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http://dx.doi.org/10.17576/jsm-2018-4712-20
Prediction of Colorectal Cancer Driver
Genes from Patients’ Genome Data
(Penentuan Gen Pemandu Kanser Kolorektum daripada
Data Genomik Pesakit)
MUHAMMAD-IQMAL ABDULLAH
& NOR AZLAN NOR MUHAMMAD*
Centre for
Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti
Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia
Received: 30 May 2018 /Accepted: 14 September
2018
ABSTRACT
Colorectal cancer refers to the
cancer that occurs in the colon and rectum. It has been established as the
third most common cancer and the forth one in causing worldwide mortality.
Cancer caused by the mutation of several genes that usually involved in the
regulation of cell proliferation, growth and cell death. The mutation that
leads to abnormal function of genes, either in enabling the genes to gain or
loss of function was termed as driver mutation and the genes with driver
mutation ability was termed as driver genes. The identification of driver genes
provides insight on mechanistic process of cancer development where this
information can be used to further understand their mode of action for causing
dysregulation in signaling pathways. In this study, two bioinformatic tools,
i.e. CGI and iCAGES were used to predict potential driver
genes from the genome of eight colorectal cancer patients with annotated
variants datasets. 44 unique driver genes and 21 pathways have been identified;
such as p53 signaling, PI3K-AKT, Endocrine resistance, MAPK and cell cycle pathways. The identification of these pathways can
lead to the identification of potential drugs targeting these pathways.
Keywords: Cancer driver genes;
colorectal cancer; pathway analysis; precision medicine
ABSTRAK
Kanser kolorektum adalah kanser yang
berlaku pada kolon dan juga rektum. Ia merupakan kanser ketiga yang
paling kerap dilaporkan serta yang keempat menjadi punca kematian
tertinggi di seluruh dunia. Kanser berlaku disebabkan oleh mutasi
daripada gen tertentu yang terlibat di dalam pengawalaturan proliferasi,
pertumbuhan dan kematian sel. Mutasi yang mencetuskan perubahan
pada fungsi gen sama ada meningkatkan atau menghilangkan fungsinya
dikenali sebagai mutasi pemandu, manakala gen yang mempunyai mutasi
pemandu dikenali sebagai gen pemandu kanser. Pengenalpastian gen
pemandu membolehkan mekanisme pembentukan kanser dapat dikenal pasti
melalui peranannya dalam pengawalaturan tapak jalan. Dalam kajian
ini, dua perisian bioinformatik iaitu CGI dan iCAGES telah digunakan
untuk mengenal pasti calon gen pemandu daripada set data varian
yang telah dianotasi daripada genom lapan pesakit kanser kolorektum.
Sebanyak 44 gen pemandu dan 21 tapak jalan terlibat telah dikenal
pasti; antaranya adalah tapak jalan pengisyaratan p53, PI3K-AKT, rintangan endokrin dan MAPK.
Kesemua tapak jalan ini berpotensi untuk dijadikan sasaran terapi.
Kata
kunci: Analisis tapak jalan; gen pemandu kanser; kanser kolorektum;
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*Corresponding author; email: norazlannm@ukm.edu.my
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