Adaptation and Experimental Validation of Clinical RNA Sequencing Protocol Oncobox for MGI DNBSEQ-G50 Platform

Buzdin, A., Sorokin, M., Garazha, A., Glusker, A., Aleshin, A., et al., RNA sequencing for research and diagnostics in clinical oncology, Semin. Cancer Biol., 2020, vol. 60, pp. 311–323. https://doi.org/10.1016/j.semcancer.2019.07.010

Article  CAS  PubMed  Google Scholar 

Wang, Y., Liu, B., Zhao, G., Lee, Y., Buzdin, A., et al., Spatial transcriptomics: Technologies, applications and experimental considerations, Genomics, 2023, vol. 115, no. 5, p. 110671. https://doi.org/10.1016/j.ygeno.2023.110671

Article  CAS  PubMed  Google Scholar 

Szeto, C.W., Kurzrock, R., Kato, S., Goloubev, A., Veerapaneni, S., et al., Association of differential expression of immunoregulatory molecules and presence of targetable mutations may inform rational design of clinical trials, ESMO Open, 2022, vol. 7, no. 1, p. 100396. https://doi.org/10.1016/j.esmoop.2022.100396

Article  CAS  PubMed  PubMed Central  Google Scholar 

Samii, A., Sorokin, M., Kar, S., Makovskaia, L., Garazha, A., et al., Case of multifocal glioblastoma with four fusion transcripts of ALK, FGFR2, NTRK2, and NTRK3 genes stresses the need for tumor tissue multisampling for transcriptomic analysis, Cold Spring Harbor Mol. Case Stud., 2021, vol. 7, no. 4, p. a006100. https://doi.org/10.1101/mcs.a006100

Article  CAS  Google Scholar 

Tsimberidou, A.M., Fountzilas, E., Bleris, L., and Kurzrock, R., Transcriptomics and solid tumors: The next frontier in precision cancer medicine, Semin. Cancer Biol., 2022, vol. 84, pp. 50–59. https://doi.org/10.1016/j.semcancer.2020.09.007

Article  CAS  PubMed  Google Scholar 

Lazar, V., Zhang, B., Magidi, S., Le Tourneau, C., Raymond, E., et al., A transcriptomics approach to expand therapeutic options and optimize clinical trials in oncology, Ther. Adv. Med. Oncol., 2023, vol. 15, p. 17588359231156382. https://doi.org/10.1177/17588359231156382

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sorokin, M., Buzdin, A.A., Guryanova, A., Efimov, V., Suntsova, M.V., et al., Large-scale assessment of pros and cons of autopsy-derived or tumor-matched tissues as the norms for gene expression analysis in cancers, Comput. Struct. Biotechnol. J., 2023, vol. 21, pp. 3964–3986. https://doi.org/10.1016/j.csbj.2023.07.040

Article  CAS  PubMed  PubMed Central  Google Scholar 

Carithers, L.J., Ardlie, K., Barcus, M., Branton, P.A., Britton, A., et al., A novel approach to high-quality postmortem tissue procurement: The GTEx project, Biopreserv. Biobanking, 2015, vol. 13, no. 5, pp. 311–319. https://doi.org/10.1089/bio.2015.0032

Article  Google Scholar 

Suntsova, M., Gaifullin, N., Allina, D., Reshetun, A., Li, X., et al., Atlas of RNA sequencing profiles for normal human tissues, Sci. Data, 2019, vol. 6, no. 1, p. 36. https://doi.org/10.1038/s41597-019-0043-4

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sorokin, M., Gorelyshev, A., Efimov, V., Zotova, E., Zolotovskaia, M., et al., RNA sequencing data for FFPE tumor blocks can be used for robust estimation of tumor mutation burden in individual biosamples, Front. Oncol., 2021, vol. 11, p. 732644. https://doi.org/10.3389/fonc.2021.732644

Article  CAS  PubMed  PubMed Central  Google Scholar 

Markham, J.F., Fellowes, A.P., Green, T., et al., Predicting response to immune checkpoint blockade in NSCLC with tumour-only RNA-seq, Br. J. Cancer, 2023, vol. 128, pp. 1148–1154. https://doi.org/10.1038/s41416-022-02105-w

Article  CAS  PubMed  Google Scholar 

Sorokin, M., Rabushko, E., Efimov, V., Poddubskaya, E., Sekacheva, M., et al., Experimental and meta-analytic validation of RNA sequencing signatures for predicting status of microsatellite instability, Front. Mol. Biosci., 2021, vol. 8, p. 737821. https://doi.org/10.3389/fmolb.2021.737821

Article  CAS  PubMed  PubMed Central  Google Scholar 

Na, W., Lee, I.J., Koh, I., Kwon, M., Song, Y.S., et al., Cancer-specific functional profiling in microsatellite-unstable (MSI) colon and endometrial cancers using combined differentially expressed genes and biclustering analysis, Medicine (Baltimore), 2023, vol. 102, no. 19, p. e33647. https://doi.org/10.1097/MD.0000000000033647

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zheng, L., Zhang, J., Ye, Y., Shi, Z., Huang, Y., et al., Construction of a novel cancer-associated fibroblast-related signature to predict clinical outcome and immune response in colon adenocarcinoma, Aging (N. Y.), 2023, vol. 15, no. 18, pp. 9521–9543. https://doi.org/10.18632/aging.205032

Article  Google Scholar 

Sorokin, M., Ignatev, K., Poddubskaya, E., Vladimirova, U., Gaifullin, N., et al., RNA sequencing in comparison to immunohistochemistry for measuring cancer biomarkers in breast cancer and lung cancer specimens, Biomedicines, 2020, vol. 8, no. 5, p. 114. https://doi.org/10.3390/biomedicines8050114

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pedersen, C.B., Campos, B., Krishnan, N.M., Panda, B., Vitting-Seerup, K., et al., Building flexible and robust analysis frameworks for molecular subtyping of cancers, bioRxiv, 2023, p. 538907.https://doi.org/10.1101/2023.05.01.538907

McAvera, R., Quinn, J., Murphy, P., and Glavey, S., Genetic abnormalities in extramedullary multiple myeloma, Int. J. Mol. Sci., 2023, vol. 24, no. 14, p. 11259. https://doi.org/10.3390/ijms241411259

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sorokin, M., Kholodenko, I., Kalinovsky, D., Shamanskaya, T., Doronin, I., et al., RNA sequencing-based identification of ganglioside GD2-positive cancer phenotype, Biomedicines, 2020, vol. 8, no. 6, p. 142. https://doi.org/10.3390/biomedicines8060142

Article  CAS  PubMed  PubMed Central  Google Scholar 

Adamyan, L., Aznaurova, Y., Stepanian, A., Nikitin, D., Garazha, A., et al., Gene expression signature of endometrial samples from women with and without endometriosis, J. Minimally Invasive Gynecol., 2021, vol. 28, no. 10, pp. 1774–1785. https://doi.org/10.1016/j.jmig.2021.03.011

Article  Google Scholar 

Borisov, N., Sergeeva, A., Suntsova, M., Raevskiy, M., Gaifullin, N., et al., Machine learning applicability for classification of PAD/VCD chemotherapy response using 53 multiple myeloma RNA sequencing profiles, Front. Oncol., 2021, vol. 11, p. 652063. https://doi.org/10.3389/fonc.2021.652063

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tsyganov, M.M., Rodionov, E.O., Ibragimova, M.K., Miller, S.V., Cheremisina, O.V., et al., Personalized prescription of chemotherapy based on assessment of mRNA expression of BRCA1, RRM1, ERCC1, TOP1, TOP2α, TUBβ3, TYMS, and GSTP1 genes in tumors compared to standard chemotherapy in the treatment of non-small-cell lung cancer, J. Pers. Med., 2022, vol. 12, no. 10, p. 1647. https://doi.org/10.3390/jpm12101647

Article  PubMed  PubMed Central  Google Scholar 

Castellano, G., Giugliano, F., Curigliano, G., and Marra, A., Clinical utility of genomic signatures for the management of early and metastatic triple-negative breast cancer, Curr. Opin. Oncol., 2023, vol. 35, no. 6, pp. 479–490. https://doi.org/10.1097/CCO.0000000000000989

Article  CAS  PubMed  Google Scholar 

Pustovalova, M., Malakhov, P., Guryanova, A., Sorokin, M., Suntsova, M., et al., Transcriptome-based traits of radioresistant sublines of non-small cell lung cancer cells, Int. J. Mol. Sci., 2023, vol. 24, no. 3, p. 3042. https://doi.org/10.3390/ijms24033042

Article  CAS  PubMed  PubMed Central  Google Scholar 

Skvortsova, I.I. and Span, P.N., Editorial: Advances in biological understanding of tumor radiation resistance, Front. Oncol., 2020, vol. 10, p. 754. https://doi.org/10.3389/fonc.2020.00754

Article  PubMed  PubMed Central  Google Scholar 

Beretta, G.L. and Zaffaroni, N., Radiotherapy-induced ferroptosis for cancer treatment, Front. Mol. Biosci., 2023, vol. 10, p. 1216733. https://doi.org/10.3389/fmolb.2023.1216733

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhu, Q., Izumchenko, E., Aliper, A.M., Makarev, E., Paz, K., et al., Pathway activation strength is a novel independent prognostic biomarker for cetuximab sensitivity in colorectal cancer patients, Hum. Genome Var., 2015, vol. 2, p. 15009. https://doi.org/10.1038/hgv.2015.9

Article  PubMed  PubMed Central  Google Scholar 

Gudkov, A., Shirokorad, V., Kashintsev, K., Sokov, D., Nikitin, D., et al., Gene expression-based signature can predict sorafenib response in kidney cancer, Front. Mol. Biosci., 2022, vol. 9, p. 753318.

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