Table 2.
Mixed-model analysis of GWAS-associated SNPs on continuous GDS
| Ancestry Group | Model Component | Effects | |||||
|---|---|---|---|---|---|---|---|
| Model 1. Selected SNPs and Haplogroups Only (Reduced Model) | |||||||
| European Descent N=440 | (R) 20 SNPs | 0.226 (0.074) | |||||
| (F) Haplogroup | H 0.010 (0.087) | J −0.040 (0.105) | T 0.117 (0.109) | UK −0.041 (0.096) | Other Referent | ||
| Model p-value | 1.731e-20 | ||||||
| Admixed Hispanic N=101 | (R) 20 SNPs | 0.304 (0.124) | |||||
| (F) Haplogroup | A 0.113 (0.105) | B −0.164 (0.121) | C 0.098 (0.132) | Other Referent | |||
| Model p-value | 7.198e-05 | ||||||
| African Descent N=484 | (R) 20 SNPs | 0.12 (0.047) | |||||
| (F) Haplogroup | L1 −0.003 (0.057) | L2 0.012 (0.053) | L3 −0.027 (0.052) | Other Referent | |||
| Model p-value | 1.803e-09 | ||||||
| Model 2. Selected SNPs with Haplogroup Interactions (Full Model) | |||||||
| European Descent N=440 | (R) 20 SNPs | 0.151 (0.096) | |||||
| (F) Haplogroup | H 0.027 (0.087) | J −0.030 (0.105) | T 0.145 (0.105) | UK −0.035 (0.096) | Other Referent | ||
| (R) SNPxHaplogroup | H 0.024 (0.032) | J 0.005 (0.043) | T 0.012 (0.047) | UK 0.041 (0.049) | Other Referent | ||
| variance explained | 0.236 (0.071) | ||||||
| LRT p-value | 0.052 | ||||||
| Admixed Hispanic N=101 | (R) 20 SNPs | 0.013 (0.249) | |||||
| (F) Haplogroup | A 0.131 (0.098) | B −0.141 (0.119) | C 0.095 (0.121) | Other Referent | |||
| (R) SNPxHaplogroup | A 0.191 (0.161) | B 0.245 (0.217) | C 0.008 (0.121) | Other | Referent | ||
| variance explained | 0.364 (0.125) | ||||||
| LRT p-value | 0.50 | ||||||
| African Descent N=484 | (R) 20 SNPs | 0.094 (0.059) | |||||
| (F) Haplogroup | L1 0.004 (0.058) | L2 0.015 (0.053) | L3 −0.023 (0.052) | Other Referent | |||
| (R) SNPxHaplogroup | L1 0.012 (0.037) | L2 0.011 (0.030) | L3 0.015 (0.030) | Other Referent | |||
| variance explained | 0.133 (0.050) | ||||||
| LRT p-value | 0.025 | ||||||
Random effects are denoted by (R) and units are in proportion of GDS variance explained, Fixed effects are denoted by (F) and units are change in GDS relative to Referent. Fixed effects for comorbidity, CART use, plasma viral load, reading ability, nadir CD4+ count and principal components are not shown. LRT: Likelihood Ratio Test between full and reduced model.