Annotations
The HIV Brain Sequence Database contains three categories of annotations: publication references, patient and sampling information, and sequence properties (see table below).
The publication annotations include bibliographic information identifying the study that generated the sequences. Patient sampling annotations contain information describing the individual patients, as well as clinical information at the time of sampling.
This information was obtained by manual curation of the original publications and in some cases direct communications with the study authors. In cases where multiple studies examined tissue samples from the same patient, the resulting sequences are linked to the same patient code to increase statistical power.
Sample timepoint annotations describe the patient’s clinical health status, neuropathological, neurocognitive status, CD4 counts, viral load, and anti-retroviral treatment history at the time of sampling. Clone and sequence annotations describe the individual sequences and the tissue from which they were cloned.
This includes the sequence start and end locations numbered based on alignment to the HXB2 reference genome, and tissue source coded using terms from a formal anatomical ontology. Alignment to HXB2 was performed using the HIV Sequence Locator tool located at the LANL HIV Sequence Database.
| Patient | |
|---|---|
| Patient code | patient code |
| Sex | gender |
| Risk factor | HIV risk factor |
| Tissue bank | Tissue bank distributing samples |
| Patient year of death | patient year of death |
| Sampling timepoint | |
|---|---|
| Sampling geo-region | patient geo-region at time of sampling |
| Sampling country | patient country at time of sampling |
| Sampling city | patient city at time of sampling |
| Patient age | patient age at sampling |
| Health status | patient health status at sampling |
| Subtype | predominant subtype at time of sampling |
| Drug naive | has patient had ART |
| Antiretroviral treatment | patient ART history |
| Viral load plasma (copies/mL) | plasma viral load |
| Viral load brain (copies/million cells) | brain viral load |
| Viral load lymphoid (copies/million cells) | lymphoid viral load |
| CD4 count (cells/uL) | CD4 count |
| Neurocognitive diagnosis | neurocognitive diagnosis |
| Neuropathological diagnosis | neuropathological diagnosis |
| Giant cells | were giant cells present in the brain |
| Sequence | |
|---|---|
| Genbank accession | Genbank accession number |
| GI | Genbank GI number |
| PubMed ID | Pubmed ID for original publicaiton |
| Sequence length | sequence length |
| Clone name | publication assigned clone name |
| Sample tissue class | global tissue class (Brain, Blood & Lymphoid, etc…) |
| Sample tissue name | tissue source |
| Sample tissue FMA code | tissue FMA code |
| Nucleic acid type | was proviral DNA or viral RNA sequenced |
| Start and end coordinates | sequence start and end referenced to HXB2 |
| Sequence | viral sequence |