RAREMETAL METHOD

Conditional Analysis

The key idea behind meta-analysis with RAREMETAL is that various gene-level test statistics can be reconstructed from single variant score statistics and that, when the linkage disequilibrium relationships between variants are known, the distribution of these gene-level statistics can be derived and used to evaluate signifi-cance. Single variant statistics are calculated using the Cochran-Mantel-Haenszel method. The main formulae are tabulated in the following:

Formulae for RAREMETAL

Test	Statistics	Null Distribution	Notation
Single Variant	$T=\sum _{i=1}^n{U}_i/\sqrt{\sum _{i=1}^n{V}_i}$	$T\sim \mathbf{𝐍}(0,1)$	$U_i\text{ is the score statistic from study }i;$$V_i\text{ is the variance of }{U}_i.$
un-weighted Burden	$T_b=\sum _{i=1}^n{\mathbf{U}}_{\mathbf{𝐢}}/\sqrt{\sum _{i=1}^n{\mathbf{V}}_{\mathbf{𝐢}}}$	$T_b\sim \mathbf{𝐍}(0,1)$	${\mathbf{U}}_{\mathbf{𝐢}}\text{ is the vector of score statistics from study }i,or$ ${\mathbf{U}}_{\mathbf{𝐢}}=\{U_{i1},...,U_{im}\};$ ${\mathbf{V}}_{\mathbf{𝐢}}\text{ is the covariance of }{\mathbf{U}}_{\mathbf{𝐢}}.$
Weighted Burden	$T_{wb}={\mathbf{𝐰}}^{\mathbf{𝐓}}\sum _{i=1}^n{\mathbf{U}}_{\mathbf{𝐢}}/\sqrt{{\mathbf{𝐰}}^{\mathbf{𝐓}}\left(\sum _{i=1}^n{\mathbf{V}}_{\mathbf{𝐢}}\right)\mathbf{𝐰}}$	$T_{wb}\sim \mathbf{𝐍}(0,1)$	${\mathbf{𝐰}}^{\mathbf{𝐓}}=\{w_1,w_2,...,w_m{\}}^T\text{ is the weight vector.}$
VT	$T_{VT}=\max (T_{b\left(f_1\right)},T_{b\left(f_2\right)},\dots ,T_{b\left(f_m\right)}),\text{ where}$$T_{b\left(f_j\right)}={\mathit{\varphi }}_{f_j}^{\mathbf{𝐓}}\sum _{i=1}^n{\mathbf{U}}_{\mathbf{𝐢}}/\sqrt{{\mathit{\varphi }}_{f_j}^{\mathbf{𝐓}}\left(\sum _{i=1}^n{\mathbf{V}}_{\mathbf{𝐢}}\right){\mathit{\varphi }}_{f_j}}$	$(T_{b\left(f_1\right)},T_{b\left(f_2\right)},\dots ,T_{b\left(f_m\right)})$$\sim \mathbf{𝐌}\mathbf{𝐕}\mathbf{𝐍}(\mathbf{𝟎},\mathrm{\Omega })\text{,}$$\text{where }{\mathrm{\Omega }}_{\mathit{i}\mathit{j}}=\frac{{\mathit{\varphi }}_{f_i}^T\left(\sum _{i=1}^n{\mathbf{V}}_{\mathbf{𝐢}}\right){\mathit{\varphi }}_{f_j}}{\sqrt{{\mathit{\varphi }}_{f_i}^T\left(\sum _{i=1}^n{\mathbf{V}}_{\mathbf{𝐢}}\right){\mathit{\varphi }}_{f_i}}\sqrt{{\mathit{\varphi }}_{f_j}^T\left(\sum _{i=1}^n{\mathbf{V}}_{\mathbf{𝐢}}\right){\mathit{\varphi }}_{f_j}}}$	${\mathit{\varphi }}_{f_j}\text{ is a vector of }0\text{s and }1\text{s,}$ $\text{indicating the inclusion of a variant using threshold }{f}_j;$
SKAT	$\mathbf{𝐐}=\left(\sum _{i=1}^n{𝐔}_{\mathbf{𝐢}}^{\mathbf{𝐓}}\right)\mathbf{𝐖}\left(\sum _{i=1}^n{\mathbf{U}}_{\mathbf{𝐢}}\right)$	$\mathbf{𝐐}\sim \sum _{i=1}^m{\lambda }_i{\chi }_{1,i}^2,\text{ where}$ $({\lambda }_1,{\lambda }_2,\dots ,{\lambda }_m)\text{ are eigen values of}$${\left(\sum _{i=1}^n{\mathbf{V}}_{\mathbf{𝐢}}\right)}^{\frac{1}{2}}\mathbf{𝐖}{\left(\sum _{i=1}^n{\mathbf{V}}_{\mathbf{𝐢}}\right)}^{\frac{1}{2}}$	$\mathbf{𝐖}\text{ is a diagonal matrix of weights.}$