Development of a Gelatin-Based Genomic Reference Material for Halal Authentication Using Real-Time PCR
Article Sidebar
Keywords:
-
Halal Authentication, Reference Material (RM), Genomic DNA, Gelatin, qPCR, Pharmaceutical Products
Abstract
Indonesia, home to over 270 million people, has the largest Muslim population globally, with approximately 87.18% adhering to Islam, driving significant demand for halal products, particularly in the food and pharmaceutical sectors. Gelatin, commonly used in medicinal capsules, often originates from porcine sources, necessitating precise halal authentication methods. This study presents the development of a novel genomic DNA-based Reference Material (RM) for gelatin, specifically for porcine DNA detection, employing Real-Time Polymerase Chain Reaction (qPCR) techniques. The methodology encompassed in-silico primer design, sample extraction optimization, DNA quality and quantity analysis, linearity assessment, limit of detection (LoD) and quantification (LoQ) determination, and RM characterization. Results indicated that the designed primers could reliably and efficiently detect porcine DNA, with optimal annealing at 58°C and primer concentration at 500 nM, achieving a PCR efficiency of 96.74%. The LoD and LoQ for pork meat samples were determined to be 0.02 pg/uL and 0.004 pg/uL, respectively, while the LoD for porcine gelatin was 0.27 ng/uL. The RMs exhibited robust homogeneity (Sig. 0.052), significant intergroup differences (Sig. 0.000), and low variation (CV 0.96%). Short-term storage at -80°C and -20°C preserved Ct value stability and consistency. Conclusively, this study successfully developed a novel gelatin-based genomic DNA RM for halal authentication, offering a scientifically validated tool that strengthens the halal assurance system, addressing Indonesian consumers’ demand for porcine-free products. These findings hold substantial implications for regulatory authorities, especially in Indonesia, and could inform the development of standardized qPCR RMs for porcine DNA detection in halal compliance testing.
References
Al-Kahtani, H. A., E. A. Ismail, and M. Asif Ahmed (2017). Pork Detection in Binary Meat Mixtures and Some Commercial Food Products Using Conventional and Real-Time PCR Techniques. Food Chemistry, 219; 54–60.
Al-Nimry, S., A. A. Dayah, I. Hasan, and R. Daghmash (2021). Cosmetic, Biomedical and Pharmaceutical Applications of Fish Gelatin/Hydrolysates. Marine Drugs, 19(3); 145.
Ali, M. E., M. A. Razzak, S. B. A. Hamid, M. M. Rahman, M. A. Amin, N. R. A. Rashid, and Asing (2015). Multiplex PCR Assay for the Detection of Five Meat Species Forbidden in Islamic Foods. Food Chemistry, 177; 214–224.
Aminfar, Z., B. Rabiei, M. Tohidfar, and M. H. Mirjalili (2019). Selection and Validation of Reference Genes for Quantitative Real-Time PCR in Rosmarinus Officinalis L. In Various Tissues and Under Elicitation. Biocatalysis and Agricultural Biotechnology, 20; 101246.
Ananta, A., E. Nurvidya Arifin, and M. Sairi Hasbullah (2015). Demography of Indonesia’s Ethnicity. ISEAS Publishing.
Arachchige, C. N. P. G., L. A. Prendergast, and R. G. Staudte (2022). Robust Analogs to the Coefficient of Variation. Journal of Applied Statistics, 49(2); 268–290.
Asif, M., D. Zhiyong, A. Iram, and M. Nisar (2021). Linguistic Analysis of Neologism Related to Coronavirus (COVID-19). Social Sciences & Humanities Open, 4(1); 100201.
Bento, C. S. A., S. Alarico, N. Empadinhas, H. C. de Sousa, and M. E. M. Braga (2022). Sequential ScCO2 Drying and Sterilisation of Alginate-Gelatine Aerogels for Biomedical Applications. The Journal of Supercritical Fluids, 184; 105570.
Borah, J. C. (2015). Shikimic Acid: A Highly Prospective Molecule in Pharmaceutical Industry. Current Science, 109(9); 1672–1679.
Bridgeman, S., G. Ellison, P. Newsholme, and C. Mamotte (2021). The HDAC Inhibitor Butyrate Impairs B Cell Function and Activates the Disallowed Gene Hexokinase I. International Journal of Molecular Sciences, 22(24); 13330.
Broeders, S., I. Huber, L. Grohmann, G. Berben, I. Taverniers, M. Mazzara, N. Roosens, and D. Morisset (2014). Guidelines for Validation of Qualitative Real-Time PCR Methods. Trends in Food Science & Technology, 37(2); 115–126.
Browne, P. D., T. K. Nielsen, W. Kot, A. Aggerholm, M. T. P. Gilbert, L. Puetz, M. Rasmussen, A. Zervas, and L. H. Hansen (2020). GC Bias Affects Genomic and Metagenomic Reconstructions, Underrepresenting GC-Poor Organisms. GigaScience, 9(2).
Bustin, S. and J. Huggett (2017). qPCR Primer Design Revisited. Biomolecular Detection and Quantification, 14; 19–28.
Cai, H., X. Gu, M. S. Scanlan, D. H. Ramatlapeng, and C. R. Lively (2012). Real-Time PCR Assays for Detection and Quantitation of Porcine and Bovine DNA in Gelatin Mixtures and Gelatin Capsules. Journal of Food Composition and Analysis, 25(1); 83–87.
Cheman, Y. (2005). Analysis of Potential Lard Adulteration in Chocolate and Chocolate Products Using Fourier Transform Infrared Spectroscopy. Food Chemistry, 90(4); 815–819.
Chen, F., Y. P. Hsieh, and R. C. Bridgman (2004). Monoclonal Antibody–Based Sandwich Enzyme-Linked Immunosorbent Assay for Sensitive Detection of Prohibited Ruminant Proteins in Feedstuffs. Journal of Food Protection, 67(3); 544–549.
Chen, K., Y. Zhou, K. Li, and J. Xiao (2017). Multiplex PCR with the Blunt Hairpin Primers for Next Generation Sequencing. Biotechnology and Bioprocess Engineering, 22(3); 347–351.
Corliss, J. O., M. Aikawa, and C. R. Sterling (1977). The Science and Technology of Gelatin. Academic Press, London (UK).
Dewantoro, A., A. Safarrida, D. Rahmasari, U. Nuraeni, R. D. Susmiarni, R. Damacena, and M. M. Amin (2023). Verification of Porcine Detection Method Based on SNI ISO/TS 20224-3:2020 on the Gelatin Matrix. Jurnal Standardisasi, 25(2); 79.
Di Leo, G. and F. Sardanelli (2020). Statistical Significance: p Value, 0.05 Threshold, and Applications to Radiomics—Reasons for a Conservative Approach. European Radiology Experimental, 4(1); 18.
Dragon, A. H., C. J. Rowe, A. M. Rhodes, O. L. Pak, T. A. Davis, and E. Ronzier (2023). Systematic Identification of the Optimal Housekeeping Genes for Accurate Transcriptomic and Proteomic Profiling of Tissues Following Complex Traumatic Injury. Methods and Protocols, 6(2); 22.
Erwanto, Y. (2018). Molecular Based Method Using PCR Technology on Porcine Derivative Detection for Halal Authentication. IntechOpen.
Forootan, A., R. Sjöback, J. Björkman, B. Sjögreen, L. Linz, and M. Kubista (2017). Methods to Determine Limit of Detection and Limit of Quantification in Quantitative Real-Time PCR (qPCR). Biomolecular Detection and Quantification, 12; 1–6.
Green, M. R. and J. Sambrook (2020). Cloning in Plasmid Vectors: Directional Cloning. Cold Spring Harbor Protocols, 2020(11); 485–488.
Guo, Y., Q. Cao, Z. Hong, Y. Tan, S. Chen, H. Jin, K. Tan, D. Wang, and Y. Yan (2020). The Origin, Transmission and Clinical Therapies on Coronavirus Disease 2019 (COVID-19) Outbreak an Update on the Status. Military Medical Research, 7(1); 11.
Hassan, N., T. Ahmad, and N. M. Zain (2018). Chemical and Chemometric Methods for Halal Authentication of Gelatin: An Overview. Journal of Food Science, 83(12); 2903–2911.
Hays, A., M. Wissel, K. Colletti, R. Soon, M. Azadeh, J. Smith, R. Doddareddy, M. Chalfant, W. Adamowicz, S. S. Ramaswamy, et al. (2024). Recommendations for Method Development and Validation of qPCR and dPCR Assays in Support of Cell and Gene Therapy Drug Development. The AAPS Journal, 26(1); 24.
Hikmah, N. N., A. Guntarti, and N. Salamah (2024). Concentration of Isolated DNA Face Masks Made of Gelatin for Halal Authentication. Journal of Halal Science and Research, 5(1); 1–5.
Hung, J. and Z. Weng (2016). Designing Polymerase Chain Reaction Primers Using Primer3Plus. Cold Spring Harbor Protocols, 2016(9); 093096.
International Organization for Standardization (ISO) (2017). Reference Materials - Guidance for Characterization and Assessment of Homogeneity and Stability. ISO Guide:35.
Jones, R. T. (2004). Manufacture and Physio-Chemical Properties. Pharmaceutical Press, second edition.
Kang, S. S. N., H. G. Lee, and H. Kim (2018). Development and Comparison of a Porcine Gelatin Detection System Targeting Mitochondrial Markers for Halal Authentication. LWT, 97; 697–702.
Karimi, K., M. Arzanlou, and I. Pertot (2020). Development of Novel Species-Specific Primers for the Specific Identification of Colletotrichum nymphaeae Based on Conventional PCR and LAMP Techniques. European Journal of Plant Pathology, 156(2); 463–475.
Karunakaran, D., A. W. Turner, A. Duchez, S. Soubeyrand, A. Rasheed, D. Smyth, D. P. Cook, M. Nikpay, J. W. Kandiah, C. Pan, et al. (2020). RIPK1 Gene Variants Associate with Obesity in Humans and Can Be Therapeutically Silenced to Reduce Obesity in Mice. Nature Metabolism, 2(10); 1113–1125.
Kesmen, Z., A. Gulluce, F. Sahin, and H. Yetim (2009). Identification of Meat Species by Taqman-Based Real-Time PCR Assay. Meat Science, 82(4); 444–449.
Khayyira, A. S., V. M. Estepane, and A. Malik (2018). Rapid PCR-Based Detection Optimization of Porcine DNA in Gelatin Capsule Shell. International Journal of Applied Pharmaceutics, 10(6); 217.
Kim, M., I. Yoo, S.-Y. Lee, Y. Hong, and H.-Y. Kim (2016). Quantitative Detection of Pork in Commercial Meat Products by Taqman® Real-Time PCR Assay Targeting the Mitochondrial D-Loop Region. Food Chemistry, 210; 102–106.
Klymus, K. E., C. M. Merkes, M. J. Allison, C. S. Goldberg, C. C. Helbing, M. E. Hunter, C. A. Jackson, R. F. Lance, A. M. Mangan, E. M. Monroe, A. J. Piaggio, J. P. Stokdyk, C. C. Wilson, and C. A. Richter (2020). Reporting the Limits of Detection and Quantification for Environmental DNA Assays. Environmental DNA, 2(3); 271–282.
Kumar, A. and N. Chordia (2015). In Silico PCR Primer Designing and Validation. PCR Primer Design, pages 143–151.
Lanzilao, I., F. Burgalassi, S. Fancelli, M. Settimelli, and R. Fani (2005). Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Analysis of Mitochondrial Cytb Gene from Species of Dairy Interest. Journal of AOAC International, 88(1); 128–135.
Lear, G., I. Dickie, J. Banks, S. Boyer, H. L. Buckley, T. R. Buckley, R. Cruickshank, A. Dopheide, K. M. Handley, S. Hermans, J. Kamke, C. K. Lee, R. Macdiarmid, S. E. Morales, D. A. Orlovich, R. Smissen, J. Wood, and R. Holdaway (2018). Methods for the Extraction, Storage, Amplification and Sequencing of DNA from Environmental Samples. New Zealand Journal of Ecology, 42(1).
León, C. M., M. Munoz, C. Hernández, M. S. Ayala, C. Flórez, A. Teherán, J. R. Cubides, and J. D. Ramírez (2017). Analytical Performance of Four Polymerase Chain Reaction (PCR) and Real Time PCR (qPCR) Assays for the Detection of Six Leishmania Species DNA in Colombia. Frontiers in Microbiology, 8.
Levin, R. E., F.-G. C. Ekezie, and D.-W. Sun (2018). DNA-Based Technique: Polymerase Chain Reaction (PCR). In Modern Techniques for Food Authentication. Elsevier, pages 527–616.
Li, J., H. Gao, Y. Li, S. Zhai, F. Xiao, G. Wu, and Y. Wu (2024). The Development of a Series of Genomic DNA Reference Materials with Specific Copy Number Ratios for the Detection of Genetically Modified Maize DBN9936. Foods, 13(5); 747.
Li, J., L. Zhang, L. Li, X. Li, X. Zhang, S. Zhai, H. Gao, Y. Li, G. Wu, and Y. Wu (2020). Development of Genomic DNA Certified Reference Materials for Genetically Modified Rice Kefeng 6. ACS Omega, 5(34); 21602–21609.
Liang, W., L. Xu, Z. Sui, Y. Li, L. Li, Y. Wen, C. Li, S. Ren, and G. Liu (2016). Quantification of Plasmid DNA Reference Materials for Shiga Toxin-Producing Escherichia Coli Based on UV, HR-ICP-MS and Digital PCR. Chemistry Central Journal, 10(1); 55
Manen, J., O. Sinitsyna, L. Aeschbach, A. V. Markov, and A. Sinitsyn (2005). A Fully Automatable Enzymatic Method for DNA Extraction from Plant Tissues. BMC Plant Biology, 5(1); 23
Masiri, J., L. Benoit, B. Barrios-Lopez, C. Thienes, M. Meshgi, A. Agapov, A. Dobritsa, C. Nadala, and M. Samadpour (2016). Development and Validation of a Rapid Test System for Detection of Pork Meat and Collagen Residues. Meat Science, 121; 397–402
Masnaini, M., A. Achyar, M. Chatri, D. H. Putri, Y. Ahda, and Irdawati (2023). Primer Design and Optimization of PCR Methods for Detecting Mixed Rat Meat in Food Samples. In Proceedings of The International Conference on Natural Resources and Technology. pages 282–289
McDevitt, S. L., M. E. Hogan, D. J. Pappas, L. Y. Wong, and J. A. Noble (2014). DNA Storage Under High Temperature Conditions Does Not Affect Performance in Human Leukocyte Antigen Genotyping via Next-Generation Sequencing (DNA Integrity Maintained in Extreme Conditions). Biopreservation and Biobanking, 12(6); 402–408
McShane, B. B., D. Gal, A. Gelman, C. Robert, and J. L. Tackett (2019). Abandon Statistical Significance. The American Statistician, 73(sup1); 235–245
Mishra, P., U. Singh, C. Pandey, P. Mishra, and G. Pandey (2019). Application of Student’s t-Test, Analysis of Variance, and Covariance. Annals of Cardiac Anaesthesia, 22(4); 407
Mokhtar, N. F. K., S. N. Aziz, N. H. Yusoff, R. M. H. Raja Nhari, N. A. Mohamad, and A. Mohd Hashim (2024). Porcine Detection in Commercial Edible Bird Nest Beverages Using Real Time PCR Targeting Chromosomally Encoded Multiple Porcine Repetitive Elements. Journal of Food Composition and Analysis, 131; 106211
Nagy, A., L. Cerníková, E. Vitásková, V. Krivda, A. Dán, Z. Dirbáková, H. Jirincová, B. Procházka, K. Sedlák, and M. Havlícková (2016). MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay. PLoS ONE, 11(3); e0151204
Nazarenko, I. (2002). Multiplex Quantitative PCR Using Self-Quenched Primers Labeled with a Single Fluorophore. Nucleic Acids Research, 30(9); 37e–37
Nguyen, P. T. D., A. Giovanni, S. Maekawa, T. H. Pham, P. Wang, and S.-C. Chen (2023). An Integrated In Silico and In Vivo Study of Nucleic Acid Vaccine Against Nocardia seriolae Infection in Orange-Spotted Grouper Epinephelus Coioides. Fish & Shellfish Immunology, 143; 109202
Nikzad, J., S. Shahhosseini, M. Tabarzad, N. Nafissi-Varcheh, and M. Torshabi (2017). Simultaneous Detection of Bovine and Porcine DNA in Pharmaceutical Gelatin Capsules by Duplex PCR Assay for Halal Authentication. DARU Journal of Pharmaceutical Sciences, 25(1); 3
Niu, Q., X. Su, L. Lian, J. Huang, S. Xue, W. Zhou, H. Zhao, X. Lu, S. Cui, J. Chen, and B. Yang (2022). Developing Qualitative Plasmid DNA Reference Materials to Detect Mechanisms of Quinolone and Fluoroquinolone Resistance in Foodborne Pathogens. Foods, 11(2); 154
Ni’Mah, A., Y. Kartikasari, A. D. Pratama, L. R. Kartikasari, B. S. Hertanto, and M. Cahyadi (2016). Detection of Pork Contamination in Fresh and Cooked Beef Using Genetic Marker Mitochondrial-DNA Cytochrome b by Duplex-PCR. Journal of the Indonesian Tropical Animal Agriculture, 41(1); 7–12
Noguchi, A., K. Nakamura, K. Sakata, N. Sato-Fukuda, T. Ishigaki, J. Mano, R. Takabatake, K. Kitta, R. Teshima, K. Kondo, and T. Nishimaki-Mogami (2016). Development and Interlaboratory Validation of a Simple Screening Method for Genetically Modified Maize Using a ΔΔ Cq-Based Multiplex Real-Time PCR Assay. Analytical Chemistry, 88(8); 4285–4293
Nurilmala, M., N. Darmawan, E. A. W. Putri, A. M. Jacoeb, and T. T. Irawadi (2021). Pangasius Fish Skin and Swim Bladder as Gelatin Sources for Hard Capsule Material. International Journal of Biomaterials, 2021; 1–6
Oh, S. H. and C. S. Jang (2020). Development and Validation of a Real-Time PCR Based Assay to Detect Adulteration with Corn in Commercial Turmeric Powder Products. Foods, 9(7); 882
Okanti, J. R., D. H. Putri, and A. Fathoni (2020). Analysis of ZDS and LCYb Enzyme Coding Gene Related to Beta Carotene Biosynthesis in Cassava (Manihot Esculenta Crantz) Using Reverse Transcription PCR (RT-PCR). Bioscience, 4(1); 01
Pavsic, J., J. Zel, and M. Milavec (2016). Assessment of the Real-Time PCR and Different Digital PCR Platforms for DNA Quantification. Analytical and Bioanalytical Chemistry, 408(1); 107–121
Perestam, A. T., K. K. Fujisaki, O. Nava, and R. S. Hellberg (2017). Comparison of Real-Time PCR and ELISA-Based Methods for the Detection of Beef and Pork in Processed Meat Products. Food Control, 71; 346–352
Prayitno, E. and E. Nuryandani (1970). Optimization of DNA Extraction of Physic Nut (Jatropha curcas) by Selecting the Appropriate Leaf. Nusantara Bioscience, 3(1)
Purwanto, H., S. Jati, and A. Rofiq (2021). Policy Analysis of Enforcement of Halal Product Guarantee Regulations Through the Regulatory Impact Analysis (RIA) Approach. Journal of Digital Marketing and Halal Industry, 3(2); 149–164
Raso, A. and R. Biassoni (2014). Twenty Years of qPCR: A Mature Technology? In Twenty Years of qPCR: A Mature Technology? pages 1–3
Rodríguez, A., M. Rodríguez, J. J. Córdoba, and M. J. Andrade (2015). Design of Primers and Probes for Quantitative Real-Time PCR Methods. In Design of Primers and Probes for Quantitative Real-Time PCR Methods. pages 31–56
Liang, W., L. Xu, Z. Sui, Y. Li, L. Li, Y. Wen, C. Li, S. Ren, and G. Liu (2016). Quantification of Plasmid DNA Reference Materials for Shiga Toxin-Producing Escherichia Coli Based on UV, HR-ICP-MS and Digital PCR. Chemistry Central Journal, 10(1), 55.
Manen, J., O. Sinitsyna, L. Aeschbach, A. V. Markov, and A. Sinitsyn (2005). A Fully Automatable Enzymatic Method for DNA Extraction from Plant Tissues. BMC Plant Biology, 5(1), 23.
Masiri, J., L. Benoit, B. Barrios-Lopez, C. Thienes, M. Meshgi, A. Agapov, A. Dobritsa, C. Nadala, and M. Samadpour (2016). Development and Validation of a Rapid Test System for Detection of Pork Meat and Collagen Residues. Meat Science, 121, 397–402.
Masnaini, M., A. Achyar, M. Chatri, D. H. Putri, Y. Ahda, and Irdawati (2023). Primer Design and Optimization of PCR Methods for Detecting Mixed Rat Meat in Food Samples. In Proceedings of The International Conference on Natural Resources and Technology, 282–289.
McDevitt, S. L., M. E. Hogan, D. J. Pappas, L. Y. Wong, and J. A. Noble (2014). DNA Storage Under High Temperature Conditions Does Not Affect Performance in Human Leukocyte Antigen Genotyping via Next-Generation Sequencing (DNA Integrity Maintained in Extreme Conditions). Biopreservation and Biobanking, 12(6), 402–408.
McShane, B. B., D. Gal, A. Gelman, C. Robert, and J. L. Tackett (2019). Abandon Statistical Significance. The American Statistician, 73(sup1), 235–245.
Mishra, P., U. Singh, C. Pandey, P. Mishra, and G. Pandey (2019). Application of Student’s t-Test, Analysis of Variance, and Covariance. Annals of Cardiac Anaesthesia, 22(4), 407.
Mokhtar, N. F. K., S. N. Aziz, N. H. Yusoff, R. M. H. Raja Nhari, N. A. Mohamad, and A. Mohd Hashim (2024). Porcine Detection in Commercial Edible Bird Nest Beverages Using Real Time PCR Targeting Chromosomally Encoded Multiple Porcine Repetitive Elements. Journal of Food Composition and Analysis, 131, 106211.
Nagy, A., L. Cerníková, E. Vitásková, V. Krivda, A. Dán, Z. Dirbáková, H. Jirincová, B. Procházka, K. Sedlák, and M. Havlícková (2016). MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay. PLoS ONE, 11(3), e0151204.
Nazarenko, I. (2002). Multiplex Quantitative PCR Using Self-Quenched Primers Labeled with a Single Fluorophore. Nucleic Acids Research, 30(9), 37e–37.
Nguyen, P. T. D., A. Giovanni, S. Maekawa, T. H. Pham, P. Wang, and S.-C. Chen (2023). An Integrated In Silico and In Vivo Study of Nucleic Acid Vaccine Against Nocardia seriolae Infection in Orange-Spotted Grouper Epinephelus Coioides. Fish & Shellfish Immunology, 143, 109202.
Nikzad, J., S. Shahhosseini, M. Tabarzad, N. Nafissi-Varcheh, and M. Torshabi (2017). Simultaneous Detection of Bovine and Porcine DNA in Pharmaceutical Gelatin Capsules by Duplex PCR Assay for Halal Authentication. DARU Journal of Pharmaceutical Sciences, 25(1), 3.
Niu, Q., X. Su, L. Lian, J. Huang, S. Xue, W. Zhou, H. Zhao, X. Lu, S. Cui, J. Chen, and B. Yang (2022). Developing Qualitative Plasmid DNA Reference Materials to Detect Mechanisms of Quinolone and Fluoroquinolone Resistance in Foodborne Pathogens. Foods, 11(2), 154.
Ni’Mah, A., Y. Kartikasari, A. D. Pratama, L. R. Kartikasari, B. S. Hertanto, and M. Cahyadi (2016). Detection of Pork Contamination in Fresh and Cooked Beef Using Genetic Marker Mitochondrial-DNA Cytochrome b by Duplex-PCR. Journal of the Indonesian Tropical Animal Agriculture, 41(1), 7–12.
Noguchi, A., K. Nakamura, K. Sakata, N. Sato-Fukuda, T. Ishigaki, J. Mano, R. Takabatake, K. Kitta, R. Teshima, K. Kondo, and T. Nishimaki-Mogami (2016). Development and Interlaboratory Validation of a Simple Screening Method for Genetically Modified Maize Using a ΔΔ Cq-Based Multiplex Real-Time PCR Assay. Analytical Chemistry, 88(8), 4285–4293.
Nurilmala, M., N. Darmawan, E. A. W. Putri, A. M. Jacoeb, and T. T. Irawadi (2021). Pangasius Fish Skin and Swim Bladder as Gelatin Sources for Hard Capsule Material. International Journal of Biomaterials, 2021, 1–6.
Oh, S. H. and C. S. Jang (2020). Development and Validation of a Real-Time PCR Based Assay to Detect Adulteration with Corn in Commercial Turmeric Powder Products. Foods, 9(7), 882.
Okanti, J. R., D. H. Putri, and A. Fathoni (2020). Analysis of ZDS and LCYb Enzyme Coding Gene Related to Beta Carotene Biosynthesis in Cassava (Manihot Esculenta Crantz) Using Reverse Transcription PCR (RT-PCR). Bioscience, 4(1), 01.
Pavsic, J., J. Zel, and M. Milavec (2016). Assessment of the Real-Time PCR and Different Digital PCR Platforms for DNA Quantification. Analytical and Bioanalytical Chemistry, 408(1), 107–121.
Perestam, A. T., K. K. Fujisaki, O. Nava, and R. S. Hellberg (2017). Comparison of Real-Time PCR and ELISA-Based Methods for the Detection of Beef and Pork in Processed Meat Products. Food Control, 71, 346–352.
Prayitno, E. and E. Nuryandani (1970). Optimization of DNA Extraction of Physic Nut (Jatropha curcas) by Selecting the Appropriate Leaf. Nusantara Bioscience, 3(1).
Purwanto, H., S. Jati, and A. Rofiq (2021). Policy Analysis of Enforcement of Halal Product Guarantee Regulations Through the Regulatory Impact Analysis (RIA) Approach. Journal of Digital Marketing and Halal Industry, 3(2), 149–164.
Raso, A. and R. Biassoni (2014). Twenty Years of qPCR: A Mature Technology? In Twenty Years of qPCR: A Mature Technology?, 1–3.
Rodríguez, A., M. Rodríguez, J. J. Córdoba, and M. J. Andrade (2015). Design of Primers and Probes for Quantitative Real-Time PCR Methods. In Design of Primers and Probes for Quantitative Real-Time PCR Methods, 31–56.
Rohland, N. and M. Hofreiter (2007). Comparison and Optimization of Ancient DNA Extraction. BioTechniques, 42(3), 343–352.
Romano, S., A. Brandao, J. Gumpinger, M. Gschweitl, and S. Beretta (2017). Qualification of AM Parts: Extreme Value Statistics Applied to Tomographic Measurements. Materials & Design, 131, 32–48.
Ruijter, J. M., R. J. Barnewall, I. B. Marsh, A. N. Szentirmay, J. C. Quinn, R. van Houdt, Q. D. Gunst, and M. J. B. van den Hoff (2021). Efficiency Correction Is Required for Accurate Quantitative PCR Analysis and Reporting. Clinical Chemistry, 67(6), 829–842.
Ruiz-Villalba, A., van Pelt-Verkuil, E., Gunst, Q. D., Ruijter, J. M., & van den Hoff, M. J. (2017). Amplification of nonspecific products in quantitative polymerase chain reactions (qPCR). Biomolecular Detection and Quantification, 14, 7–18.
Sabina, J., & Leamon, J. H. (2015). Bias in whole genome amplification: Causes and considerations. In Whole genome amplification: Methods and protocols (pp. 15–41). Springer.
Sanchez, J. M. (2020). Linear calibrations in chromatography: The incorrect use of ordinary least squares for determinations at low levels, and the need to redefine the limit of quantification with this regression model. Journal of Separation Science, 43(13), 2708–2717.
Sasmito, D. E. K., Kurniawan, R., & Muhimmah, I. (2014). Karakteristik primer pada polymerase chain reaction (PCR) untuk sekuensing DNA: Mini review. In Seminar Informatika Medis 2014 (pp. 93–102). (in Indonesia)
Schurch, N. J., Schofield, P., Gierlinski, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K. G., Simpson, G. G., Owen-Hughes, T., Blaxter, M., & Barton, G. J. (2016). How many biological replicates are needed in an RNA-Seq experiment and which differential expression tool should you use? RNA, 22(6), 839–851.
Sentandreu, M. A., & Sentandreu, E. (2014). Authenticity of meat products: Tools against fraud. Food Research International, 60, 19–29.
Shabani, H., Mehdizadeh, M., Mousavi, S. M., Dezfouli, E. A., Solgi, T., Khodaverdi, M., Rabiei, M., Rastegar, H., & Alebouyeh, M. (2015). Halal authenticity of gelatin using species-specific PCR. Food Chemistry, 184, 203–206.
Shuhaimi, M., & Sam-on, M. F. S. (2022). Rapid DNA-based analytical techniques to verify the authenticity of halal food. Journal of Halal Studies, 4(1), 1–23.
Soares, S., Amaral, J. S., Oliveira, M. B. P. P., & Mafra, I. (2013). A SYBR Green real-time PCR assay to detect and quantify pork meat in processed poultry meat products. Meat Science, 94(1), 115–120.
Sultana, S., Hossain, M. A. M., Azlan, A., Johan, M. R., Chowdhury, Z. Z., & Ali, M. E. (2020). TaqMan probe based multiplex quantitative PCR assay for determination of bovine, porcine and fish DNA in gelatin admixture, food products and dietary supplements. Food Chemistry, 325, 126756.
Svec, D., Tichopad, A., Novosadova, V., Pfaffl, M. W., & Kubista, M. (2015). How good is a PCR efficiency estimate: Recommendations for precise and robust qPCR efficiency assessments. Biomolecular Detection and Quantification, 3, 9–16.
Tan, L. L., Ahmed, S. A., Ng, S. K., Citartan, M., Raabe, C. A., Rozhdestvensky, T. S., & Tang, T. H. (2020). Rapid detection of porcine DNA in processed food samples using a streamlined DNA extraction method combined with the SYBR Green real-time PCR assay. Food Chemistry, 309, 125654.
Tan, S. C., & Yiap, B. C. (2009). DNA, RNA, and protein extraction: The past and the present. BioMed Research International, 2009, 1–10.
Tasrip, N. A., Mohd Desa, M. N., Khairil Mokhtar, N. F., Sajali, N., Mohd Hashim, A., Ali, M. E., & Kqueen, C. Y. (2021). Rapid porcine detection in gelatin-based highly processed products using loop-mediated isothermal amplification. Journal of Food Science and Technology, 58(12), 4504–4513.
Tretiakov, M. Y., Tokhtar, V. K., Ivleva, A. E., Kurkina, J. N., Batlutskaya, I. V., & Lyashenko, I. V. (2022). Optimizing the dry plant sample preparation method for efficient DNA extraction in Syringa vulgaris. International Journal of Ecosystems and Ecology Science (IJEES), 12(1), 201–206.
Vallejo, C. V., Tere, C. P., Calderon, M. N., Arias, M. M., & Leguizamon, J. E. (2021). Development of a genomic DNA reference material for Salmonella enteritidis detection using polymerase chain reaction. Molecular and Cellular Probes, 55, 101690.
VanInsberghe, M., Zahn, H., White, A. K., Petriv, O. I., & Hansen, C. L. (2018). Highly multiplexed single-cell quantitative PCR. PLoS ONE, 13(1), e0191601.
Vyhnánek, T., Trojan, V., Štiasna, K., Presinszká, M., Mrkvičová, E., Hrivna, L., & Havel, L. (2015). Testing of DNA isolation for the identification of hemp. Potravinarstvo Slovak Journal of Food Sciences, 9(1), 393–397.
Xie, N. G., Wang, M. X., Song, P., Mao, S., Wang, Y., Yang, Y., Luo, J., Ren, S., & Zhang, D. Y. (2022). Designing highly multiplex PCR primer sets with simulated annealing design using dimer likelihood estimation (SADDLE). Nature Communications, 13(1), 1–12.
Xu, L., & Kasprzyk-Hordern, B. (2023). Assessment of the stability of antimicrobials and resistance genes during short- and long-term storage condition: Accounting for uncertainties in bioanalytical workflows. Analytical and Bioanalytical Chemistry, 415(24), 6027–6038.
Yuniarti, H., Rinanti, A., & Bambang Cholis, S. (2020). Optimization of primary annealing temperature with BigDye reagent in sequencing reaction. International Journal of Scientific and Technology Research, 9(3), 1431–1434.
Zehra, A., & Kaur, S. (2023). Virus concentration and TaqMan real-time polymerase chain reaction (qPCR) quantification of adenoviral DNA for detection of sewage and farm wastewater-associated adenoviral markers: Optimization and validation of virus concentration methods. Journal of Soil Salinity and Water Quality, 15(1), 115–126.
Zhao, Z. (2014). Optimal GC content for PCR primers designed for the detection of bacterial and viral pathogens. Journal of Microbiological Methods, 98(3), 289–295.
Zia, Q., Alawami, M., Mokhtar, N. F. K., Nhari, R. M. H. R., & Hanish, I. (2020). Current analytical methods for porcine identification in meat and meat products. Food Chemistry, 324, 126664.
Al-Nimry, S., A. A. Dayah, I. Hasan, and R. Daghmash (2021). Cosmetic, Biomedical and Pharmaceutical Applications of Fish Gelatin/Hydrolysates. Marine Drugs, 19(3); 145.
Ali, M. E., M. A. Razzak, S. B. A. Hamid, M. M. Rahman, M. A. Amin, N. R. A. Rashid, and Asing (2015). Multiplex PCR Assay for the Detection of Five Meat Species Forbidden in Islamic Foods. Food Chemistry, 177; 214–224.
Aminfar, Z., B. Rabiei, M. Tohidfar, and M. H. Mirjalili (2019). Selection and Validation of Reference Genes for Quantitative Real-Time PCR in Rosmarinus Officinalis L. In Various Tissues and Under Elicitation. Biocatalysis and Agricultural Biotechnology, 20; 101246.
Ananta, A., E. Nurvidya Arifin, and M. Sairi Hasbullah (2015). Demography of Indonesia’s Ethnicity. ISEAS Publishing.
Arachchige, C. N. P. G., L. A. Prendergast, and R. G. Staudte (2022). Robust Analogs to the Coefficient of Variation. Journal of Applied Statistics, 49(2); 268–290.
Asif, M., D. Zhiyong, A. Iram, and M. Nisar (2021). Linguistic Analysis of Neologism Related to Coronavirus (COVID-19). Social Sciences & Humanities Open, 4(1); 100201.
Bento, C. S. A., S. Alarico, N. Empadinhas, H. C. de Sousa, and M. E. M. Braga (2022). Sequential ScCO2 Drying and Sterilisation of Alginate-Gelatine Aerogels for Biomedical Applications. The Journal of Supercritical Fluids, 184; 105570.
Borah, J. C. (2015). Shikimic Acid: A Highly Prospective Molecule in Pharmaceutical Industry. Current Science, 109(9); 1672–1679.
Bridgeman, S., G. Ellison, P. Newsholme, and C. Mamotte (2021). The HDAC Inhibitor Butyrate Impairs B Cell Function and Activates the Disallowed Gene Hexokinase I. International Journal of Molecular Sciences, 22(24); 13330.
Broeders, S., I. Huber, L. Grohmann, G. Berben, I. Taverniers, M. Mazzara, N. Roosens, and D. Morisset (2014). Guidelines for Validation of Qualitative Real-Time PCR Methods. Trends in Food Science & Technology, 37(2); 115–126.
Browne, P. D., T. K. Nielsen, W. Kot, A. Aggerholm, M. T. P. Gilbert, L. Puetz, M. Rasmussen, A. Zervas, and L. H. Hansen (2020). GC Bias Affects Genomic and Metagenomic Reconstructions, Underrepresenting GC-Poor Organisms. GigaScience, 9(2).
Bustin, S. and J. Huggett (2017). qPCR Primer Design Revisited. Biomolecular Detection and Quantification, 14; 19–28.
Cai, H., X. Gu, M. S. Scanlan, D. H. Ramatlapeng, and C. R. Lively (2012). Real-Time PCR Assays for Detection and Quantitation of Porcine and Bovine DNA in Gelatin Mixtures and Gelatin Capsules. Journal of Food Composition and Analysis, 25(1); 83–87.
Cheman, Y. (2005). Analysis of Potential Lard Adulteration in Chocolate and Chocolate Products Using Fourier Transform Infrared Spectroscopy. Food Chemistry, 90(4); 815–819.
Chen, F., Y. P. Hsieh, and R. C. Bridgman (2004). Monoclonal Antibody–Based Sandwich Enzyme-Linked Immunosorbent Assay for Sensitive Detection of Prohibited Ruminant Proteins in Feedstuffs. Journal of Food Protection, 67(3); 544–549.
Chen, K., Y. Zhou, K. Li, and J. Xiao (2017). Multiplex PCR with the Blunt Hairpin Primers for Next Generation Sequencing. Biotechnology and Bioprocess Engineering, 22(3); 347–351.
Corliss, J. O., M. Aikawa, and C. R. Sterling (1977). The Science and Technology of Gelatin. Academic Press, London (UK).
Dewantoro, A., A. Safarrida, D. Rahmasari, U. Nuraeni, R. D. Susmiarni, R. Damacena, and M. M. Amin (2023). Verification of Porcine Detection Method Based on SNI ISO/TS 20224-3:2020 on the Gelatin Matrix. Jurnal Standardisasi, 25(2); 79.
Di Leo, G. and F. Sardanelli (2020). Statistical Significance: p Value, 0.05 Threshold, and Applications to Radiomics—Reasons for a Conservative Approach. European Radiology Experimental, 4(1); 18.
Dragon, A. H., C. J. Rowe, A. M. Rhodes, O. L. Pak, T. A. Davis, and E. Ronzier (2023). Systematic Identification of the Optimal Housekeeping Genes for Accurate Transcriptomic and Proteomic Profiling of Tissues Following Complex Traumatic Injury. Methods and Protocols, 6(2); 22.
Erwanto, Y. (2018). Molecular Based Method Using PCR Technology on Porcine Derivative Detection for Halal Authentication. IntechOpen.
Forootan, A., R. Sjöback, J. Björkman, B. Sjögreen, L. Linz, and M. Kubista (2017). Methods to Determine Limit of Detection and Limit of Quantification in Quantitative Real-Time PCR (qPCR). Biomolecular Detection and Quantification, 12; 1–6.
Green, M. R. and J. Sambrook (2020). Cloning in Plasmid Vectors: Directional Cloning. Cold Spring Harbor Protocols, 2020(11); 485–488.
Guo, Y., Q. Cao, Z. Hong, Y. Tan, S. Chen, H. Jin, K. Tan, D. Wang, and Y. Yan (2020). The Origin, Transmission and Clinical Therapies on Coronavirus Disease 2019 (COVID-19) Outbreak an Update on the Status. Military Medical Research, 7(1); 11.
Hassan, N., T. Ahmad, and N. M. Zain (2018). Chemical and Chemometric Methods for Halal Authentication of Gelatin: An Overview. Journal of Food Science, 83(12); 2903–2911.
Hays, A., M. Wissel, K. Colletti, R. Soon, M. Azadeh, J. Smith, R. Doddareddy, M. Chalfant, W. Adamowicz, S. S. Ramaswamy, et al. (2024). Recommendations for Method Development and Validation of qPCR and dPCR Assays in Support of Cell and Gene Therapy Drug Development. The AAPS Journal, 26(1); 24.
Hikmah, N. N., A. Guntarti, and N. Salamah (2024). Concentration of Isolated DNA Face Masks Made of Gelatin for Halal Authentication. Journal of Halal Science and Research, 5(1); 1–5.
Hung, J. and Z. Weng (2016). Designing Polymerase Chain Reaction Primers Using Primer3Plus. Cold Spring Harbor Protocols, 2016(9); 093096.
International Organization for Standardization (ISO) (2017). Reference Materials - Guidance for Characterization and Assessment of Homogeneity and Stability. ISO Guide:35.
Jones, R. T. (2004). Manufacture and Physio-Chemical Properties. Pharmaceutical Press, second edition.
Kang, S. S. N., H. G. Lee, and H. Kim (2018). Development and Comparison of a Porcine Gelatin Detection System Targeting Mitochondrial Markers for Halal Authentication. LWT, 97; 697–702.
Karimi, K., M. Arzanlou, and I. Pertot (2020). Development of Novel Species-Specific Primers for the Specific Identification of Colletotrichum nymphaeae Based on Conventional PCR and LAMP Techniques. European Journal of Plant Pathology, 156(2); 463–475.
Karunakaran, D., A. W. Turner, A. Duchez, S. Soubeyrand, A. Rasheed, D. Smyth, D. P. Cook, M. Nikpay, J. W. Kandiah, C. Pan, et al. (2020). RIPK1 Gene Variants Associate with Obesity in Humans and Can Be Therapeutically Silenced to Reduce Obesity in Mice. Nature Metabolism, 2(10); 1113–1125.
Kesmen, Z., A. Gulluce, F. Sahin, and H. Yetim (2009). Identification of Meat Species by Taqman-Based Real-Time PCR Assay. Meat Science, 82(4); 444–449.
Khayyira, A. S., V. M. Estepane, and A. Malik (2018). Rapid PCR-Based Detection Optimization of Porcine DNA in Gelatin Capsule Shell. International Journal of Applied Pharmaceutics, 10(6); 217.
Kim, M., I. Yoo, S.-Y. Lee, Y. Hong, and H.-Y. Kim (2016). Quantitative Detection of Pork in Commercial Meat Products by Taqman® Real-Time PCR Assay Targeting the Mitochondrial D-Loop Region. Food Chemistry, 210; 102–106.
Klymus, K. E., C. M. Merkes, M. J. Allison, C. S. Goldberg, C. C. Helbing, M. E. Hunter, C. A. Jackson, R. F. Lance, A. M. Mangan, E. M. Monroe, A. J. Piaggio, J. P. Stokdyk, C. C. Wilson, and C. A. Richter (2020). Reporting the Limits of Detection and Quantification for Environmental DNA Assays. Environmental DNA, 2(3); 271–282.
Kumar, A. and N. Chordia (2015). In Silico PCR Primer Designing and Validation. PCR Primer Design, pages 143–151.
Lanzilao, I., F. Burgalassi, S. Fancelli, M. Settimelli, and R. Fani (2005). Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Analysis of Mitochondrial Cytb Gene from Species of Dairy Interest. Journal of AOAC International, 88(1); 128–135.
Lear, G., I. Dickie, J. Banks, S. Boyer, H. L. Buckley, T. R. Buckley, R. Cruickshank, A. Dopheide, K. M. Handley, S. Hermans, J. Kamke, C. K. Lee, R. Macdiarmid, S. E. Morales, D. A. Orlovich, R. Smissen, J. Wood, and R. Holdaway (2018). Methods for the Extraction, Storage, Amplification and Sequencing of DNA from Environmental Samples. New Zealand Journal of Ecology, 42(1).
León, C. M., M. Munoz, C. Hernández, M. S. Ayala, C. Flórez, A. Teherán, J. R. Cubides, and J. D. Ramírez (2017). Analytical Performance of Four Polymerase Chain Reaction (PCR) and Real Time PCR (qPCR) Assays for the Detection of Six Leishmania Species DNA in Colombia. Frontiers in Microbiology, 8.
Levin, R. E., F.-G. C. Ekezie, and D.-W. Sun (2018). DNA-Based Technique: Polymerase Chain Reaction (PCR). In Modern Techniques for Food Authentication. Elsevier, pages 527–616.
Li, J., H. Gao, Y. Li, S. Zhai, F. Xiao, G. Wu, and Y. Wu (2024). The Development of a Series of Genomic DNA Reference Materials with Specific Copy Number Ratios for the Detection of Genetically Modified Maize DBN9936. Foods, 13(5); 747.
Li, J., L. Zhang, L. Li, X. Li, X. Zhang, S. Zhai, H. Gao, Y. Li, G. Wu, and Y. Wu (2020). Development of Genomic DNA Certified Reference Materials for Genetically Modified Rice Kefeng 6. ACS Omega, 5(34); 21602–21609.
Liang, W., L. Xu, Z. Sui, Y. Li, L. Li, Y. Wen, C. Li, S. Ren, and G. Liu (2016). Quantification of Plasmid DNA Reference Materials for Shiga Toxin-Producing Escherichia Coli Based on UV, HR-ICP-MS and Digital PCR. Chemistry Central Journal, 10(1); 55
Manen, J., O. Sinitsyna, L. Aeschbach, A. V. Markov, and A. Sinitsyn (2005). A Fully Automatable Enzymatic Method for DNA Extraction from Plant Tissues. BMC Plant Biology, 5(1); 23
Masiri, J., L. Benoit, B. Barrios-Lopez, C. Thienes, M. Meshgi, A. Agapov, A. Dobritsa, C. Nadala, and M. Samadpour (2016). Development and Validation of a Rapid Test System for Detection of Pork Meat and Collagen Residues. Meat Science, 121; 397–402
Masnaini, M., A. Achyar, M. Chatri, D. H. Putri, Y. Ahda, and Irdawati (2023). Primer Design and Optimization of PCR Methods for Detecting Mixed Rat Meat in Food Samples. In Proceedings of The International Conference on Natural Resources and Technology. pages 282–289
McDevitt, S. L., M. E. Hogan, D. J. Pappas, L. Y. Wong, and J. A. Noble (2014). DNA Storage Under High Temperature Conditions Does Not Affect Performance in Human Leukocyte Antigen Genotyping via Next-Generation Sequencing (DNA Integrity Maintained in Extreme Conditions). Biopreservation and Biobanking, 12(6); 402–408
McShane, B. B., D. Gal, A. Gelman, C. Robert, and J. L. Tackett (2019). Abandon Statistical Significance. The American Statistician, 73(sup1); 235–245
Mishra, P., U. Singh, C. Pandey, P. Mishra, and G. Pandey (2019). Application of Student’s t-Test, Analysis of Variance, and Covariance. Annals of Cardiac Anaesthesia, 22(4); 407
Mokhtar, N. F. K., S. N. Aziz, N. H. Yusoff, R. M. H. Raja Nhari, N. A. Mohamad, and A. Mohd Hashim (2024). Porcine Detection in Commercial Edible Bird Nest Beverages Using Real Time PCR Targeting Chromosomally Encoded Multiple Porcine Repetitive Elements. Journal of Food Composition and Analysis, 131; 106211
Nagy, A., L. Cerníková, E. Vitásková, V. Krivda, A. Dán, Z. Dirbáková, H. Jirincová, B. Procházka, K. Sedlák, and M. Havlícková (2016). MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay. PLoS ONE, 11(3); e0151204
Nazarenko, I. (2002). Multiplex Quantitative PCR Using Self-Quenched Primers Labeled with a Single Fluorophore. Nucleic Acids Research, 30(9); 37e–37
Nguyen, P. T. D., A. Giovanni, S. Maekawa, T. H. Pham, P. Wang, and S.-C. Chen (2023). An Integrated In Silico and In Vivo Study of Nucleic Acid Vaccine Against Nocardia seriolae Infection in Orange-Spotted Grouper Epinephelus Coioides. Fish & Shellfish Immunology, 143; 109202
Nikzad, J., S. Shahhosseini, M. Tabarzad, N. Nafissi-Varcheh, and M. Torshabi (2017). Simultaneous Detection of Bovine and Porcine DNA in Pharmaceutical Gelatin Capsules by Duplex PCR Assay for Halal Authentication. DARU Journal of Pharmaceutical Sciences, 25(1); 3
Niu, Q., X. Su, L. Lian, J. Huang, S. Xue, W. Zhou, H. Zhao, X. Lu, S. Cui, J. Chen, and B. Yang (2022). Developing Qualitative Plasmid DNA Reference Materials to Detect Mechanisms of Quinolone and Fluoroquinolone Resistance in Foodborne Pathogens. Foods, 11(2); 154
Ni’Mah, A., Y. Kartikasari, A. D. Pratama, L. R. Kartikasari, B. S. Hertanto, and M. Cahyadi (2016). Detection of Pork Contamination in Fresh and Cooked Beef Using Genetic Marker Mitochondrial-DNA Cytochrome b by Duplex-PCR. Journal of the Indonesian Tropical Animal Agriculture, 41(1); 7–12
Noguchi, A., K. Nakamura, K. Sakata, N. Sato-Fukuda, T. Ishigaki, J. Mano, R. Takabatake, K. Kitta, R. Teshima, K. Kondo, and T. Nishimaki-Mogami (2016). Development and Interlaboratory Validation of a Simple Screening Method for Genetically Modified Maize Using a ΔΔ Cq-Based Multiplex Real-Time PCR Assay. Analytical Chemistry, 88(8); 4285–4293
Nurilmala, M., N. Darmawan, E. A. W. Putri, A. M. Jacoeb, and T. T. Irawadi (2021). Pangasius Fish Skin and Swim Bladder as Gelatin Sources for Hard Capsule Material. International Journal of Biomaterials, 2021; 1–6
Oh, S. H. and C. S. Jang (2020). Development and Validation of a Real-Time PCR Based Assay to Detect Adulteration with Corn in Commercial Turmeric Powder Products. Foods, 9(7); 882
Okanti, J. R., D. H. Putri, and A. Fathoni (2020). Analysis of ZDS and LCYb Enzyme Coding Gene Related to Beta Carotene Biosynthesis in Cassava (Manihot Esculenta Crantz) Using Reverse Transcription PCR (RT-PCR). Bioscience, 4(1); 01
Pavsic, J., J. Zel, and M. Milavec (2016). Assessment of the Real-Time PCR and Different Digital PCR Platforms for DNA Quantification. Analytical and Bioanalytical Chemistry, 408(1); 107–121
Perestam, A. T., K. K. Fujisaki, O. Nava, and R. S. Hellberg (2017). Comparison of Real-Time PCR and ELISA-Based Methods for the Detection of Beef and Pork in Processed Meat Products. Food Control, 71; 346–352
Prayitno, E. and E. Nuryandani (1970). Optimization of DNA Extraction of Physic Nut (Jatropha curcas) by Selecting the Appropriate Leaf. Nusantara Bioscience, 3(1)
Purwanto, H., S. Jati, and A. Rofiq (2021). Policy Analysis of Enforcement of Halal Product Guarantee Regulations Through the Regulatory Impact Analysis (RIA) Approach. Journal of Digital Marketing and Halal Industry, 3(2); 149–164
Raso, A. and R. Biassoni (2014). Twenty Years of qPCR: A Mature Technology? In Twenty Years of qPCR: A Mature Technology? pages 1–3
Rodríguez, A., M. Rodríguez, J. J. Córdoba, and M. J. Andrade (2015). Design of Primers and Probes for Quantitative Real-Time PCR Methods. In Design of Primers and Probes for Quantitative Real-Time PCR Methods. pages 31–56
Liang, W., L. Xu, Z. Sui, Y. Li, L. Li, Y. Wen, C. Li, S. Ren, and G. Liu (2016). Quantification of Plasmid DNA Reference Materials for Shiga Toxin-Producing Escherichia Coli Based on UV, HR-ICP-MS and Digital PCR. Chemistry Central Journal, 10(1), 55.
Manen, J., O. Sinitsyna, L. Aeschbach, A. V. Markov, and A. Sinitsyn (2005). A Fully Automatable Enzymatic Method for DNA Extraction from Plant Tissues. BMC Plant Biology, 5(1), 23.
Masiri, J., L. Benoit, B. Barrios-Lopez, C. Thienes, M. Meshgi, A. Agapov, A. Dobritsa, C. Nadala, and M. Samadpour (2016). Development and Validation of a Rapid Test System for Detection of Pork Meat and Collagen Residues. Meat Science, 121, 397–402.
Masnaini, M., A. Achyar, M. Chatri, D. H. Putri, Y. Ahda, and Irdawati (2023). Primer Design and Optimization of PCR Methods for Detecting Mixed Rat Meat in Food Samples. In Proceedings of The International Conference on Natural Resources and Technology, 282–289.
McDevitt, S. L., M. E. Hogan, D. J. Pappas, L. Y. Wong, and J. A. Noble (2014). DNA Storage Under High Temperature Conditions Does Not Affect Performance in Human Leukocyte Antigen Genotyping via Next-Generation Sequencing (DNA Integrity Maintained in Extreme Conditions). Biopreservation and Biobanking, 12(6), 402–408.
McShane, B. B., D. Gal, A. Gelman, C. Robert, and J. L. Tackett (2019). Abandon Statistical Significance. The American Statistician, 73(sup1), 235–245.
Mishra, P., U. Singh, C. Pandey, P. Mishra, and G. Pandey (2019). Application of Student’s t-Test, Analysis of Variance, and Covariance. Annals of Cardiac Anaesthesia, 22(4), 407.
Mokhtar, N. F. K., S. N. Aziz, N. H. Yusoff, R. M. H. Raja Nhari, N. A. Mohamad, and A. Mohd Hashim (2024). Porcine Detection in Commercial Edible Bird Nest Beverages Using Real Time PCR Targeting Chromosomally Encoded Multiple Porcine Repetitive Elements. Journal of Food Composition and Analysis, 131, 106211.
Nagy, A., L. Cerníková, E. Vitásková, V. Krivda, A. Dán, Z. Dirbáková, H. Jirincová, B. Procházka, K. Sedlák, and M. Havlícková (2016). MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay. PLoS ONE, 11(3), e0151204.
Nazarenko, I. (2002). Multiplex Quantitative PCR Using Self-Quenched Primers Labeled with a Single Fluorophore. Nucleic Acids Research, 30(9), 37e–37.
Nguyen, P. T. D., A. Giovanni, S. Maekawa, T. H. Pham, P. Wang, and S.-C. Chen (2023). An Integrated In Silico and In Vivo Study of Nucleic Acid Vaccine Against Nocardia seriolae Infection in Orange-Spotted Grouper Epinephelus Coioides. Fish & Shellfish Immunology, 143, 109202.
Nikzad, J., S. Shahhosseini, M. Tabarzad, N. Nafissi-Varcheh, and M. Torshabi (2017). Simultaneous Detection of Bovine and Porcine DNA in Pharmaceutical Gelatin Capsules by Duplex PCR Assay for Halal Authentication. DARU Journal of Pharmaceutical Sciences, 25(1), 3.
Niu, Q., X. Su, L. Lian, J. Huang, S. Xue, W. Zhou, H. Zhao, X. Lu, S. Cui, J. Chen, and B. Yang (2022). Developing Qualitative Plasmid DNA Reference Materials to Detect Mechanisms of Quinolone and Fluoroquinolone Resistance in Foodborne Pathogens. Foods, 11(2), 154.
Ni’Mah, A., Y. Kartikasari, A. D. Pratama, L. R. Kartikasari, B. S. Hertanto, and M. Cahyadi (2016). Detection of Pork Contamination in Fresh and Cooked Beef Using Genetic Marker Mitochondrial-DNA Cytochrome b by Duplex-PCR. Journal of the Indonesian Tropical Animal Agriculture, 41(1), 7–12.
Noguchi, A., K. Nakamura, K. Sakata, N. Sato-Fukuda, T. Ishigaki, J. Mano, R. Takabatake, K. Kitta, R. Teshima, K. Kondo, and T. Nishimaki-Mogami (2016). Development and Interlaboratory Validation of a Simple Screening Method for Genetically Modified Maize Using a ΔΔ Cq-Based Multiplex Real-Time PCR Assay. Analytical Chemistry, 88(8), 4285–4293.
Nurilmala, M., N. Darmawan, E. A. W. Putri, A. M. Jacoeb, and T. T. Irawadi (2021). Pangasius Fish Skin and Swim Bladder as Gelatin Sources for Hard Capsule Material. International Journal of Biomaterials, 2021, 1–6.
Oh, S. H. and C. S. Jang (2020). Development and Validation of a Real-Time PCR Based Assay to Detect Adulteration with Corn in Commercial Turmeric Powder Products. Foods, 9(7), 882.
Okanti, J. R., D. H. Putri, and A. Fathoni (2020). Analysis of ZDS and LCYb Enzyme Coding Gene Related to Beta Carotene Biosynthesis in Cassava (Manihot Esculenta Crantz) Using Reverse Transcription PCR (RT-PCR). Bioscience, 4(1), 01.
Pavsic, J., J. Zel, and M. Milavec (2016). Assessment of the Real-Time PCR and Different Digital PCR Platforms for DNA Quantification. Analytical and Bioanalytical Chemistry, 408(1), 107–121.
Perestam, A. T., K. K. Fujisaki, O. Nava, and R. S. Hellberg (2017). Comparison of Real-Time PCR and ELISA-Based Methods for the Detection of Beef and Pork in Processed Meat Products. Food Control, 71, 346–352.
Prayitno, E. and E. Nuryandani (1970). Optimization of DNA Extraction of Physic Nut (Jatropha curcas) by Selecting the Appropriate Leaf. Nusantara Bioscience, 3(1).
Purwanto, H., S. Jati, and A. Rofiq (2021). Policy Analysis of Enforcement of Halal Product Guarantee Regulations Through the Regulatory Impact Analysis (RIA) Approach. Journal of Digital Marketing and Halal Industry, 3(2), 149–164.
Raso, A. and R. Biassoni (2014). Twenty Years of qPCR: A Mature Technology? In Twenty Years of qPCR: A Mature Technology?, 1–3.
Rodríguez, A., M. Rodríguez, J. J. Córdoba, and M. J. Andrade (2015). Design of Primers and Probes for Quantitative Real-Time PCR Methods. In Design of Primers and Probes for Quantitative Real-Time PCR Methods, 31–56.
Rohland, N. and M. Hofreiter (2007). Comparison and Optimization of Ancient DNA Extraction. BioTechniques, 42(3), 343–352.
Romano, S., A. Brandao, J. Gumpinger, M. Gschweitl, and S. Beretta (2017). Qualification of AM Parts: Extreme Value Statistics Applied to Tomographic Measurements. Materials & Design, 131, 32–48.
Ruijter, J. M., R. J. Barnewall, I. B. Marsh, A. N. Szentirmay, J. C. Quinn, R. van Houdt, Q. D. Gunst, and M. J. B. van den Hoff (2021). Efficiency Correction Is Required for Accurate Quantitative PCR Analysis and Reporting. Clinical Chemistry, 67(6), 829–842.
Ruiz-Villalba, A., van Pelt-Verkuil, E., Gunst, Q. D., Ruijter, J. M., & van den Hoff, M. J. (2017). Amplification of nonspecific products in quantitative polymerase chain reactions (qPCR). Biomolecular Detection and Quantification, 14, 7–18.
Sabina, J., & Leamon, J. H. (2015). Bias in whole genome amplification: Causes and considerations. In Whole genome amplification: Methods and protocols (pp. 15–41). Springer.
Sanchez, J. M. (2020). Linear calibrations in chromatography: The incorrect use of ordinary least squares for determinations at low levels, and the need to redefine the limit of quantification with this regression model. Journal of Separation Science, 43(13), 2708–2717.
Sasmito, D. E. K., Kurniawan, R., & Muhimmah, I. (2014). Karakteristik primer pada polymerase chain reaction (PCR) untuk sekuensing DNA: Mini review. In Seminar Informatika Medis 2014 (pp. 93–102). (in Indonesia)
Schurch, N. J., Schofield, P., Gierlinski, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K. G., Simpson, G. G., Owen-Hughes, T., Blaxter, M., & Barton, G. J. (2016). How many biological replicates are needed in an RNA-Seq experiment and which differential expression tool should you use? RNA, 22(6), 839–851.
Sentandreu, M. A., & Sentandreu, E. (2014). Authenticity of meat products: Tools against fraud. Food Research International, 60, 19–29.
Shabani, H., Mehdizadeh, M., Mousavi, S. M., Dezfouli, E. A., Solgi, T., Khodaverdi, M., Rabiei, M., Rastegar, H., & Alebouyeh, M. (2015). Halal authenticity of gelatin using species-specific PCR. Food Chemistry, 184, 203–206.
Shuhaimi, M., & Sam-on, M. F. S. (2022). Rapid DNA-based analytical techniques to verify the authenticity of halal food. Journal of Halal Studies, 4(1), 1–23.
Soares, S., Amaral, J. S., Oliveira, M. B. P. P., & Mafra, I. (2013). A SYBR Green real-time PCR assay to detect and quantify pork meat in processed poultry meat products. Meat Science, 94(1), 115–120.
Sultana, S., Hossain, M. A. M., Azlan, A., Johan, M. R., Chowdhury, Z. Z., & Ali, M. E. (2020). TaqMan probe based multiplex quantitative PCR assay for determination of bovine, porcine and fish DNA in gelatin admixture, food products and dietary supplements. Food Chemistry, 325, 126756.
Svec, D., Tichopad, A., Novosadova, V., Pfaffl, M. W., & Kubista, M. (2015). How good is a PCR efficiency estimate: Recommendations for precise and robust qPCR efficiency assessments. Biomolecular Detection and Quantification, 3, 9–16.
Tan, L. L., Ahmed, S. A., Ng, S. K., Citartan, M., Raabe, C. A., Rozhdestvensky, T. S., & Tang, T. H. (2020). Rapid detection of porcine DNA in processed food samples using a streamlined DNA extraction method combined with the SYBR Green real-time PCR assay. Food Chemistry, 309, 125654.
Tan, S. C., & Yiap, B. C. (2009). DNA, RNA, and protein extraction: The past and the present. BioMed Research International, 2009, 1–10.
Tasrip, N. A., Mohd Desa, M. N., Khairil Mokhtar, N. F., Sajali, N., Mohd Hashim, A., Ali, M. E., & Kqueen, C. Y. (2021). Rapid porcine detection in gelatin-based highly processed products using loop-mediated isothermal amplification. Journal of Food Science and Technology, 58(12), 4504–4513.
Tretiakov, M. Y., Tokhtar, V. K., Ivleva, A. E., Kurkina, J. N., Batlutskaya, I. V., & Lyashenko, I. V. (2022). Optimizing the dry plant sample preparation method for efficient DNA extraction in Syringa vulgaris. International Journal of Ecosystems and Ecology Science (IJEES), 12(1), 201–206.
Vallejo, C. V., Tere, C. P., Calderon, M. N., Arias, M. M., & Leguizamon, J. E. (2021). Development of a genomic DNA reference material for Salmonella enteritidis detection using polymerase chain reaction. Molecular and Cellular Probes, 55, 101690.
VanInsberghe, M., Zahn, H., White, A. K., Petriv, O. I., & Hansen, C. L. (2018). Highly multiplexed single-cell quantitative PCR. PLoS ONE, 13(1), e0191601.
Vyhnánek, T., Trojan, V., Štiasna, K., Presinszká, M., Mrkvičová, E., Hrivna, L., & Havel, L. (2015). Testing of DNA isolation for the identification of hemp. Potravinarstvo Slovak Journal of Food Sciences, 9(1), 393–397.
Xie, N. G., Wang, M. X., Song, P., Mao, S., Wang, Y., Yang, Y., Luo, J., Ren, S., & Zhang, D. Y. (2022). Designing highly multiplex PCR primer sets with simulated annealing design using dimer likelihood estimation (SADDLE). Nature Communications, 13(1), 1–12.
Xu, L., & Kasprzyk-Hordern, B. (2023). Assessment of the stability of antimicrobials and resistance genes during short- and long-term storage condition: Accounting for uncertainties in bioanalytical workflows. Analytical and Bioanalytical Chemistry, 415(24), 6027–6038.
Yuniarti, H., Rinanti, A., & Bambang Cholis, S. (2020). Optimization of primary annealing temperature with BigDye reagent in sequencing reaction. International Journal of Scientific and Technology Research, 9(3), 1431–1434.
Zehra, A., & Kaur, S. (2023). Virus concentration and TaqMan real-time polymerase chain reaction (qPCR) quantification of adenoviral DNA for detection of sewage and farm wastewater-associated adenoviral markers: Optimization and validation of virus concentration methods. Journal of Soil Salinity and Water Quality, 15(1), 115–126.
Zhao, Z. (2014). Optimal GC content for PCR primers designed for the detection of bacterial and viral pathogens. Journal of Microbiological Methods, 98(3), 289–295.
Zia, Q., Alawami, M., Mokhtar, N. F. K., Nhari, R. M. H. R., & Hanish, I. (2020). Current analytical methods for porcine identification in meat and meat products. Food Chemistry, 324, 126664.
Authors
Rahma, A. A., Meilani, N. D., Sulistiawati, Ainaputri, A. S., Damara, D. S., & Malau, J. (2025). Development of a Gelatin-Based Genomic Reference Material for Halal Authentication Using Real-Time PCR. Science and Technology Indonesia, 10(1), 27–42. https://doi.org/10.26554/sti.2025.10.1.27-42
This work is licensed under a Creative Commons Attribution 4.0 International License.