Sains Malaysiana 51(12)(2022): 4019-4030

http://doi.org/10.17576/jsm-2022-5112-12

A Review of Mitochondrial SNP Determination using Allele-Specific PCR in Forensic Identification

(Suatu Tinjauan Penentuan SNP Mitokondria menggunakan PCR Khusus-Alel dalam Pengecaman Forensik)

SHALINI PARTHIPAN, MOHITHA SANDRASAGRAN & SERI MIRIANTI ISHAR^*

Forensic Science Program, Faculty of Health Sciences, Forensics UKM, Basement 1 PTSL, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

Received: 9 May 2022/Accepted: 12 August 2022

Abstract

Allele-specific polymerase chain reaction (AS-PCR) is a rapid and cost-effective single nucleotide polymorphism (SNP) genotyping method compared to multiplex or real-time PCR. The SNPs occurring in mitochondrial DNA (mtSNPs) is the most abundant polymorphism in humans and can be used in human identification involving mass fatality incidents. Nevertheless, the application of AS-PCR has yet to be widely applicable in forensic investigations because this method requires further development due to its limitations. This review aims to relate the applications of AS-PCR, the combination of AS-PCR with other PCR techniques and improvements imposed on this technique in past studies. A narrative literature review was carried out over 70 studies related to the mtDNA, SNP, AS-PCR, and forensic DNA. The findings suggested that AS-PCR with new adaptations in technology such as incorporating additional mismatch, choosing allele-specific primer with either common forward or reverse, gel free real-time AS-PCR analysis, and usage of fluorescence probes can improve the specificity of SNP genotyping in forensic applications. This review concludes that AS-PCR and its combination with other improvised techniques can be applied in human identification to successfully analyze degraded or low quantity samples. Nevertheless, development of more SNP loci is required to implement AS-PCR in human identification to match the current gold standard STR typing method.

Keywords: Allele-specific PCR; human identification; mitochondrial DNA; single nucleotide polymorphism

Abstrak

Tindak balas rantai polimerase khusus alel (AS-PCR) merupakan kaedah pengecapjarian polimorfisme nukleotida tunggal (SNP) yang cepat dan murah berbanding multipleks PCR atau tindak balas berantai polimerase masa nyata. SNP berlaku dalam DNA mitokondria (mtSNPs) adalah polimorfisme yang paling banyak diperhatikan pada manusia dan boleh digunakan untuk pengecaman mangsa dari bencana. Namun demikian, kaedah PCR khusus alel masih belum dipraktikkan secara meluas dalam kajian forensik kerana beberapa had AS-PCR menyebabkan kaedah ini masih memerlukan penambahbaikan seterusnya. Oleh yang demikian, kajian ini bertujuan untuk menghubungkan beberapa aplikasi AS-PCR, gabungan AS-PCR dengan teknik lain dan penambahbaikan yang dilakukan terhadap kaedah ini daripada kajian lepas. Tinjauan naratif ini dijalankan terhadap lebih daripada 70 kajian berdasarkan kata kunci mtDNA, SNP, AS-PCR dan DNA forensik. Hasil tinjauan mencadangkan bahawa AS-PCR dengan penyesuaian baharu dalam kaedah tersebut seperti menambahkan bes ketidaksepadan dalam pencetus khusus alel, pemilihan pencetus umum daripada pencetus kehadapan atau berbalik, AS-PCR dengan analisis masa nyata bebas daripada penggunaan gel serta penggunaan prob pendarfluor boleh meningkatkan kekhususan AS-PCR terhadap aplikasi forensik. Kesimpulannya, AS-PCR dengan gabungan beberapa teknik penambahbaikan boleh digunakan untuk menganalisis sampel manusia terurai atau berkuantiti DNA rendah daripada tempat kejadian. Namun demikian, pembangunan lebih banyak lokus SNP harus dilakukan untuk mempraktikkan kaedah AS-PCR dalam pengecaman manusia supaya kaedah ini sepadan dengan pengecapjarian STR semasa.

Kata kunci: DNA mitokondria; PCR khusus alel; pengecaman manusia; polimorfisme nukleotida tunggal

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^*Corresponding author; email: seri.ishar@ukm.edu.my