SeqURE – a new copy-capture based method for sequencing of unknown Retroposition events

Table 3 Candidate tumor-specific Alu insertions

Sample	RE family	Chromosome	Position	UMI count in 5′ flank library	3′ flank Length	UMI count in 3′ flank library	PCR validation
CCC8	AluYa5	8	137,710,278	4	44	0	No
	AluYa5	1	39,888,222	2	544	0	No
	AluYb8	5	94,414,349	2	218	0	No
CCC9	AluYb8	5	77,457,780	2	89	148(+ 397)^a	–
CCC9	AluYb8	7	43,035,359	3	137	2(+ 1)^a	No^b
CCC11	AluYa5	8	80,855,361	2	212	456(+ 283)^a	–
	AluYa5	4	103,090,594	2	20	0	No
	AluYa5	1	9,512,325	2	108	0	N/A
CCC13	AluYa5	16	70,789,164	2	123	0	No
CCC14	AluYa5	10	80,758,919	2	423	0	No

^a also found in corresponding normal sample
^b - PCR product detected in both tumor and normal samples
N/A – impossible to design primers due to insertion into other repetitive sequences

ISSN: 1759-8753