Explore the HIV and the Antibody Repertoire



HIV Diversity

Measured as π. This is a measure of the amount of differences between the sequences in a sample. Specifically, this is the mean genetic distance between all pairs of sequences in a sample

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Antibody Repertoire Diversity

Antibody Repertoire Diversity – Same as HIV Diversity. Measured as π. This is a measure of the amount of differences between the sequences in a sample. Specifically, this is the mean genetic distance between all pairs of sequences in a sample

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HIV + Antibody Diversity

Measured as π. This is a measure of the amount of differences between the sequences in a sample. Specifically, this is the mean genetic distance between all pairs of sequences in a sample

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HIV Non-Synonymous Divergence

Measures the amount of coding mutations in the sequences of a sample when compared to some reference sequence. Specifically, this is the rate of non-synonymous mutations (often referred to as dN), relative to the most numerous sequence of the first time-point. This is averaged across all sequences in a sample.

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HIV Synonymous Divergence

Measures the amount of silent mutations in the sequences of a sample when compared to some reference sequence. Specifically, this is the rate of synonymous mutations (often referred to as dS), relative to the most numerous sequence of the first time-point. This is averaged across all sequences in a sample.

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Antibody Repertoire Divergence

The proportion of mutations in a sequence, relative to its inferred naïve ancestor sequence. The naïve ancestor sequence is inferred using Change-O. This is averaged across all sequences in a sample.

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HIV Selection

A measure of the selective pressure on non-synonymous mutations in sequences. Estimated as the non-synonymous mutation rate normalized by the synonymous mutation rate (or dN/dS). Values less than 1 indicate purifying selection, and values greater than 1 indicate positive selection. This is averaged across all sequences in a sample.

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Antibody Repertoire Selection

A measure of the amount of mutations that help a given sequence (or B cell) generate offspring. Estimated using BASELINe. This compares the number of observed mutations in a sequence to the number of mutations that would be expected if there were no selection (i.e. neutrality). Values less than 0 indicate purifying selection, and values greater than 0 indicate positive selection.

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Antibody Repertoire Selection

A measure of the amount of mutations that help a given sequence (or B cell) generate offspring. Estimated using BASELINe. This compares the number of observed mutations in a sequence to the number of mutations that would be expected if there were no selection (i.e. neutrality). Values less than 0 indicate purifying selection, and values greater than 0 indicate positive selection.

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CD4 T cell count

Measures the number of CD4 positive T cells in the peripheral blood of a sample.

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Viral Load

Measures the concentration of HIV virions in the peripheral blood of a sample.

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