The Precision Medicine in Liver Cancer across an Asia-pacific NETwork (PLANET)

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
EGAD00001006570	The clinical relevance of immune landscape intratumoural heterogeneity (immune-ITH) and its role in tumour evolution remain largely unexplored. Here, we uncover significant spatial and phenotypic immune–ITH from multiple tumour sectors and decipher its relationship with tumour evolution and disease progression in hepatocellular carcinomas (HCC). Immune–ITH is associated with tumour transcriptomic-ITH, mutational burden, and distinct immune microenvironments. Tumours with low immune–ITH experience higher immunoselective pressure and escape via loss of heterozygosity in human leukocyte antigens and immunoediting. Instead, the tumours with high immune-ITH evolve to a more immunosuppressive/exhausted microenvironment. This gradient of immune pressure along with immune-ITH represents a hallmark of tumour evolution, which is closely linked to the transcriptome-immune networks that contributes to disease progression and immune inactivation. Remarkably, high immune-ITH and its transcriptomic signature are predictive for worse clinical outcome in HCC patients. This in-depth investigation of ITH provides evidence on tumour-immune co-evolution along HCC progression.	HiSeq X Ten Illumina HiSeq 4000	70
EGAD00001008647	This dataset includes WGS data of samples from our paper titled "Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in Hepatocellular Carcinoma: The PLANET study." (National Science Review, nwab192. https://doi.org/10.1093/nsr/nwab192)	HiSeq X Ten Illumina HiSeq 4000	-
EGAD00001008648	This dataset includes RNA-seq data of samples from our paper titled "Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in Hepatocellular Carcinoma: The PLANET study." (National Science Review, nwab192. https://doi.org/10.1093/nsr/nwab192)	Illumina HiSeq 4000	-
EGAD00001009041	This dataset includes RNA-seq, DNA and Chip-Seq data of samples from our paper.		-
EGAD00001009042	This dataset includes RNA-seq data of samples from our paper.		18
EGAD00001009858	WGS data of multi-region samples from PLANET 123 Patient cohort	HiSeq X Ten Illumina HiSeq 4000	12
EGAD00001009859	RNA-seq data of multi-region samples from PLANET 123 Patient cohort	Illumina HiSeq 4000	-

Publications	Citations
Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in hepatocellular carcinoma: the PLANET study. Zhai W, Lai H, Kaya NA, Chen J, Yang H, Lu B, Lim JQ, Ma S, Chew SC, Chua KP, Alvarez JJS, Chen PJ, Chang MM, Wu L, Goh BKP, Chung AY, Chan CY, Cheow PC, Lee SY, Kam JH, Kow AW, Ganpathi IS, Chanwat R, Thammasiri J, Yoong BK, Ong DB, de Villa VH, Dela Cruz RD, Loh TJ, Wan WK, Zeng Z, Skanderup AJ, Pang YH, Madhavan K, Lim TK, Bonney G, Leow WQ, Chew V, Dan YY, Tam WL, Toh HC, Foo RS, Chow PK. Natl Sci Rev 9: 2022 nwab192	13
Pan-cancer pervasive upregulation of 3' UTR splicing drives tumourigenesis. Chan JJ, Zhang B, Chew XH, Salhi A, Kwok ZH, Lim CY, Desi N, Subramaniam N, Siemens A, Kinanti T, Ong S, Sanchez-Mejias A, Ly PT, An O, Sundar R, Fan X, Wang S, Siew BE, Lee KC, Chong CS, Lieske B, Cheong WK, Goh Y, Fam WN, Ooi MG, Koh BTH, Iyer SG, Ling WH, Chen J, Yoong BK, Chanwat R, Bonney GK, Goh BKP, Zhai W, Fullwood MJ, Wang W, Tan KK, Chng WJ, Dan YY, Pitt JJ, Roca X, Guccione E, Vardy LA, Chen L, Gao X, Chow PKH, Yang H, Tay Y. Nat Cell Biol 24: 2022 928-939	20
Multi-region sampling with paired sample sequencing analyses reveals sub-groups of patients with novel patient-specific dysregulation in Hepatocellular Carcinoma. Jeon AJ, Teo YY, Sekar K, Chong SL, Wu L, Chew SC, Chen J, Kendarsari RI, Lai H, Ling WH, Kaya NA, Lim JQ, Ramasamy A, Oguz G, Chung AY, Chan CY, Cheow PC, Kam JH, Madhavan K, Kow A, Ganpathi IS, Lim TKH, Leow WQ, Loong S, Loh TJ, Wan WK, Soon GST, Pang YH, Yoong BK, Ong DB, Lim J, de Villa VH, Cruz RDD, Chanwat R, Thammasiri J, Bonney GK, Goh BKP, Tucker-Kellogg G, Foo RSY, Chow PKH. BMC Cancer 23: 2023 118	1
A genomic enhancer signature associates with hepatocellular carcinoma prognosis. Jeon AJ, Anene-Nzelu CG, Teo YY, Chong SL, Sekar K, Wu L, Chew SC, Chen J, Kendarsari RI, Lai H, Ling WH, Kaya NA, Lim JQ, Chung AYF, Cheow PC, Kam JH, Madhavan K, Kow A, Ganpathi IS, Lim TKH, Leow WQ, Loong S, Loh TJ, Wan WK, Soon GST, Pang YH, Yoong BK, Bee-Lan Ong D, Lim J, de Villa VH, Dela Cruz RD, Chanwat R, Thammasiri J, Bonney GK, Goh BKP, Foo RSY, Chow PK. JHEP Rep 5: 2023 100715	2