Table 2 SVAs RIPs that are associated with clinical features and markers of progression of PD in the PPMI cohort. The FDR corrected p value from the linear mixed-effects model is reported for each SVA. The mean and 95% confidence intervals (CI) are reported for each genotype at each visit with data available and Tukey adjusted p values from the pairwise analysis are shown for each pair of genotypes. (Bold highlights significant p values in pairwise analysis).

From: Reference SVA insertion polymorphisms are associated with Parkinson’s Disease progression and differential gene expression

SVA ID Associated feature Time of visit (months) FDR corrected p value from lme model AA mean (95% CI) PA mean (95% CI) PP mean (95% CI) AA vs PA p-value AA vs PP p-value PA vs PP p-value
SVA_7 MDS-UPDRS Part III 0 0.04 24.5 (9.5–39.5) 20.9 (18.5–23.3) 21.0 (19.8–22.3) 0.88 0.89 0.99
Score (OFF) 12   28.5 (13.5–43.5) 23.9 (21.4–26.4) 25.6 (24.2–26.9) 0.82 0.92 0.49
  24   27.0 (12.1–42.0) 26.0 (23.4–28.7) 27.5 (26.1–29.0) 0.99 0.99 0.57
  36   10.0 (−4.96–25.0) 28.4 (25.7–31.1) 29.5 (28.1–31.0) 0.05 0.03 0.75
SVA_11 MDS-UPDRS Part II 0 0.003 6.3 (5.1–7.52) 5.6 (4.9-6.3) 6.2 (5.0–7.5) 0.57 >0.99 0.62
Score 12   7.4 (6.1–8.6) 7.2 (6.5–7.8) 7.9 (6.7–9.2) 0.95 0.82 0.55
  24   8.3 (7.1–9.6) 7.9 (7.2–8.5) 7.5 (6.2–8.8) 0.79 0.61 0.85
  36   10.9 (9.6–12.2) 8.9 (8.2–9.6) 7.6 (6.3–8.9) 0.02 0.001 0.16
SVA_24 Categorical Hoehn 0 0.04 2.62 (2.55–2.69) 2.53 (2.44–2.62) 2.47 (2.31–2.64) 0.30 0.26 0.82
& Yahr 12   2.76 (2.68–2.84) 2.77 (2.67–2.87) 2.62 (2.44–2.81) 0.99 0.38 0.37
  24   2.79 (2.71–2.88) 2.86 (2.75–2.96) 2.61 (2.43–2.79) 0.62 0.18 0.06
  36   2.87 (2.78–2.96) 3.07 (2.96–3.18) 2.78 (2.60–2.97) 0.02 0.70 0.03
SVA_36 Ipsilateral count 0 0.02 2.39 (1.98–2.79) 2.40 (2.22–2.58) 2.43 (2.27–2.59) >0.99 0.98 0.96
density ratio 12   3.36 (2.93–3.79) 2.55 (2.36–2.74) 2.64 (2.48–2.81) 0.003 0.007 0.77
(caudate/putamen) 24   3.72 (3.28–4.17) 2.63 (2.44–2.82) 2.68 (2.51–2.86) <0.0001 0.0001 0.91
SVA_47 Ipsilateral count 0 0.008 2.40 (2.29–2.52) 2.69 (2.15–3.23) 2.53 (1.27–3.78) 0.57 0.98 0.97
density ratio 12   2.64 (2.51–2.76) 3.39 (2.85–3.93) 2.89 (1.40–4.38) 0.02 0.94 0.81
(caudate/putamen) 24   2.66 (2.54 –2.79) 4.44 (3.87–5.01) 3.18 (1.18–5.19) <0.0001 0.87 0.46
SVA_67 Ipsilateral count 0 1.97 × 10-6 2.64 (2.04–3.24) 2.43 (2.24–2.62) 2.38 (2.24–2.53) 0.79 0.69 0.91
density ratio 12   3.81 (3.12–4.51) 2.63 (2.43–2.83) 2.64 (2.49–2.79) 0.004 0.004 >0.99
(caudate/putamen) 24   5.10 (4.43–5.76) 2.67 (2.46–2.88) 2.66 (2.51–2.81) <0.0001 <0.0001 >0.99
SVA_79 Contralateral count 0 0.03 3.26 (2.75–3.78) 2.87 (2.76–2.98) 0.14
density ratio 12   2.40 (1.87–2.93) 2.93 (2.82–3.04) 0.06
(caudate/putamen) 24   2.18 (1.67–2.69) 2.93 (2.81–3.04) 0.005