Frequency and methylation status of selected retrotransposition competent L1 loci in amyotrophic lateral sclerosis

Table 1 Retrotransposition competent L1 elements chosen for genotyping and methylation analysis in ALS cohort

Name	Percentage of retrotransposition activity of L1RP [11, 14, 42]	Ref/non-ref	Insertion Allele Frequency [11, 15]	Number of germline offspring elements from 3′ transduction analysis [15]	Number of 3′ transduction somatic insertions in cancer [17]	Chromosomal loci
L1_chr2_q24.1	150	Non-ref RIP	na,0.16	41/121	21/655	chr2:156,527,848 intergenic
L1_chr6_q24.1	141	Non-ref RIP	na,0.18	14/121	98/655	chr6:13,191,033 Intron PHACTR1
L1_chrX_p22.2	132	Ref RIP	0.34,0.74	1/121	20/655	chrX:11,953,208 intergenic
L1_chr6_p22.3	112.7	Ref RIP	0.30,0.61	2/121	2/655	chr6:24,811,907 Intron FAM65B
L1_chr8_q24.22	89.4	Ref RIP	0.44,1	2/121	4/655	chr8:135,082,987 intergenic
L1_chr1_p12	–	Ref	1,1	13/121	7/655	chr1:119,394,974 intergenic
L1_chr22_q12.1	13.8	Ref	1,1	2/121	137/655	chr22:29,059,272 Intron TTC28

The RC-L1 elements were shortlisted based on their high level of activity in a cellular retrotransposition assay [11, 14, 42], high number of germline offspring elements from 3′ transductions analysis [15] or high number of somatic insertions in cancer from 3′ transductions analysis [17]. Non-ref RIP: L1s that are not in the human reference genome and are polymorphic for their presence/absence. Ref RIP: L1s that are present in the human reference genome and are polymorphic for their presence/absence. Ref: L1s present in the human reference genome and there is currently no evidence that they are polymorphic for their presence/absence

ISSN: 1756-6606