Table 1.
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 | CTNNB1, AXIN1, PTEN, RB1, ARID2, TERT | (7) |
| Single | WES | Disruption of cellular pathways | Genetic alterations | HCC | TP53, CTNNB1, KEAP1, C16orf62, MLL4, RAC2 | (83) |
| Single | WES | Recurrently mutated genes in fitness and regeneration | Accumulation of mutations | Cirrhotic livers | PKD1, KMT2D, ARID1A | (84) |
| Single | WGS | Early oncogenesis | Mutations in sets of driver genes | Cancer | TP53, KRAS, TERT, PIK3CA, APC, SMAD4, MEN1, DAXX, EGFR | (86) |
| Single | RRBS | Tumorigenesis | Hypomethylaion on Upregulated region | HCC | Mst1r, Slpi | (105) |
| Single | RNA-Seq | Pro-oncogenic properties such as cellular growth and proliferation, movement | CNV alterations and gene expression change | Cancer | TP53, KRAS, CTNNB1 | (78) |
| Single | RNA-Seq | Inhibition of Growth, Migration, and Invasion of HCC | Overexpression | HCC | ZKSCAN1 | (80) |
| Single | RNA-Seq | Treated FASN related to liver disease | Overexpression | NAFLD | PKLR, PNPLA3, PCSK9 | (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 | GOT2 | (81) |
| Multiple | RNA-Seq, ChIP-Seq | Cancer cell proliferation and tumorigenesis | Demethylation of promoter is associated with the gene expression | Cancer | LIN28B | (79) |
| Multiple | RNA-seq, WGS | Identification of Genomic mutations and transcriptomic abberations | p53 signaling related regulation | HCC | TTK | (2) |
| Multiple | RNA-Seq, small RNA-Seq | Metastasis and tumorigenesis | Deregulation of lncRNAs related with DNA methylation on genomic alterations | HCC | HAND2-AS1 | (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 | IMP2 | (93) |
| Multiple | RNA-Seq, miRNA-seq | Identification of Genomic mutations and transcriptomic abberations | Regulation of multiple metabolic pathways | HCC | TP53, AXIN1, ARID2, RPS6KA3, HNF4A, CPS1, TSC1, THRAP3 | (101) |
| Multiple | RNA-Seq, WES | Different oncogenic pathways result in distinct tumour phenotypes | Mutation-altered gene regulation | HCC | CTNNB1, TP53, TSC1/TSC2, TERT | (102) |
| Multiple | RNA-Seq, DNA-Seq | Sorafenib response | Oncogene mutational burden in tumor / Overexpression | HCC | TGFa, PECAM1, NRG1 | (103) |
| Multiple | RNA-Seq, RRBS | Observation of phenotypes in pFFC-FFC cohort | Overexpression with Hypomethylation | NASH | PDGFRβ | (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.