. Author manuscript; available in PMC: 2017 Dec 1.

Published in final edited form as: Epidemiol Methods. 2016 Jan 23;5(1):93–112. doi: 10.1515/em-2015-0007

Table 2.

Estimation of the Terms in the Transport Formula for Bridging RV144 to Estimation of VE^*(t = 39) in HVTN 702

Term

Data Source

Method

(v, x) Level

(0,0)

(0,1)

(1,0)

(1,1)

\hat{V E} (t = 39, v ∣ s_{1}, x)

RV144

Structural MLR

Figure 1

0.0¹

{\hat{mrisk}}_{0} (t = 39, v ∣ s_{1}, x)

RV144

From above²

Not shown

F̂^*(s₁|x)

HVTN 100³

Empirical NPMLEs

Figure 2

Ĥ^*(x) for x = 0 (CC) and x = 1 (CT/TT)

Host genetics database

Frequency of CC, CT/TT in n = 131 Black South Africans

0.51

0.49

0.51

0.49

ŵ_Inc(t = 39|x) numer:

{\hat{risk}}_{0}^{*} (t = 39 ∣ x)

HVTN 503 trial in RSA (2007–2013) (Gray et al., 2014)

IPW Kaplan-Meier NPMLEs

0.121⁴

ŵ_Inc(t = 39|x) denom:

{\hat{risk}}_{0} (t = 39 ∣ x)

RV144

IPW Aalen-Johansen

0.0070

0.012

0.0070

0.012

ŵ_Inc(t = 39|x)

17.3

10.08

17.3

10.08

ŵ_V(t = 39, v|x) numer:

{\hat{risk}}_{0}^{*} (t = 39, v ∣ x) / {risk}_{0}^{*} (t = 39 ∣ x)

HIV sequence database

Frequency of v = 0 (169K) and v = 1 (X169K) in the RSA IPW Aalen-Johansen + database

0.60⁵

0.40⁵

ŵ_V(t = 39, v|x) denom:

{\hat{risk}}_{0} (t = 39, v ∣ x) / {\hat{risk}}_{0} (t = 39 ∣ x)

RV144

0.70⁶

0.76⁶

0.33⁶

0.20⁶

ŵ_V(t = 39, v|x)

0.86

0.79

1.22

2.03

Estimated as 0.0 because $\hat{V E} (t = 39, v = 1) = - 0.55$ (95% CI = −2.58 to 0.33) and the belief that the vaccine did not increase infection risk.

Estimated as part of the method for estimating $\hat{V E} (t = 39, v ∣ s_{1}, x)$ (details in Supplementary Appendix B).

Because HVTN 100 has not yet completed, the data from RV144 were used.

⁴

The estimates are the same for x = 0 and x = 1 because data on X were not available in the HVTN 503 trial.

⁵

The estimates are the same for v = 0 and v = 1 because data on X were not available in HVTN 503; the estimates are empirical fractions from 254 HIV-1 sequences of South Africans in the LANL database from 2008 to 2013.

⁶

Initial estimates from RV144 (IPW Aalen-Johansen) and final estimates using empirical fractions from 207 HIV-1 sequences of Thais in the LANL database from 2003 to 2009 (See Supplementary Appendix B).