Biomarkers for liver disease identified using NGS technique
| Approach of NGS | Applied techniques | Biological meaning | Detected alteration | Target disease | Biomarkers | Reference |
|---|---|---|---|---|---|---|
| Single | WGS | Distinct relationships with environmental factors and transcription, and driver genes | Mutational and structural rearragement signatures | Liver Cancer | (7) | |
| Single | WES | Disruption of cellular pathways | Genetic alterations | HCC | (83) | |
| Single | WES | Recurrently mutated genes in fitness and regeneration | Accumulation of mutations | Cirrhotic livers | (84) | |
| Single | WGS | Early oncogenesis | Mutations in sets of driver genes | Cancer | (86) | |
| Single | RRBS | Tumorigenesis | Hypomethylaion on Upregulated region | HCC | (105) | |
| Single | RNA-Seq | Pro-oncogenic properties such as cellular growth and proliferation, movement | CNV alterations and gene expression change | Cancer | (78) | |
| Single | RNA-Seq | Inhibition of Growth, Migration, and Invasion of HCC | Overexpression | HCC | (80) | |
| Single | RNA-Seq | Treated FASN related to liver disease | Overexpression | NAFLD | (87) | |
| Single | Small RNA-Seq | Controlling epithelial mesenchymal transition (EMT) and metastasis | Low expression levels | HCC and HCA | miR-200a, miR-429, miR-490-3p, miR-452, miR-766, miR-1180 | (88) |
| Single | miRNA-Seq | Distinguishing early HCC from LC | Comparing expression by ROC curve analysis | HCC | miR-122, miR-148a | (89) |
| Single | miRNA-Seq | Acceleration of cell migration oand invasion | Overexpression | HBV-associated HCC | miR-21 | (90) |
| Single | DNA-Seq | 3’ UTF variant related to MetS features | Genetic variations in aminotransferase loci | NAFLD | (81) | |
| Multiple | RNA-Seq, ChIP-Seq | Cancer cell proliferation and tumorigenesis | Demethylation of promoter is associated with the gene expression | Cancer | (79) | |
| Multiple | RNA-seq, WGS | Identification of Genomic mutations and transcriptomic abberations | p53 signaling related regulation | HCC | (2) | |
| Multiple | RNA-Seq, small RNA-Seq | Metastasis and tumorigenesis | Deregulation of lncRNAs related with DNA methylation on genomic alterations | HCC | (91) | |
| Multiple | Total RNA-Seq, miRNA-seq | Altered gene expression levels for multiple pathway related with cancer and non-cancer | Correlation between complex ncRNA-miRNA-mRNA network | HCC | CECR7, LINC00346, MAPKAPK5-AS1, LOC338651, FLJ90757, LOC283663 | (92) |
| Multiple | RNA-Seq, miRNA-Seq | Induce steatosis-like phenotypes and Enhance risks of HCC | Overexpression of mRNA effects to miRNA regulatory system | Murine microsteatosis | (93) | |
| Multiple | RNA-Seq, miRNA-seq | Identification of Genomic mutations and transcriptomic abberations | Regulation of multiple metabolic pathways | HCC | (101) | |
| Multiple | RNA-Seq, WES | Different oncogenic pathways result in distinct tumour phenotypes | Mutation-altered gene regulation | HCC | (102) | |
| Multiple | RNA-Seq, DNA-Seq | Sorafenib response | Oncogene mutational burden in tumor / Overexpression | HCC | (103) | |
| Multiple | RNA-Seq, RRBS | Observation of phenotypes in pFFC-FFC cohort | Overexpression with Hypomethylation | NASH | (104) |
List of biomarkers organized by approach of NGS, application methods in liver disease. WGS: Whole Genome Sequencing; WES: Whole Exome Sequencing; RRBS: Reduced Representation Bisulfite Sequencing; RNA-Seq: RNA Sequencing; miRNA-Seq: micro RNA-Seq; ChIP-Seq: Chromatin Immunoprecipitation Sequencing; MAPS: Massive Anchored Parallel Sequencing.