Gene networks and transcriptional regulators associated with liver cancer development and progression

Meier, Tatiana; Timm, Max; Montani, Matteo; Wilkens, Ludwig

doi:10.1186/s12920-021-00883-5

BMC Medical Genomics

Table 1 Chromosomal aberrations in hepatocellular carcinoma (HCC) tumours compared to adjacent non-tumourous tissues (NT)

From: Gene networks and transcriptional regulators associated with liver cancer development and progression

Chr	Arm	Type of aberration		Significant^a	Non-neoplastic tissues (NT)		HCC
Chr	Arm	NT	HCC	Significant^a	Size^b of intervals	% cases affected	Size^b of intervals	% cases affected
1	p	–	Loss	Yes	0	0	407	27.3–31.8
1	q	–	Gain	Yes	2108	7.7–23.1	2108	54.5–77.3
2	q	–	Gain	Yes	0	0	206	27.3–36.4
3	p	–	Gain	Yes	173	15.4–23.1	173	54.5–73.6
4	q	–	Loss	Yes	0	0	689	27.3–31.8
5	p	–	Gain	Yes	0	0	12	27.3
5	q	–	Loss	Yes	0	0	673	27.3–31.8
5	q	–	Gain	Yes	0	0	154	27.3
6	p	–	Gain	Yes	525	7.7–15.4	1061	31.8–68.2
6	q	–	Loss	Yes	0	0	26	27.3
7	p	–	Gain	Yes	100	7.7–15.4	810	27.3–68.2
7	q	Gain	Gain	Yes	96	23.1–30.8	146	36.4–72.7
7	q	Gain	Gain	No	94	30.7–53.8	94	63.6–72.7
8	p	–	Loss	Yes	103	7.7	525	31.8–63.6
8	q	–	Gain	Yes	14	7.7	1456	27.3–50
8	q	Gain	Gain	Yes	22	46.2	22	81.8
8	q	Gain	Gain	No	54	38.4–69.2	54	72.7–81.8
9	q	–	Gain	Yes	10	15.4	10	63.6
9	q	Gain	Gain	No	276	30.7	276	63.6
10	q	–	Gain	Yes	12	7.7	51	27.3–50
10	q	–	Loss	Yes	0	0	13	27.3
11	q	Gain	Gain	Yes	80	38.5	80	77.3
11	p/q	Gain	Gain	No	373	38.4–53.8	373	59.1–72.7
12	p	–	Gain	Yes	0	0	38	36.4
12	q	–	Gain	Yes	323	15.4	323	54.5–63.6
13	q	–	Loss	Yes	23	7.7	996	27.3–50.0
13	q	–	Gain	Yes	21	7.7	21	45.5–50.0
14	q	–	Gain	Yes	158	7.7–23.1	158	45.5–59.1
15	q	–	Gain	Yes	38	15.4	498	27.3–54.5
16	p	–	Gain	Yes	221	7.7	221	40.9–50.5
16	q	–	Loss	Yes	15	7.7	15	31.8
17	p/q	–	Gain	Yes	1802	7.7–15.4	1802	40.9–63.6
18	q	–	Loss	Yes	0	0	759	27.3–36.4
19	q	–	Gain	Yes	10	7.7	10	45.5
19	p	Gain	Gain	No	652	53.8	652	68.2–77.3
19	q	Gain	Gain	No	999	30.8–46.2	999	63.6–68.2
20	p/q	–	Gain	Yes	820	7.7–23.1	1125	31.8–63.6
21	q	–	Gain	Yes	0	0	235	27.3–36.4
22	q	–	Gain	Yes	810	7.7–15.4	810	59.1–63.6

The table only includes aberrations that spanned more than 10 probes. Known chromosomal imbalances in HCC are marked in bold. Common aberrations found in both HCC (n = 22) and adjacent NT (n = 17) samples were included when they affected > 50% of cases in one tissue set and > 30% of cases in the other; they are presented in italics
Chr chromosome
^aDifferential aberrations between HCC and NT samples were considered statistically significant when P < 0.05 in differential aberration analysis
^bThe interval size is expressed as the total number of probes that spanned the aberration interval

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