euL1db - The European database of L1-HS retrotransposon insertions in humans

Description
In this study enhanced retrotransposon capture sequencing (RC-seq) was applied to 19 hepatocellular carcinoma (HCC) genomes and elucidated two archetypal L1-mediated mechanisms enabling tumorigenesis. In the first example, 4/19 (21.1%) donors presented germline retrotransposition events in the tumor suppressor mutated in colorectal cancers (MCC). MCC expression was ablated in each case, enabling oncogenic b-cate- nin/Wnt signaling. In the second example, suppression of tumorigenicity 18 (ST18) was activated by a tumor-specific L1 insertion. Experimental assays confirmed that the L1 interrupted a negative feedback loop by blocking ST18 repression of its enhancer. ST18 was also frequently amplified in HCC nodules from Mdr2-/- mice, supporting its assignment as a candidate liver oncogene. These proof-of-principle results substantiate L1-mediated retrotransposition as an important etiological factor in HCC.

Mapped assembly	Original assembly	Browse by SRIP	Browse by MRIP
hg19_NCBI37	hg19_NCBI37	SRIP	MRIP

Sample ID	Sample name	Relationship	Clinical	Anatomopathology	Tissue	Sub Tissue	WGA	Size
171	12T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
172	12NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
173	15T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
174	15NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
175	21T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
176	21NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
177	29T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
178	29NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
179	32T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
180	32NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
181	33T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
182	33NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
183	35T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
184	35NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
185	42T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
186	42NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
187	47T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
188	47NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
189	48T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
190	48NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
191	49T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
192	49NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
193	60T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
194	60NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
195	62T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
196	62NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
197	70T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
198	70NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
199	86T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
200	86NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
201	89T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
202	89NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
203	95T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
204	95NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
205	106T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
206	106NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool
207	116T	Pair	Hepatocellular_Carcinoma	Cancerous	Liver	Epithelial	no	cell-pool
208	116NT	Pair	Hepatocellular_Carcinoma	Normal	Liver	Epithelial	no	cell-pool

Individual Name	Gender	Population	Clinical	Disease	Relationship	Father	Mother
12	Male	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
15	Male	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
21	Male	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
29	Male	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
32	Male	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
33	Female	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
35	Female	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
42	Female	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
47	Male	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
48	Male	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
49	Male	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
60	Male	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
62	Male	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
70	Male	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
86	Female	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
89	Male	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
95	Male	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
106	Male	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.
116	Male	Caucasian	Cancerous	Hepatocellular_Carcinoma	Unrelated	.	.

euL1db The European database of L1-HS retrotransposon insertions in humans

euL1db

The European database of L1-HS retrotransposon insertions in humans