Sieve analysis data API

Sieve analysis is a statistical methodology for identifying evidence of vaccine-induced selective immune pressure on "breakthrough" pathogens in a vaccine efficacy trial. See this review by Edlefsen et al. or these lecture slides from Peter Gilbert for more details. This service can be used to download all the neccesary files for performing a sieve analysis of a vaccine efficacy trial.

HIV-1 vaccine efficacy trials available for download:

API specification

A full dataset consists of a treatment assignment file (all patient identifiers are PUB_IDs) and an alignment of all breakthrough genetic sequences and the vaccine immunogen sequence (i.e. the reference).

Each file is available through an encoded URI:

An additional file is available to obtain a list of valid protein:reference codes for each study

You can also download the site-wise distance matrix for all sequences in an alignment relative to the vaccine reference sequence, using a vaccine mismatch distance (i.e. hamming distance)

Published results including site-specific effect magnitudes, p-values and q-values are also available in CSV format: