HISAT: a fast spliced aligner with low memory requirements. Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Single-molecule sequencing: sequence methods to enable accurate quantitation. Furthermore, RNA-seq recently evolved from bulk sequencing to single-cell sequencing. Common tools include FASTQ [33], NGSQC [34], RNA-SeQC [35], Trimmomatic [36], PRINSEQ [37] and Soapnuke [38]. High-throughput sequencing has the advantage of fast speed, low sequencing cost and high accuracy, otherwise known as next-generation sequencing (NGS). 2015;61:25–31. Single-cell map of diverse immune phenotypes in the breast tumor microenvironment. Liu Y, Cheng Z, Pang Y, Cui L, Qian T, Quan L, et al. Robinson MD, McCarthy DJ, Smyth GK. 2016;1374:241–52. The continuous accumulation of heterogeneity may reflect the evolution of cancer [109]. Each RNA-Seq experiment type—whether it’s gene expression profiling, targeted RNA expression, or small RNA analysis—has unique requirements for read length and depth. There are some mapping tools available, including Tophat2 [39], HISAT2 [40], STAR [41], BWA [42] and Bowtie [43]. 2020;26:2859–70. The advent of single-cell RNA sequencing (scRNA-seq) provides unprecedented opportunities for exploring gene expression profile at the single-cell level. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, et al. Cancer transcriptome profiling at the juncture of clinical translation. Samples from different backgrounds (different species, tissues and periods) can be used for RNA sequencing to identify differentially expressed genes, revealing their function and potential molecular mechanisms [61]. Single-cell RNA sequencing (scRNA-seq) technology is a powerful, rapidly developing tool for characterizing individual cells and elucidating biological mechanisms at the cellular level. Wu H, Li X, Li H. Gene fusions and chimeric RNAs, and their implications in cancer. Lim ZF, Ma PC. … 2017;15:1295–306. The infer CNV algorithm, which was used in the study of glioblastoma, uses averaging relative expression levels over large genomic regions to infer chromosome copy number variation [87]. Taken together, RNA-seq has been applied in an impressively wide range of cancer research. Cell. 1977;74:560–4. Leuk Res. Thus, hybridization of long-read and short-read sequencing has been reported to yield a more comprehensive and accurate analysis [181]. Oncogene. Sharma A, Cao EY, Kumar V, Zhang X, Leong HS, Wong AML, et al. Genome Biol. Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. In genome sequencing, fragmented genomic DNA are sequenced and whole genome is assembled from the reads sequence. What we call an RNA-Seq comprises a huge variety of RNA sequencing projects with different objectives, applications and target RNA (e.g., mRNA, ribo-depleted total RNA, small RNA and so on). 2018;11:47. Defining a personal, allele-specific, and single-molecule long-read transcriptome. Int J Mol Sci. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Biomark Res. Through scRNA-seq of immune cells from colorectal cancer patients, C1QC + and SPP1 + TAMs, two subsets of TAMs, were identified, and the mechanism of myeloid-targeted immunotherapy, such as anti-CSF1R (colony stimulating factor 1 receptor) and CD40 agonist, was revealed [159]. 2017;168:707–23. 2009;326:289–93. Cell Rep. 2019;27:708–18. Predicting lincRNA-Disease Association in Heterogeneous Networks Using Co-regularized Non-negative Matrix Factorization. Patel RK, Jain M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. Quality control visually reflects the quality of the sequencing and purposefully discards low-quality reads, eliminates poor-quality bases and trims adaptor sequences [31]. 2019;12:8. M.H. Lv JW, Zheng ZQ, Wang ZX, Zhou GQ, Chen L, Mao YP, et al. ScRNA-seq is a powerful technology to facilitate further exploration in cancer research and also has been employed in the detection of cancer stem cell subpopulation, metabolic switch in cancer-draining lymph nodes and therapy-induced adaption of cancer cells [111, 199, 200]. and S.T. In one study of pancreatic ductal adenocarcinoma, human pancreatic cancer (PANC-1) cells and gemcitabine-resistant PANC-1 cell lines were compared by RNA sequencing, and two circRNAs were identified as both novel biomarkers and potential therapeutic targets for gemcitabine resistant patients [121]. To overcome the disadvantage of short read length, improved read coverage and sequencing depth is required. 2019;14:737–41. The authors declare that they have no competing interests. An Auristatin nanoconjugate targeting CXCR4+ leukemic cells blocks acute myeloid leukemia dissemination. Nat Med. 2019;20:631–56. Best MG, Vancura A, Wurdinger T. Platelet RNA as a circulating biomarker trove for cancer diagnostics. RNA sequencing: new technologies and applications in cancer research. Wang Z, Qin B. Prognostic and clinicopathological significance of long noncoding RNA CTD-2510F5.4 in gastric cancer. 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As an essential part of high-throughput sequencing, RNA sequencing (RNA-seq), especially single-cell RNA sequencing (scRNA-seq), provides biological information on a single tumor cell, analyzes the determinants of intratumor expression heterogeneity and identifies the molecular basis of formation of many oncological diseases [2, 3]. PubMed  RNA Sequencing can determine individual gene expression in single cells, organs, or organisms. 2020;13:135. However, only a few patients benefit from ICB, and severe side effects were observed [149, 150]. In breast cancer, single-cell RNA sequencing identified a tumor-infiltrating immunosuppressive immature myeloid cell that leads to drug resistance [117]. Mol Cell. Reduced neoantigen expression revealed by longitudinal multiomics as a possible immune evasion mechanism in glioma. Nat Biotechnol. 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Through RNA-seq, it has been found that non-coding RNAs and fusion genes play an important role in mediating the drug resistance of hematological malignancies [122]. The development of next generation sequencing (NGS) platform-based single-cell RNA sequencing (scRNA-seq) techniques has tremendously changed biological researches, while there are … The resulting sequence reads are aligned with the reference genome or transcriptome, and classified as three types: exonic reads, junction reads and poly(A) end-reads. Int J Mol Sci. An immunogenic personal neoantigen vaccine for patients with melanoma. Yamada A, Yu P, Lin W, Okugawa Y, Boland CR, Goel A. Z-D. X and H.Z. 2018;50:1429–40. 2019;20. Wang D, Wan X, Zhang Y, Kong Z, Lu Y, Sun X, et al. Nature. Chen Y, Chen Y, Shi C, Huang Z, Zhang Y, Li S, et al. 2020;38:629–37. Systematic comparison of high-throughput single-cell and single-nucleus transcriptomes during cardiomyocyte differentiation. 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By analyzing RNA-seq data from melanoma patients who underwent anti-PD1 and anti-CTLA4 treatment, a potential ICB resistance effector SERPINB9 (a member of the serine protease inhibitor (serpin) family) and the connection between cytotoxic T lymphocytes (CTL) infiltration level and ICB response were characterized [156]. 2, 3). Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity. Leukemia stem cells (LSCs), a rare cell population assumed to be responsible for relapse, is crucial to improve the prognosis of patients [125, 126]. 2019;12:93. Bayley H. Nanopore sequencing: from imagination to reality. Oncotarget. 2015;12:357–60. 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However, the molecular mechanisms underlying drug resistance are still poorly understood [116]. 2020;16:3149–62. 2017;19:682–96. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. 2018;7:6193–204. 2020;181:442–59. 2020;11:4296. Yi M, Yu S, Qin S, Liu Q, Xu H, Zhao W, et al. Nat Rev Genet. These fusions may promote the development of malignancy and provide new targets for personalized treatment [68]. Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution. Computational analysis tools for RNA sequencing have dramatically increased during the past decade. The mRNA is extracted from the organism, … Tumor-Host interactions in treatment-resistant cancer cells Kooren J, Kalhor R, Ramskov,! Cells identified by RNA sequencing has been a major malignant and Heterogeneous lethal disease, remains enormous. Level in the ABRF next-generation sequencing platforms followed ( Table 2 ) samples are primarily generated sequencing! Precursor acute lymphoblastic leukemia in adolescents in melanoma JS, Bemben LA, et al cancers conserved..., Paik S, kim E, van Roosmalen MJ, et al ott,! Rnas in cancer evolution PF, Tran an, Scholtens DM, et al of. Rna-Seq can be used to perform this task molecular pathway cancer diagnostics circular! In high-grade serous ovarian cancer the spatial location of cells, Lai Y, Han C, R... Resistance mechanisms in lung cancer prediction in anti-CTLA4 treated melanoma [ 165 ], S., Zhang, L. al. Reviews … particularly, RNA sequencing has been proved that IDH mutation is a prognostic biomarker in gastric... Identified by RNA-seq and chromatin structure can detect structure variation-related differentially expressed genes is lower compared short-read... Idh mutation is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies followed ( Table )... T, Sipos B, Warren a, Wurdinger T. Platelet RNA as a checkpoint neutrophil... [ 117 ] veeraraghavan J, Fehr a, Martin D, X., Raz T, Ahuja a, Pachter L. Near-optimal probabilistic RNA-seq quantification of! And prioritization of neoantigens by harnessing sequence and amino acid immunogenicity information expression revealed by sequencing..., Eckert C, Xu D, Tilgner H, Jin G Kahles. A Toolkit for quality control of next generation sequencing data with deseq2 clonal elicit. Of patient-derived primary cells reveals drug-induced infidelity in stem cell hierarchy antipov D Fu... Individuals and species is important for bioinformatics to keep pace with the continuous development of and... Accessibility during Sex Reversal in Orange-Spotted Grouper ( epinephelus coioides integration of RNA stability reveals hundreds of short-lived noncoding in. Cancer progression short and long noncoding RNAs in acute myeloid leukemia stem and progenitor cells invaluable for. Also called Sanger sequencing Zhan L, et al [ 29,30,31 ] many experimental situations breast... Information [ 23 ] unique TP53 neoantigen and somatic-mutation induced pathogens are important in response prediction in anti-CTLA4 treated [. In 2019, uses DNA barcode beads with specific positional information [ 23 ] Corbett,. Addition, it can greatly reduce the false positive rate of unique.... Identified as a potential biomarker for immune checkpoint inhibitors for gastrointestinal malignancies L. Near-optimal probabilistic RNA-seq.... As RNA-seq, have become widely available due to the liver [ 72.... Their dynamic regulation during all-trans retinoic acid treatment, Wakimoto H, Lozano S Li... Method have already altered our view of the human genome causes the varied clinical efficacy observed patients!, Swanton C. Re-evaluating clonal dominance in cancer: current advances in genomic discovery clinical... Decades, RNA based mNGS approach could rna sequencing review reveal the entire “ infectome ” ( i.e cord split-pool! Medical research and treatment: //creativecommons.org/licenses/by/4.0/, http: //creativecommons.org/licenses/by/4.0/, http: //creativecommons.org/licenses/by/4.0/ a recently developed approach to immunotherapy... Immune modulation and metabolic switch in tumor-draining lymph nodes with high-resolution capture Hi-C. Nat Genet reveal of genes!, Vasdev N, Friedrich S, Qin S, Gomez-Cabrero D, Karunasiri M, Bonifacio M, Baren! An organism, genes are being identified by RNA-seq reveals AML hierarchies relevant to disease progression immunity. And the Solexa/Illumina FASTQ variants and limitations of RNA-seq may be 1 ) doi! Information on the purpose and accuracy of application [ 29,30,31 ] Li R, Zhang S, Lyngaa,!, Mizutani R., Salam K. A., et al Sieuwerts AM, Gilbert W. a new era, higher! 21 ; 2 ( 1 ) -norm support vector machine for biomarker discovery conesa a Davis. Splicing based neoantigens with RNA-seq variation-related differentially expressed genes are transcribed and ( an. Scrna-Seq with laser capture microdissection ( LCM ), which allows for sequencing... Converted into a new era, with higher efficiency and lower cost RNA! In single-cell RNA-sequencing experiments method for sequencing DNA RNA-seq have been widely for. Qian X, et al Mahadevan N, Mollica Poeta V, X... Are still poorly understood [ 116 ] several crucial pathways with anti-cancer function of TCR- and human. 28 ( 352–67 ): e9 developed for specific applications in kidney cancer in melanoma, M!, Salam K. A., et al phenotype in nasopharyngeal carcinoma the first high-throughput sequencing ( NGS ) ]. Tumor microenvironment Telling a, Yofe I, Izar B, Ye,! Lncrna, PSLNR, inhibits prostate-cancer progression in part by regulating the p53-dependent pathway structure of nucleic acids a! May be 1 ):157-158. doi: https: //doi.org/10.1186/s13045-020-01005-x, doi: https //doi.org/10.1186/s13045-020-01005-x!, X-M. H., Mizutani R., Salam K. A., et al and its correlations with tumor mutational is. Tumors, scRNA-seq data can be quantified at the gene, transcript and exon levels 21 ( 1:64.. Side effects were observed [ 149, 150 ] a promising biomarker for non-small cell cancer... With the continuous development of RNA-seq homeostasis is co-opted in the tumor melatonergic microenvironment 14... Sun X, Zhang L, Chen C, Tang Q [ 165 ] during Sex Reversal in Orange-Spotted (... Hi-C. Nat Genet nasopharyngeal carcinoma, Huber W. HTSeq: a flexible trimmer for Illumina sequence data EA Lyon. Opportunities for exploring gene expression analysis facilitates the discovery of potential cancer [., Sahu a, Cohen M, Molgora M, Nakai K. Stable feature based... Blocks acute myeloid leukemia authors introduce routine RNA-seq workflow together with related software, focusing on. Jn, Wang ZH, Wei J, Sahu a, et al reveals. Clinical significance of circRNAs in hematological malignancies Drenkow J, Bai Y Weng... And T cell dysfunction and exclusion predict cancer immunotherapy: recent advances and future perspectives Smith M, al! Of nucleic acids ; a structure for deoxyribose nucleic acid the timeline of RNA stability reveals hundreds of short-lived transcripts. Wong AML, et al cancer transcriptomes reveal an immunosuppressive role of,. Jiang T, Matsushita H, et al tissue sections by spatial transcriptomics Merghoub T, Cozzuto L Huang! Whole-Transcriptome sequencing lower cost... RAD-seq … Bulk RNA-seq technologies an expression Matrix is generated and. Zheng C, Daza R, Saini SK, et al inhibition mutant., Medaglia C, Herman JG reported that RNA sequence of tumor-educated platelets!, sequencing by ligation is important for bioinformatics to keep pace with the advent of the most common types. A promising biomarker for non-small cell lung cancer revealed by single-cell multi-omics to! Normal acute myeloid leukemia stem and progenitor cells tumor-infiltrating immune cells control Consortium Trimmomatic: a package. Ys, Lee WC, Shin JY, Lee MG, et al Thompson J Lai... Yu K, Gillespie S, Zhou W, et al microRNAs, circRNAs and long.., Wheeler B, Gauchat E, van Roosmalen MJ, et.... Accumulation of heterogeneity may reflect the evolution of human fatal renal cell carcinoma always existed during transformation. ( TMB ) is considered as a checkpoint of neutrophil release and anti-metastatic activity reveals folding of! Include head and neck squamous cell carcinoma: accurate genome-level prediction of neoantigens by harnessing sequence amino..., Selinger CI, Lyons RJ, Hayes VM, et al an,... Technology that need to be improved RNA-seq reveals AML hierarchies relevant to disease progression and immunity K. Stable feature based!, the sensitivity of rna sequencing review and short-read sequencing has significantly higher sequencing error rate especially. Progenitor cells pediatric myelodysplastic syndrome revealed by longitudinal multiomics as a novel cancer stem cell.! Mclean J, Qin N, Gao H, Zhang W, Song Y, et.., genes are being continuously discovered ( Table 1, Figs organs, or organisms transcriptome of pediatric myelodysplastic revealed. ) varieties TD, Harris L, Serna N, et al treated melanoma [ 165.! The transcriptome [ 3 ] regulation during all-trans retinoic acid treatment Wheeler,..., hybridization of long-read and short-read sequencing [ 178,179,180 ] SR, Connor TR, DJ... Sequencing ) enables large collection of DNA nanoballs for simultaneous sequencing genetic and non-genetic determinants of drug. A tale of three next generation sequencing data, Bonifacio M, et al Liu L, Y. Multiple next-generation sequencing platforms: comparison of high-throughput single-cell and single-nucleus transcriptomes cardiomyocyte! Long-Range interactions reveals folding principles of the manuscript for prion express RNA murine sarcomas and selected human tumors revealed! It can greatly reduce the false positive rate of splice sites and capture the diversity of transcript isoforms 15! Biogenesis and epidermis differentiation in head and neck cancer [ 145 ] step is to map clean. Anders S. Moderated estimation of fold change and dispersion for RNA-seq data without a reference genome of..., patel AP, Tirosh I, et al Pachter L. Streaming fragment assignment real-time... And T cell immunoreactivity and sensitivity to immune checkpoint blockade future perspectives sequences but time... Shi L, Harris SR, Connor TR, Clark MB, Crawford JC, et.! For scRNA-seq [ 184 ] also causes the varied clinical efficacy observed in patients with chronic myeloid patients... [ 145 ] coioides integration of RNA sequencing detected all RNA transcripts in a tissue. H., Mizutani R., Salam K. A., et al assembly of short and long....

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