Identification of single nucleotide polymorphisms on the D-loop region of mtDNA in Sundanese population

Wolly  Candramila; Sony Heru  Sumarsono; Bambang  Suryobroto; Maelita Ramdani  Moeis

Wolly Candramila
Sony Heru Sumarsono
Bambang Suryobroto
Maelita Ramdani Moeis

Abstract

Identification of sequence polymorphism on the D-loop region of mtDNA has been done for various purposes, including health and medical treatment. In this research, single nucleotide polymorphisms were identified in the D-loop region of mtDNA of the Sundanese population in western Java. A total of 118 unrelated and healthy Sundanese probands were collected from closed-traditional kampung adat and open communities distributed in 14 cities and regencies in western Java. DNA amplification and direct sequencing of the D-loop region were proceeded using primers L15990 and H409. Multi-alignment was conducted not only intrapopulation but also with D-loop sequence data stored in GenBank for comparison. In this research, we categorized high-frequency SNPs as less effective for identification in population studies because of their presence in other populations outside Indonesia. Meanwhile, lower-frequency SNPs showed typical variants of Sundanese haplotypes. On the other hand, rare or low-frequency SNPs should be re-examined in larger size of samples to have a better understanding of risk factors for many diseases.

References

Anderson, S., Bankier, A. T., Barrel, B. G., de Bruijn, M. H., Coulson, A. R., Drouin, J., . . . Young, I. G. (1981). Sequence and the Organization of the Human Mitochondrial Genome. Nature, 209, 457-465.

Andréasson, H., Asp, A., Alderborn, A., Gyllensten, U., & Allen, M. (2002). Mitochondrial Sequence Analysis for Forensic Identification Using Pyrosequencing Technology. Biotechniques, 32(1), 124-133.

Andrews, R. M., Kubacka, I., Chinnery, P. F., Lightowlers, R. N., Tumbull, D. M., & Howell, N. (1999). Reanalysis and Revision of the Cambridge Reference Sequence fo Human Mitochondrial DNA. Nature Genetics, 23, 147.

Babron, M.-C., de Tayrac, M., Rutledge, D. N., Zeggini, E., & Genin, E. (2012). Rare and Low Frequency Variant Stratification in the UK Population: Description and Impact on Association Tests. PLoS ONE, 7(10), e46519. doi:10.1371/journal.pone.0046519

Badan Pusat Statistik. (2011). Kewarganegaraan, Suku Bangsa, Agama, dan Bahasa Sehari-hari Penduduk Indonesia. Jakarta: Badan Pusat Statistik.

Bandelt, H. -J., & Parson, W. (2008). Consistent treatment of length variants in the human mtDNA control region: a reappraisal. International Journal of Legal Medicine, 122, 11-21.

Budowle, B., Allard, M. W., Fisher, C. L., Isenberg, A. R., Monson, K. L., Stewart, J. E., . . . Miller, K. W. (2002). HVI and HVII mitochondrial DNA data in Apaches and Navajos. International Journal of Legal Medicine, 116, 212-215. doi:10.1007/s00414-001-0283-6

Candramila, W., Sumarsono, S. H., Suryobroto, B., & Moeis, M. R. (2021). Maternal Genetic Distance Between Sundanese and Javanese Populations in Indonesia. EPiC Series in Biological Sciences (pp. 41-47). Manchester: Easy Chair.

Coble, M. D., Vallone, P. M., Just, R. S., Diegoli, T. M., Smith, B. C., & Parsons, T. J. (2006). Effective Strategies for Forensic Analysis in the Mitochondrial DNA Coding Region. International Journal of Legal Medicine, 120, 27-32. doi:10.1007/s00414-005-0044-z

Edgar, R. C. (2004). MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 1-19.

Fucharoen, G., Fucharoen, S., & Horai, S. (2001). Mitochondrial DNA Polymorphisms in Thailand. Journal of Human Genetics, 46, 115-125.

Govatati, S., Deenadayal, M., Shivaji, S., & Bhanoori, M. (2013, June). Mitochondrial displacement loop alterations are associated with endometriosis. Fertility and Sterility, 99(7), 1989e1-1986.e9. doi:10.1016/j.fertnstert.2013.02.021

Guo, Z., Zhao, S., Fan, H., Du, Y., Zhao, Y., & Wang, G. (2016). Identification of Sequence Polymorphisms in the D-loop Region of Mitochondrial DNA as a Risk Factor for Colon Cancer. Mitochondrial DNA Part A, 1-2.

Kong, D., Shi, S., & Li, Y. (2014). Single Nucleotide Polymorphisms in the D-loop Region of Mitochondrial DNA are Associated with Epithelial Ovarian Cancer Prognosis. Mitochondrial DNA Part A, 1-3.

Kryukov, G. V., Pennacchio, L. A., & Sunyaev, S. R. (2007, April). Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. American Journal of Human Genetics, 80(4), 727-739. doi:10.1085/513473

Mousavizadeh, K., Rajabi, P., Alaee, M., Dadgar, S., & Houshmand, M. (2014). Usage of mitochondrial D-loop variation to predict risk for Huntington disease. Mitochondrial DNA, 26(4), 579-582. doi:10.3109/19401736.2013.878902

Murakami, H., Ota, A., Simojo, H., Okada, M., Ajisaka, R., & Kuno, S. (2002). Polymorphisms in Control Region of mtDNA Relates to Individual Differences in Endurance Capacity or Trainability. Japanese Journal of Physiology, 52(3), 247-256.

Nishimaki, Y., Sato, K., Fang, L., Ma, M., Hasekura, H., & Boetrcher, B. (1999). Sequence polymorphism in the mtDNA HV1 Region in japanese and Chinese. Legal Medicine, 1, 238-249.

Piercy, R., Sullivan, K. M., Benson, N., & Gill, P. (1993). The application of mitochondrial DNA typing to the study of white Caucasian genetic identification. International Journal of Legal Medicine, 106, 85-90.

Ranasinghe, R., Tennekoon, K. H., Karunanayake, E. H., Lembring, M., & Allen, M. (2015). A study of genetic polymorphisms in mitochondrial DNA hypervariable regions I and II of the five major ethnic groups and Vedda population in Sri Langka. Legal Medicine, 17(6), 539-546. doi:10.1016/j.legalmed.2015.05.007

Rousselet, F., & Mangin, P. (1998). Mitochondrial DNA Polymorphisms: a study of 50 French Caucasian individuals and application to forensic casework. International Journal of Legal Medicine, 111, 292-298.

Sambrook, J., Fritsch, E. F., & Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual 2nd Edition. New York: Cold Spring Harbor Laboratory Press.

Sharma, S., Saha, A., Rai, E., Bhat, A., & Bamezai, R. (2005). Human mtDNA hypervariable regions, HVR I and II, hint at deep common maternal founder and subsequent maternal gene flow in Indian population groups. Journal of Human Genetics, 50, 497-506. doi:10.1007/s10038-005-0284-2

Sigurðardóttir, S., Helgason, A., Gulcher, J. R., Stefansson, K., & Donnelly, P. (2000). The Mutation Rate in the Human mtDNA Control Region. American Journal of Human Genetics, 66, 1599-1609.

Stoltzfus, A., & Norris, R. W. (2015). On the causes of Evolutionary Transition:Transversion Bias. Molecular Biology and Evolution, 33(3), 595-602. doi:10.1093/molbev/msv274

Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). Mega5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 28, 2731-2739.

Tsai, L. C., Lin, C. Y., Lee, J. C., Chang, J. G., Linacre, A., & Goodwin, W. (2001). Sequence polymorphism of mitochondrial D-loop DNA in the Taiwanese Han Population. Forensic Science International, 119, 239-247.

Tuladhar, B. S., Rashid, N. H., Panneerchelvam, S., & Nor, N. M. (2014, September). Sequence Polymorphism of Mitochondrial DNA Hypervariable Regions I and II in Malay Population of Malaysia. Scientific World, 12(12), 24-29. doi:10.3126_sw.v12i12.13566

Wilson, M. R., Allard, M. W., Monson, K. L., Miller, K. W., & Budowle, B. (2002). Further Discussion of the Consistent Treatment of Length Variants in the Human Mitochondrial DNA Control Region. Forensic Science Communications, 4.

Wilson, M. R., Allard, M. W., Monson, K. L., Miller, K. W., & Budowle, B. (2002). Recommendations for consistent treatment of length variants in the human mtDNA control regions. Forensic Science International, 129, 35-42.

Xu, J., Guo, Z., Bai, Y., Zhang, J., Cui, L., Zhang, H., . . . Ai, X. (2015). Single Nucleotide Polymorphisms in the D-loop Region of Mitochondrial DNA is Associated with the Kidney Survival Time in Chronic Kidney Disease Patients. Renal Failure, 37(1), 108-112. doi:10.3109/0886022X.2014.976132