Table 7. Summary of chromosomal losses in hepatocellular carcinoma, 5 studies of fibrolamellar hepatocellular carcinoma identified by comparative genomic hybridization studies, and results of whole genome sequencing.
| HCC | FL-HCC Comparative Genomic Hybridization | FL-HCC Whole Genome Sequencing | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total | Total % | Individual Studies | Events | Average | Range | |||||||
| # of cases | 785 | 30 | 11 | 10 | 5 | 3 | 1 | 10 | Involved Genes | |||
| 1p | 15% | 3 | 10% | 1 | 0 | 1 | 0 | 1 | 10 | 4.50 | 3–9 | HNRNPCL1 (heterogeneous nuclear ribonucleoprotein C-like 1) in 3/10 HSPA7 (heat shock 70kDa protein 7) in 3/10 PPIAL4B (peptidylprolyl isomerase A (cyclophilin A)-like 4B) in 3/10 PPIAL4C (peptidylprolyl isomerase A (cyclophilin A)-like 4C) in 3/10 PRAMEF2 (PRAME family member 2) in 3/10 PRAMEF4 (PRAME family member 4) in 3/10 RNVU1-19 TTC34 (tetratricopeptide repeat domain 34) in 6/10 |
| 1q | 1% | 0 | 0% | 0 | 0 | 0 | 0 | 0 | 8 | 4.13 | 0–8 | ANKRD20A12P (ankyrin repeat domain 20 family, member A12, pseudogene) in 3/10 FAM231D (family with sequence similarity 231, member D) in 3/10 FCGR1C (Fc fragment of IgG, high affinity Ic, receptor (CD64), pseudogene) in 3/10 FCGR2C (Fc fragment of IgG, low affinity IIc, receptor for (CD32) (gene/pseudogene)) in 3/10 HNRNPCL1 (heterogeneous nuclear ribonucleoprotein C-like 1) in 3/10 HSPA7 (heat shock 70kDa protein 7) in 3/10 PPIAL4B (peptidylprolyl isomerase A (cyclophilin A)-like 4B) in 3/10 PPIAL4C (peptidylprolyl isomerase A (cyclophilin A)-like 4C) in 3/10 |
| 2p | 1% | 0 | 0% | 0 | 0 | 0 | 0 | 0 | 8 | 2.38 | 0–4 | |
| 2q | 3% | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 2.83 | 0–6 | ||
| 3p | 4% | 2 | 0% | 1 | 1 | 0 | 0 | 0 | 10 | 2.00 | 1–5 | |
| 3q | 2% | 2 | 0 | 2 | 0 | 0 | 0 | 9 | 3.11 | 0–6 | MUC4 (mucin 4) in 4/10 | |
| 4p | 11% | 2 | 7% | 1 | 0 | 0 | 0 | 1 | 10 | 7.80 | 12-Mar | |
| 4q | 34% | 2 | 2 | 0 | 0 | 0 | 0 | 9 | 2.56 | 0–7 | ||
| 5p | 2% | 0 | 7% | 0 | 0 | 0 | 0 | 0 | 5 | 1.40 | 0–2 | |
| 5q | 8% | 1 | 7% | 1 | 0 | 0 | 0 | 0 | 9 | 1.44 | 0–3 | |
| 6p | 1% | 1 | 7% | 0 | 0 | 1 | 0 | 0 | 9 | 2.22 | 0–6 | |
| 6q | 15% | 1 | 0% | 1 | 0 | 0 | 0 | 0 | 9 | 2.33 | 0–3 | ADGB (androglobin) in 3/10 BCLAF1 (BCL2-associated transcription factor 1) in 4/10 |
| 7p | 1% | 0 | 3% | 0 | 0 | 0 | 0 | 0 | 8 | 1.25 | 0–2 | |
| 7q | 3% | 0 | 3% | 0 | 0 | 0 | 0 | 0 | 10 | 4.60 | 2–11 | DPP6 (dipeptidyl-peptidase 6) in 4/10 MUC12 (mucin 12) in 4/10 PTPRN2 (protein tyrosine phosphatase, receptor type, N polypeptide 2) in 6/10 |
| 8p | 38% | 5 | 3% | 2 | 3 | 0 | 0 | 0 | 8 | 1.50 | 0–3 | |
| 8q | 2% | 0 | 0% | 0 | 0 | 0 | 0 | 0 | 7 | 1.43 | 0–4 | |
| 9p | 14% | 2 | 0% | 0 | 0 | 2 | 0 | 0 | 3 | 1.67 | 0–3 | |
| 9q | 11% | 1 | 17% | 0 | 0 | 1 | 0 | 0 | 7 | 1.29 | 0–2 | |
| 10p | 3% | 0 | 0% | 0 | 0 | 0 | 0 | 0 | 3 | 1.00 | 0–1 | |
| 10q | 11% | 0 | 7% | 0 | 0 | 0 | 0 | 0 | 9 | 2.33 | 0–5 | |
| 11p | 5% | 2 | 3% | 2 | 0 | 0 | 0 | 0 | 9 | 2.22 | 0–4 | |
| 11q | 10% | 1 | 0% | 0 | 0 | 1 | 0 | 0 | 9 | 3.56 | 0–9 | GLB1L2 (galactosidase, beta 1-like 2) in 3/10 GLB1L3 (galactosidase, beta 1-like 3) in 3/10 |
| 12p | 7% | 0 | 0% | 0 | 0 | 0 | 0 | 0 | 6 | 1.83 | 0–5 | |
| 12q | 3% | 0 | 7% | 0 | 0 | 0 | 0 | 0 | 8 | 2.88 | 0–7 | DPY19L2 (dpy-19-like 2 (C. elegans)) in 3/10 TDG (thymine-DNA glycosylase) in 3/10 |
| 13p | 0% | 2 | 3% | 2 | 0 | 0 | 0 | 0 | 0 | |||
| 13q | 26% | 2 | 0% | 0 | 2 | 0 | 0 | 0 | 5 | 1.20 | 0–2 | |
| 14p | 0% | 0 | 0% | 0 | 0 | 0 | 0 | 0 | 0 | |||
| 14q | 11% | 4 | 7% | 2 | 2 | 0 | 0 | 0 | 7 | 4.00 | 0–7 | ELK2AP (ELK2A, member of ETS oncogene family, pseudogene) in 3/10 |
| 15p | 0% | 0 | 7% | 0 | 0 | 0 | 0 | 0 | 0 | |||
| 15q | 5% | 1 | 0% | 0 | 0 | 1 | 0 | 0 | 9 | 2.44 | 0–4 | TYRO3 protein tyrosine kinase) in 4/10 |
| 16p | 17% | 3 | 13% | 0 | 0 | 3 | 0 | 0 | 6 | 2.17 | 0–3 | |
| 16q | 36% | 1 | 0% | 0 | 0 | 1 | 0 | 0 | 8 | 1.88 | 0–4 | |
| 17p | 32% | 1 | 3% | 0 | 0 | 1 | 0 | 0 | 8 | 1.38 | 0–3 | MAP2K3 (mitogen-activated protein kinase kinase 3) in 3/10 NCOR1 (nuclear receptor corepressor 1) in 3/10 |
| 17q | 4% | 1 | 10% | 0 | 0 | 1 | 0 | 0 | 6 | 1.50 | 0–2 | |
| 18p | 4% | 3 | 3% | 0 | 3 | 0 | 0 | 0 | 5 | 1.60 | 0–3 | |
| 18q | 11% | 6 | 3% | 3 | 3 | 0 | 0 | 0 | 5 | 1.60 | 0–2 | |
| 19p | 7% | 0 | 3% | 0 | 0 | 0 | 0 | 0 | 10 | 1.50 | 1–4 | PRKACA, GIPC1, CD97, DDX39A, LPHN1, PKN1, ASF1B, LOC100507373, PTGER1, DNAJB1 (known genomic deletion) in 8/10 |
| 19q | 4% | 0 | 10% | 0 | 0 | 0 | 0 | 0 | 8 | 2.75 | 0–7 | |
| 20p | 2% | 1 | 20% | 0 | 1 | 0 | 0 | 0 | 6 | 1.50 | 0–2 | |
| 20q | 1% | 0 | 0% | 0 | 0 | 0 | 0 | 0 | 4 | 1.00 | 0–1 | |
| 21p | 0% | 1 | 0% | 0 | 1 | 0 | 0 | 0 | 2 | 1.00 | 0–1 | |
| 21q | 9% | 3 | 3% | 2 | 1 | 0 | 0 | 0 | 6 | 1.17 | 0–2 | |
| 22p | 0% | 0 | 0% | 0 | 0 | 0 | 0 | 0 | 0 | |||
| 22q | 6% | 1 | 3% | 1 | 0 | 0 | 0 | 0 | 8 | 2.38 | 0–5 | ADRBK2 (adrenergic, beta, receptor kinase 2) in 3/10 CRYBB2P1 (crystallin, beta B2 pseudogene 1) in 4/10 IGLL3P (immunoglobulin lambda-like polypeptide 3, pseudogene) in 4/10 LRP5L (low density lipoprotein receptor-related protein 5-like) in 4/10 |
| Xp | 5% | 1 | 10% | 0 | 0 | 1 | 0 | 0 | 6 | 1.83 | 0–3 | |
| Xq | 5% | 2 | 0% | 0 | 0 | 2 | 0 | 0 | 6 | 1.50 | 0–3 | RBMX (RNA binding motif protein, X-linked) 3/10 |
| Yp | 5% | 1 | 3% | 1 | 0 | 0 | 0 | 0 | 0 | |||
| Yq | 6% | 1 | 3% | 1 | 0 | 0 | 0 | 0 | 8 | 3.13 | 0–6 | |
| Reference | [60] | [61] | [62] | [63] | [12] | [63] | ||||||
HCC = Hepatocellular carcinoma, FL-HCC = Fibrolamellar hepatocellular carcinoma
Adapted from Ward and Waxman [44]