Table 1.
Neanderthal Selective Sweep Score; z squared logarithm regression and binomial proportion test (BPT).
| GWAS | β (Min, Max) | Std. error | p-value | C.I | BPT(p) 1%(Min, Max) |
|---|---|---|---|---|---|
| AD | −0.012(−0.029,0.012) | 0.016 | 5.00E-01 | −0.041,0.022 | 2.5E-01(8.0E-04,5.9E-01) |
| ADHD | 0.003(−0.013,0.017) | 0.013 | 8.40E-01 | −0.022,0.028 | 4.5E-01(3.6E-02,6.2E-01) |
| BD | −0.004(−0.020,0.013) | 0.01 | 7.10E-01 | −0.023,0.015 | 4.8E-01(1.4E-02,9.1E-01) |
| MDD | −0.018(−0.034,−0.006) | 0.012 | 2.00E-01 | −0.042,0.007 | 5.6E-01(1.1E-01,9.4E-01) |
| Migraine | −0.006(−0.029,−0.002) | 0.013 | 6.90E-01 | −0.032,0.020 | 7.4E-01(2.3E-01,9.2E-01) |
| MS | −0.003(−0.034,0.022) | 0.02 | 8.80E-01 | −0.042,0.035 | 5.1E-01(8.7E-03,8.5E-01) |
| SCZ 1 | −0.038(−0.052,−0.026) | 0.013 | 7.90E-03 | −0.063,−0.013 | 1.7E-01(1.8E-02,6.1E-01) |
| SCZ 2 | −0.067(−0.076,−0.056) | 0.01 | 7.30E-09 | −0.088,−0.047 | 2.4E-02(5.7E-06,3.7E-01) |
| BMI | −0.050(−0.061,−0.037) | 0.016 | 4.50E-03 | −0.079,−0.023 | 4.2E-01(6.2E-02,9.2E-01) |
| Height | −0.074(−0.098,−0.058) | 0.015 | 8.90E-06 | −0.104,−0.045 | 1.1E-01(3.9E-04,6.9E-01) |
| WHR | −0.026(−0.039,−0.019) | 0.011 | 2.50E-02 | −0.047,−0.006 | 2.3E-01(7.1E-03,5.1E-01) |
| SBP | −0.015(−0.024,−0.003) | 0.01 | 1.80E-01 | −0.036,0.005 | 3.7E-01(9.3E-02,7.3E-01) |
| TC | −0.001(−0.019,0.023) | 0.019 | 9.80E-01 | −0.037,0.039 | 5.3E-01(3.1E-01,8.6E-01) |
| TG | −0.017(−0.024,−0.003) | 0.015 | 3.30E-01 | −0.048,0.014 | 4.3E-01(8.2E-03,8.3E-01) |
| CD | −0.025(−0.049,0.003) | 0.019 | 2.50E-01 | −0.062,0.014 | 5.3E-01(2.6E-01,8.6E-01) |
| CeD | −0.000(−0.024,0.018) | 0.018 | 9.90E-01 | −0.037,0.035 | 3.7E-01(1.2E-01,8.4E-01) |
| RA | −0.004(−0.020,0.013) | 0.011 | 7.70E-01 | −0.025,0.017 | 5.7E-01(2.2E-02,8.8E-01) |
| UC | −0.017(−0.027,0.015) | 0.015 | 3.10E-01 | −0.047,0.014 | 5.3E-01(1.7E-01,9.2E-01) |
Phenotypes: psychiatric and other neurological diseases Alzheimer’s disease (AD), attention deficit hyperactivity disorder (ADHD), bipolar disorder (BD), major depressive disorder (MDD), migraine, multiple sclerosis (MS), first and second edition of the schizophrenia (SCZ) GWAS by the Psychiatric Genomic Consortium (SCZ1 and SCZ2), anthropometric measures (body mass index (BMI), height, waist-hip ratio (WHR)), cardiovascular risk factors (systolic blood pressure (SBP), total cholesterol (TC), triglycerides (TG)), immune-mediated diseases (Crohn’s disease (CD), celiac disease (CeD), rheumatoid arthritis (RA), ulcerative colitis (UC)). Squared z-scores logarithm versus Neanderthal selective sweep score (NSS) regression for various phenotypes controlling for other enrichment factors (genic annotation scores, genotypic variance, LD) and top 1% binomial proportion test (BPT) p-values.
SCZ is the only phenotype with a significant negative correlation between squared z-scores logarithms and NSS scores while controlling for other covariates. Also, in SCZ2 the top 1% SNPs include a nominally significant excess of SNPs with NSS score < 0 (Human Divergent) compared to any SNPs (BPT).