Whole transcriptome and exome sequencing of childhood ALL

Gene fusion is a major class of genomic abnormalities in childhood acute lymphoblastic leukemia (ALL) and sentinel chromosomal rearrangements involving EP300 and CREBBP may cause global epigenetic deregulation during leukemogenesis with potentials for therapeutic targeting. This dataset includes whole transcriptome sequencing of 231 children with acute lymphoblastic leukemia from a Singapore-Malaysia frontline clinical treatment protocol.

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

2 Datasets 11 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
EGAD00001002151	Whole transcriptome sequencing of 231 children with newly-diagnosed ALL	Illumina HiSeq 2000	231
EGAD00001002152	Whole exome sequencing for the matched germline and tumor DNA from 10 ALL cases with ZNF384 rearrangements.	Illumina HiSeq 2000	20

Publications	Citations
Whole-transcriptome sequencing identifies a distinct subtype of acute lymphoblastic leukemia with predominant genomic abnormalities of EP300 and CREBBP. Qian M, Zhang H, Kham SK, Liu S, Jiang C, Zhao X, Lu Y, Goodings C, Lin TN, Zhang R, Moriyama T, Yin Z, Li Z, Quah TC, Ariffin H, Tan AM, Shen S, Bhojwani D, Hu S, Chen S, Zheng H, Pui CH, Yeoh AE, Yang JJ. Genome Res 27: 2017 185-195	75
Identification of novel lncRNAs regulated by the TAL1 complex in T-cell acute lymphoblastic leukemia. Ngoc PCT, Tan SH, Tan TK, Chan MM, Li Z, Yeoh AEJ, Tenen DG, Sanda T. Leukemia 32: 2018 2138-2151	31
Mutational and transcriptomic profiling of acute leukemia of ambiguous lineage reveals obscure but clinically important lineage bias. Lao ZT, Ding LW, An O, Hattori N, Sun QY, Tan KT, Mayakonda A, Chuan WG, Madan V, Lin DC, Yang H, Koeffler HP. Haematologica 104: 2019 e200-e203	6
The Identification and Interpretation of cis-Regulatory Noncoding Mutations in Cancer. Patel MB, Wang J. High Throughput 8: 2018 E1	4
RAS-protein activation but not mutation status is an outcome predictor and unifying therapeutic target for high-risk acute lymphoblastic leukemia. Koschut D, Ray D, Li Z, Giarin E, Groet J, Alić I, Kham SK, Chng WJ, Ariffin H, Weinstock DM, Yeoh AE, Basso G, Nižetić D. Oncogene 40: 2021 746-762	5
Short H2A histone variants are expressed in cancer. Chew GL, Bleakley M, Bradley RK, Malik HS, Henikoff S, Molaro A, Sarthy J. Nat Commun 12: 2021 490	21
Distinct clinical characteristics of DUX4- and PAX5-altered childhood B-lymphoblastic leukemia. Li Z, Lee SHR, Chin WHN, Lu Y, Jiang N, Lim EH, Coustan-Smith E, Chiew KH, Oh BLZ, Koh GS, Chen Z, Kham SKY, Quah TC, Lin HP, Tan AM, Ariffin H, Yang JJ, Yeoh AE. Blood Adv 5: 2021 5226-5238	16
Epigenetic activation of the FLT3 gene by ZNF384 fusion confers a therapeutic susceptibility in acute lymphoblastic leukemia. Zhao X, Wang P, Diedrich JD, Smart B, Reyes N, Yoshimura S, Zhang J, Yang W, Barnett K, Xu B, Li Z, Huang X, Yu J, Crews K, Yeoh AEJ, Konopleva M, Wei CL, Pui CH, Savic D, Yang JJ. Nat Commun 13: 2022 5401	5
USP1 promotes the aerobic glycolysis and progression of T-cell acute lymphoblastic leukemia via PLK1/LDHA axis. Liu S, Xiang Y, Wang B, Gao C, Chen Z, Xie S, Wu J, Liu Y, Zhao X, Yang C, Yue Z, Wang L, Wen X, Zhang R, Zhang F, Xu H, Zhai X, Zheng H, Zhang H, Qian M. Blood Adv 7: 2023 3099-3112	1
TALLSorts: a T-cell acute lymphoblastic leukemia subtype classifier using RNA-seq expression data. Gu A, Schmidt B, Lonsdale A, Jalaldeen R, Kosasih HJ, Brown LM, Sadras T, Ekert PG, Oshlack A. Blood Adv 7: 2023 7402-7406	0
DUX4 is a common driver of immune evasion and immunotherapy failure in metastatic cancers. Pineda JMB, Bradley RK. Elife 12: 2024 RP89017	1