Genetic association study of synphilin-1in idiopathic Parkinson's disease

BMC Medical Genetics

Table 1 Genotype frequencies for single markers used in both direct and indirect association analysis obtained with the Haploview 3.2 software package. P-values and OR are for allelic analysis.

Exon/Intron	Nucleotide change	Chromosome location	Amino acid change	Genotypes Cases 11/12/22	Controls 11/12/22	MAF Cases/controls	Allele 1 vs. allele 2 p-value	OR (95% CI)
1	g.IVS1-70G>A	121 754 613	----	165/115/19	206/176/24	0.26/0.28	0.43	0.90 [0.71–1.15]
4	T131>C	121 786 462	Val44Ala	296/1/0	405/0/0	0.0/0.0	0.42	ND
4	C636>T	121 786 967	Pro212Pro	296/1/0	405/0/0	0.0/0.0	0.42	ND
5	g.IVS4-26G>A	121 788 920	----	153/115/32	97/181/34	0.30/0.30	0.91	0.98 [0.78–1.24]
5	C1134>T	121 789 001	Leu378Leu	295/2/0	404/1/0	0.0/0.0	0.58	2.73 [0.36–20.9]
6	g.IVS5+188A>C	121 789 313	----	133/118/42	173/181/53	0.34/0.35	0.78	0.97 [0.77–1.21]
6	g.IVS5+235A>G	121 789 360	----	151/115/33	196/183/32	0.30/0.30	0.95	1.01 [0.80–1.27]
7	g.IVS6-62G>A	121 804 161	----	291/6/0	397/8/0	0.01/0.01	1.00	1.02 [0.37–2.84]
7	g.IVS6-23T>C	121 804 200	----	154/118/27	202/179/31	0.29/0.29	0.86	0.98 [0.76–1.23]
10	C1861>T	121 814 302	Arg621Cys	293/4/0^†	395/10/0	0.01/0.01	0.42	0.54 [0.18–1.64]
10	G2125>C	121 814 565	Glu709Gln	296/1/0	401/4/0	0.0/0.0	0.40	0.34 [0.05–2.27]

^†One PSP affected (not accounted for here) was found to be homozygous for this variant. OR-Odds ratio. The SNPs used for indirect analysis were highly heterozygous; rs1946649, g.IVS1-70G>A (ObsHet; 0.41); rs2242224, g.IVS4-26G>A (ObsHet; 0.42); rs304383, g.IVS5+188A>C (ObsHet; 0.43); rs2242223, g.IVS5+235A>G (ObsHet; 0.42) and rs22900987, g.IVS6-23T>C (0.42).

ISSN: 1471-2350