruited from the hospitals. Multivariate analysis showed that a family history of NPC and current smoking were significantly associated with the risk of NPC (p < 0.05). Further analysis revealed a significant association between the risk of NPC in smokers with no family history of NPC (p < 0.05). Conclusions: This preliminary study suggests that family history and smoking are factors associated with the development of NPC in Pahang, which was consistent with previous studies.
Quantile Normalization for High Throughput Circulating MicroRNA Expression Study using TaqMan® Low Density Array Panels: Supporting Evidence Ahmad, Azmir; Mohamed, Syarah Syamimi; Tumian, Afidalina; Tolos, Siti Marponga; Sivanesan, Vijaya Mohan; Leman, Wan Ishlah; Abdullah, Kahairi; Mohamad, Irfan; Wan Zainon, Wan Mohd. Nazri; Rosla, Luqman; Syed Yussof, Sharifah Nor Ezura; Mark, Paul; Mohamed@Awang, Kamariah; Ramli, Rosdi; Omar, Eshamsol Kamar; Mohd. Yassin, Mohd. Wardah; Mohamad, Mohd. Amin Marwan; Kaderi, Mohd. Arifin
HAYATI Journal of Biosciences Vol. 31 No. 3 (2024): May 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.3.432-442

Abstract

In searching for new biomarkers, high throughput technique has been widely used by researchers, including for gene expression study. However, the reliability and accuracy of results from high throughput study critically depends on appropriate data management, including normalization methods. Data driven normalization has been introduced as a normalization method for high throughput gene expression study. Thus, this study was conducted to evaluate the performance of various data driven and reference genes normalization methods using a high throughput circulating microRNA expression dataset. A quantification cycle (Cq) dataset generated from a high throughput circulating microRNA study was used to test the normalization methods using HTqPCR package in R software. The normalized Cq generated from different methods were compared descriptively using box plot analysis and coefficient of variance. The box plot analysis showed that quantile normalization produced more homogenous Cq distribution, lesser outliers and reduced coefficient of variance as compared to other normalization methods in screening and validation phases. The overview on quantile normalized Cq showed consistency in its level of expression before and after 2-∆∆Cq calculation indicating the reliability of quantile normalized Cq. Quantile normalization is suggested to be used in high throughput miRNA expression study due to its performance in homogenizing the data, reduce outliers and coefficient of variance.
Co-Authors Abdullah, Kahairi Abdullah, Kahari Ahmad, Azmir Awang, Kamariah Mohamed Basha, Muzaitul Akma Mustapa Kamal Leman, Wan Ishlah Mark, Paul Mohamad, Irfan Mohamad, Mohd. Amin Marwan Mohamed Awang, Kamariah Mohamed, Syarah Syamimi Mohamed@Awang, Kamariah Mohd. Shiyuti, Muhammad Izani Mohd. Yassin, Mohd. Wardah Omar, Eshamsol Kamar Paul, Mark Rahman, Nor Azlina A. Ramli, Rosdi Rosla, Luqman Sivanesan, Vijaya Mohan Syed Yussof, Sharifah Nor Ezura Tolos, Siti Marponga Tumian, Afidalina Wan Zainon, Wan Mohd. Nazri Yassin, Wardah Mohd. Yussof, Sharifah Nor Ezura Syed