Curing AIDS,
with programming

Andrew Grimm

Curing AIDS Understanding HIV,
with programming

Andrew Grimm

What's AIDS?

Disease caused by HIVIf untreated, damages the immune systemDamage of immune system can cause death

Whats HIV?

VirusCannot live independentlyHijacks the cells of living creatures to reproduce itselfGenome is 9749 letters long Human genome is 3 billion letters longHas two copies of the genomeHumans also have two copies of their genome

Impact of AIDS

PrevalenceAnnual deaths

Worldwide35 million1.5 million

Australia18,000100

Japan8,100100

What am I studying?

Two types of mutationPoint mutationRecombination

Point mutation

One letter of the genome changing to another letter

Recombination

Swapping equivalent portions of the two copies of the genome

Why study mutation?

It enables HIV to escape the immune systemIt enables HIV to become resistant to drugs

Laboratory component

Start with viruses with a known genomeInfect cells with virusesLet them reproduce for one generationDetermine the sequence of new virusesNone of this done by me!

Analysis component

Compare sequences against the sequences of the original

Challenges faced

New questions and analyses

Questions lead to new analysesNew analyses lead to new insightsNew insights lead to new questions

Performance

Initially only dealt with hundreds of sequencesNow deal with millions of sequences

Breaking of assumptions

I used to assume a sequence would be either wild type or marker type, or a mixtureNow I have to handle wild type or marker type 1 or marker type 2

Questions?

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