Identification of point mutations, expression perturbations, and gene fusions in T-cell acute lymphoblastic leukemia by RNA-seq

RNA-seq is a promising technology to re-sequence protein-coding genes for the identification of single nucleotide variants, while simultaneously obtaining information on structural variations and gene expression perturbations. T-cell acute lymphoblastic leukemia (T-ALL) is caused by a combination of gene fusions leading to the over-expression of transcription factors reinforced by point mutations in oncogenes and tumor suppressor genes. We asked whether RNA-seq is suitable for the detection of driver mutations in these leukemias. We analyzed 31 T-ALL patient samples and 18 T-ALL cell lines by high-coverage paired-end RNA-seq.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 5 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001000849	None	Illumina HiSeq 2000	50

Publications	Citations
Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia. Atak ZK, Gianfelici V, Hulselmans G, De Keersmaecker K, Devasia AG, Geerdens E, Mentens N, Chiaretti S, Durinck K, Uyttebroeck A, Vandenberghe P, Wlodarska I, Cloos J, Foà R, Speleman F, Cools J, Aerts S. PLoS Genet 9: 2013 e1003997	81
Synthetic modeling reveals HOXB genes are critical for the initiation and maintenance of human leukemia. Kusakabe M, Sun AC, Tyshchenko K, Wong R, Nanda A, Shanna C, Gusscott S, Chavez EA, Lorzadeh A, Zhu A, Hill A, Hung S, Brown S, Babaian A, Wang X, Holt RA, Steidl C, Karsan A, Humphries RK, Eaves CJ, Hirst M, Weng AP. Nat Commun 10: 2019 2913	5
β-Catenin activity induces an RNA biosynthesis program promoting therapy resistance in T-cell acute lymphoblastic leukemia. García-Hernández V, Arambilet D, Guillén Y, Lobo-Jarne T, Maqueda M, Gekas C, González J, Iglesias A, Vega-García N, Sentís I, Trincado JL, Márquez-López I, Heyn H, Camós M, Espinosa L, Bigas A. EMBO Mol Med 15: 2023 e16554	2
The circadian clock circuitry modulates leukemia initiating cell activity in T-cell acute lymphoblastic leukemia. Murgo E, De Santis E, Sansico F, Melocchi V, Colangelo T, Padovano C, Colucci M, Carbone A, Totti B, Basti A, Gottschlich L, Relogio A, Capitanio N, Bianchi F, Mazzoccoli G, Giambra V. J Exp Clin Cancer Res 42: 2023 218	0
Decoding the genetic symphony: Profiling protein-coding and long noncoding RNA expression in T-acute lymphoblastic leukemia for clinical insights. Verma D, Kapoor S, Kumari S, Sharma D, Singh J, Benjamin M, Bakhshi S, Seth R, Nayak B, Sharma A, Pramanik R, Palanichamy JK, Sivasubbu S, Scaria V, Arora M, Kumar R, Chopra A. PNAS Nexus 3: 2024 pgae011	0