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
Diserahkan:
9 Mei 2022/Diterima: 12 Ogos 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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*Pengarang untuk surat-menyurat; email: seri.ishar@ukm.edu.my
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