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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
Published on: August 4, 2016
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Transcriptomic Characterization of North Queensland Hepatocellular Carcinoma
Rhys Gillman1,2, Miriam Wankell1, Eun Jin Sun1,2
1Department of Biomedical Sciences and Molecular and Cell Biology, College of Medicine and Dentistry, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia.
Oncology
|December 22, 2025
Summary
Hepatocellular carcinoma (HCC) in rural Australia shares molecular features with larger cohorts, validating transcriptome-based precision oncology for remote settings. This study confirms findings from The Cancer Genome Atlas (TCGA) in a regional cohort.
Area of Science:
- Genomics
- Oncology
- Bioinformatics
Background:
- Hepatocellular carcinoma (HCC) presents a growing health challenge, particularly in underserved rural and remote populations.
- Existing cancer genomic databases, like The Cancer Genome Atlas (TCGA), lack representation from these communities.
- The applicability of TCGA findings to HCC in remote settings remains uncertain.
Purpose of the Study:
- To investigate the molecular characteristics of HCC in a rural Australian cohort.
- To compare the molecular profile of this cohort with the TCGA Liver Hepatocellular Carcinoma (LIHC) cohort.
- To evaluate a transcriptome-based pipeline for low-cost drug target prediction in precision oncology.
Main Methods:
- Paired tumor and adjacent non-tumor liver biopsies from 19 rural Australian patients were analyzed using RNA-sequencing (RNA-seq).
- Transcriptomic and mutational features were characterized and compared against the TCGA LIHC cohort.
- A transcriptome-only adaptation of the TARGET-SL pipeline was employed for drug target prediction.
Main Results:
- Differential gene expression analysis revealed 923 altered genes, with 64% overlap with TCGA-LIHC data; cohort gene expression showed strong correlation (Spearman Rho = 0.96).
- Somatic variant calling identified CTNNB1 (47%) and TP53 (21%) as frequently mutated genes, consistent with TCGA findings.
- Copy number inference detected deletions on 8p, 6q, and 17p; the TARGET-SL pipeline identified potential drug candidates for 63% of patients.
Conclusions:
- Hepatocellular carcinoma in North Queensland (NQ) exhibits core molecular features similar to larger TCGA cohorts.
- A transcriptome-based approach is feasible for supporting precision oncology in resource-limited regional areas.
- This study highlights the potential for targeted therapies in underserved populations based on genomic profiling.
