Computational protocol: Association between proto-oncogene mutations and clinicopathologic characteristics and overall survival in colorectal cancer in East Azerbaijan, Iran

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Protocol publication

[…] Program conditions were 3 minutes at 94°C, followed by 30 cycles of 20 seconds at 94°C, 150 seconds at 61°C, 20 seconds at 72°C, and 3 minutes at 72°C. PCR products were analyzed by 1.5% agarose-gel electrophoresis and visualized by ethidium bromide staining, using UVItec (Cambridge, UK) equipment.Sanger sequencing was performed after purification of PCR products with a PCR product-purification kit (MBST, Tehran, Iran) as per the manufacturer’s protocol. The forward primers of PCR amplification of KRAS and BRAF genes were used for sequencing, using a genetic analyzer (ABI 4-capillary 3130; Thermo Fisher Scientific).Sequencing electropherograms were analyzed using Chroma 233, FinchTV, and DNAman software. Mutation status and probable nucleotide changes in the specific exon were determined using “Database Nucleotide Collection Blast” in NCBI/BLAST. All sequence results (normal and tumor) were compared with the significant KRAS- and BRAF-gene mutations in the My Cancer Genome database of CRC, to identify mutations and the presence of new mutations. […]

Pipeline specifications

Software tools FinchTV, DNAMAN, BLASTN
Databases MCG
Application Sanger sequencing
Organisms Homo sapiens
Diseases Colonic Neoplasms, Neoplasms, Colorectal Neoplasms