Deep longitudinal data
- 10 patients
- more than 80 time points
- defined time of infection
- 4.5 - 16 years follow-up without therapy
- 6 - 12 samples per patient
- whole genome
- coverage >1000 with quantified template input
How to access and explore
- browse data by patient
- compare patients and genomic regions
- the sequencing methods and quality controls
- download the cleaned reads
Table: Overview of patient specific data.
Example: Phylogeny of samples in the p17 region, colored by patient.
Reference sequences are colored black.
Rationale and methods
We extracted viral RNA from frozen serum samples from 11 untreated HIV patients, with approximately 8 time points per patient, spanning at least five years from an established time of infection. To maximize sensitivity, depth and coverage, we developed a protocol for whole-genome sequencing using six overlapping primer sets. We optimized the library preparation protocol to obtain long inserts starting from less than 1 ng of DNA and sequenced all samples on the Illumina MiSeq platform, obtaining around 10,000x coverage. We are able to call minor alleles as rare as 0.2% in the viral population and preserve linkage information over 500 bp.
This deep whole genome data set covering many years in 11 patients provides a comprehensive portrait of HIV-1 intra-patient evolution that should be suitable for many different types of analyses. We are planning to release the dataset soon and will in addition to raw reads provide pre-analyzed data such as consensus sequences, minor single nucleotide variant frequencies and tools to extract haplotypes up to 500 bp in length in most regions of the HIV-1 genome.
Data use
Population genomics of intrapatient HIV-1 evolution
Fabio Zanini, Johanna Brodin, Lina Thebo, Christa Lanz, Jan Albert and Richard Neher. eLIFE, e11282.