Genetic Profiling of Tumor Specimens

Tumour DNA was extracted from tumour specimens with NucleoSpin® Tissue (MACHEREY-NAGEL, Düren, Germany). Regions of interest for driver genes [23 (link), 27 (link)–30 (link)] were amplified by PCR with gene-specific primers (Supplementary Table 1) and TaKaRa Ex Taq® (TAKARA BIO, Shiga, Japan) (IDH1/2, H3F3A, and HIST1H3B) or AmpliTaq Gold 360 (Thermo Fisher Scientific, Waltham, MA) (TERTp, KRAS, HRAS, and NRAS) using Applied Biosystems GeneAmp PCR System 9700 (Thermo Fisher Scientific). PCR products were purified by ExoSAP-IT (Affymetrix, Santa Clara, CA), then sequenced with sequencing primer (IDH1) or PCR forward primer as a sequencing primer (IDH2, H3F3A, HIST1H3B, TERTp, and exons 2 and 3 of KRAS, HRAS, and NRAS) and BigDye® Terminator V1.1 Cycle Sequencing Kit (Thermo Fisher Scientific) using the ABI 3130xL Genetic Analyzer (Thermo Fisher Scientific).

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Makino Y., Arakawa Y., Yoshioka E., Shofuda T., Minamiguchi S., Kawauchi T., Tanji M., Kanematsu D., Nonaka M., Okita Y., Kodama Y., Mano M., Hirose T., Mineharu Y., Miyamoto S, & Kanemura Y. (2021). Infrequent RAS mutation is not associated with specific histological phenotype in gliomas. BMC Cancer, 21, 1025.

Publication 2021

NucleoSpin® Tissue Ex Taq AmpliTaq Gold 360 Applied Biosystems GeneAmp PCR System 9700 ExoSAP-IT BigDye® Terminator V1.1 Cycle Sequencing Kit ABI 3130xL Genetic Analyzer

Exons Gene Genetic Gold Hras Idh2 Kras Nras Primer Tissue Tumour Tumour dna

Corresponding Organization :

Other organizations : Kyoto University, Osaka National Hospital, Hyogo Prefectural Cancer Center

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Variable analysis

independent variables

Regions of interest for driver genes [23, 27–30] were amplified by PCR with gene-specific primers

dependent variables

Tumour DNA was extracted from tumour specimens

control variables

NucleoSpin® Tissue (MACHEREY-NAGEL, Düren, Germany) was used to extract tumour DNA
TaKaRa Ex Taq® (TAKARA BIO, Shiga, Japan) was used for PCR amplification of IDH1/2, H3F3A, and HIST1H3B
AmpliTaq Gold 360 (Thermo Fisher Scientific, Waltham, MA) was used for PCR amplification of TERTp, KRAS, HRAS, and NRAS
Applied Biosystems GeneAmp PCR System 9700 (Thermo Fisher Scientific) was used for PCR amplification
ExoSAP-IT (Affymetrix, Santa Clara, CA) was used to purify PCR products
Sequencing was performed using sequencing primer (IDH1) or PCR forward primer (IDH2, H3F3A, HIST1H3B, TERTp, and exons 2 and 3 of KRAS, HRAS, and NRAS) and BigDye® Terminator V1.1 Cycle Sequencing Kit (Thermo Fisher Scientific) using the ABI 3130xL Genetic Analyzer (Thermo Fisher Scientific)

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