Retrotransposition in tumors and brains

Table 1 Summary of published evidence for tumor-specific somatic retrotransposition ^a

Study	Cancer type	Tumor–normal pairs, n	Tumors with somatic insertions, n	Tumor-only somatic insertions, n				Normal-only somatic insertions		Method
				Detected	Validated as tumor-specific			Detected	Validated
					By PCR	By sequencing
					By PCR	3′ end only	3′ + 5′ ends
Iskow et al. [6]	Lung	20	6	L1: 9	8/9	8	0	0		Pyrosequencing
	Brain	10	0							Pyrosequencing
Lee et al. [9]	Glioblastoma	16	0	L1: 183	38/39	6	2	0		Paired-end WGS
	Ovarian	9	5	Alu: 10	1/3
	Colorectal	5	5	ERV1: 1	1/1		1
	Prostate	7	6
	Multiple myeloma	7	1
	Normal (Trio)	3	0
Solyom et al. [10]	Colorectal	16	13	L1: 107	69/107	34	35	12	0	L1-Seq
Shukla et al. [11]	Hepatocarcinoma	19	5	L1: 17	12/17	2	10	21	1	RC-Seq
				Alu: 27	0/13
				SVA: 1	0/1
Ewing et al. [12]^b	Acute myeloid leukemia	24	0	0						Paired-end WGS
	Breast	12	0	0
	Colorectal adenocarcinoma	5	0	0
	Glioblastoma	15	0	0
	Lung	19	2	GRIP: 3	0/0
	Ovarian	10	0	0

^aERV1, Endogenous retrovirus1 (PABL_A type); L1-seq, Hemi-specific PCR coupled to Illumina sequencing [14]; RC-seq, Retrotransposon capture sequencing, involving hybridization of fragmented genomic DNA to custom retrotransposon sequence capture arrays followed by deep sequencing [15]; Trio, mother, father and child; WGS, Whole-genome sequencing. ^bEwing et al. examined only gene retrocopy insertion polymorphisms (GRIPs), which are processed gene transcripts present as retrotransposed insertions in one or more individuals but absent from the reference genome.

ISSN: 1759-8753