TY - JOUR
T1 - Genomic profiles of Indonesian colorectal cancer patients
AU - Abdullah, Murdani
AU - Meilany, Sofy
AU - Trimarsanto, Hidayat
AU - Malik, Safarina G.
AU - Sukartini, Ninik
AU - Idrus, Firhat
AU - Nursyirwan, Saskia A.
AU - Muzellina, Virly N.
AU - Pribadi, Rabbinu R.
AU - Maulahela, Hasan
AU - Syam, Ari F.
AU - Utari, Amanda Pitarini
N1 - Funding Information:
This study was supported by the Indonesian Ministry of Research, Technology, and Higher Education through the World Class Research (WCR) 2019 Program Contract NKB-1086/UN2.R3.1/HKP.05.00/2019.
Publisher Copyright:
Copyright: © 2023 Abdullah M et al.
PY - 2023
Y1 - 2023
N2 - Background: Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide and genetic mutation plays a vital role in CRC development. A previous study has suggested that genetic alterations among Indonesian patients with CRC might differ from those known in developed countries. This study aimed to describe the genomic profiles of Indonesian patients with CRC. Methods: A total of 13 patients were recruited for this study from May to July 2019. Tissue samples were collected, and genomic DNA was extracted from the samples. AmpliSeq for Illumina Cancer HotSpot Panel v2 Next-generation sequencing was used for DNA sequencing and a genome analysis toolkit was used for local realignment around the discovered variants. Results: A total of 45 genes comprising 391 single nucleotide variants (SNVs) with a depth >10 were observed. The genes with the most variants were STK11, SMAD4, EGFR, and ERBB4 and the genes with the most non-synonymous variants were SMAD4, TP53, FGFR3, CDKN2A, and STK11. Genes and SNVs in at least 90% of all samples consisted of 43 genes comprising 286 variants. Genes with the most non-synonymous SNVs were EGFR, SMO, FGFR3, TP53, STK11, CDKN2A. Genes related to the chromosomal instability pathway, such as TP53, SMAD4, KRAS, and APC, are also found in the analysis. Conclusions: Our findings showed that all patients with CRC in this study had genetic mutations in the chromosomal instability pathway. Analysis of genetic mutation of Indonesian patients with CRC might be crucial for advanced targeted therapy and for better clinical outcomes.
AB - Background: Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide and genetic mutation plays a vital role in CRC development. A previous study has suggested that genetic alterations among Indonesian patients with CRC might differ from those known in developed countries. This study aimed to describe the genomic profiles of Indonesian patients with CRC. Methods: A total of 13 patients were recruited for this study from May to July 2019. Tissue samples were collected, and genomic DNA was extracted from the samples. AmpliSeq for Illumina Cancer HotSpot Panel v2 Next-generation sequencing was used for DNA sequencing and a genome analysis toolkit was used for local realignment around the discovered variants. Results: A total of 45 genes comprising 391 single nucleotide variants (SNVs) with a depth >10 were observed. The genes with the most variants were STK11, SMAD4, EGFR, and ERBB4 and the genes with the most non-synonymous variants were SMAD4, TP53, FGFR3, CDKN2A, and STK11. Genes and SNVs in at least 90% of all samples consisted of 43 genes comprising 286 variants. Genes with the most non-synonymous SNVs were EGFR, SMO, FGFR3, TP53, STK11, CDKN2A. Genes related to the chromosomal instability pathway, such as TP53, SMAD4, KRAS, and APC, are also found in the analysis. Conclusions: Our findings showed that all patients with CRC in this study had genetic mutations in the chromosomal instability pathway. Analysis of genetic mutation of Indonesian patients with CRC might be crucial for advanced targeted therapy and for better clinical outcomes.
KW - colorectal cancer
KW - genetics
KW - Indonesia
KW - mutation
KW - sequencing
UR - http://www.scopus.com/inward/record.url?scp=85152915431&partnerID=8YFLogxK
U2 - 10.12688/f1000research.109136.2
DO - 10.12688/f1000research.109136.2
M3 - Article
AN - SCOPUS:85152915431
SN - 2046-1402
VL - 11
JO - F1000Research
JF - F1000Research
M1 - 443
ER -