Table 2.

Allele frequencies of polymorphic RC-L1s are similar using PCR or tagging SNPs to determine L1 genotype

L1 (Tagging SNP)	IAF of L1 based on PCR		p value based on PCR genotypes	r2,D’	IAF of L1 based on SNP		p value based on SNP genotypes
L1_chr2_q24.1 (rs7594648)	Controls (243)	0.30	0.67	0.95,0.98	Controls (386)	0.32	0.38
	SALS (220)	0.29			SALS (1331)	0.30
L1_chr6_q24.1 (rs1150602)	Controls (494)	0.14	0.32	0.90,1.00	Controls (340)	0.17	0.36
	SALS (445)	0.16			SALS (1178)	0.18
L1_chr6_p22.3 (rs6932875)	Controls (180)	0.14	0.39	0.90,0.97	Controls (357)	0.16	0.99
	SALS (179)	0.12			SALS (1227)	0.15
L1_chr8_q24.22 (rs7844570)	Controls (176)	0.45	0.66	0.99,1.00	Controls (385)	0.46	0.34
	SALS (177)	0.44			SALS (1330)	0.44
L1_chrX_p22.2 (rs6640825)	Female controls (114)	0.57	0.31	0.94,0.99	Female controls (233)	0.59	0.56
	Female SALS (54)	0.51			Female SALS (509)	0.57
	Male controls (64)	0.56			Male controls (139)	0.58
	Male SALS (119)	0.55			Male SALS (740)	0.60

Each polymorphic RC-L1 was genotyped using PCR and then expanded into the larger cohort of the UK Project MinE samples using tagging SNPs as a proxy for the L1 genotype and each method demonstrated a similar insertion allele frequency (IAF). The RC-L1s were in strong LD with their respective tagging SNPs demonstrated by the r² values. There was no significant association of any of the RC-L1s with SALS by either genotyping method (chi-squared test). Number in brackets in columns IAF of L1 based on PCR and IAF of L1 based on SNP indicate the number of individuals per cohort