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Author Topic: Great tools to understand your genotype, choose you drug (Standford) etc  (Read 1701 times)

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Offline John2038

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  • Posts: 1,529
  • Happiness is a journey, not a destination.
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Very interesting programs, to understand the impact of the mutations and choose the drug.


http://hivdb6.stanford.edu/asi/deployed/hiv_central.pl?program=hivdb&action=showMutationForm

Genotype (HIVdb Program)

Provide Mutation Scores, Mutations comments and Mutation List Analysis

Example of input data

Reverse Transcriptase
K103N V108IV M184V T215FIST T39N S48T V60I K122P D123E I135M S162C D177E G196E Q197K T200A Q207E R211K L228R

Protease
T12S I15V G16E L19I M36I L63T H69K I72IV I93L

Output
Quote

PI Major Resistance Mutations:   None
PI Minor Resistance Mutations:   None
Other Mutations:   T12S, I15V, G16E, L19I, M36I, L63T, H69K, I72IV, I93L

Protease Inhibitors

ATV....Susceptible
DRV....Susceptible
FPV....Susceptible
IDV....Susceptible
LPV....Susceptible
NFV....Susceptible
SQV....Susceptible
TPV....Susceptible

PR Comments

* The following 2 of the 21 tipranavir RESIST study mutations were present: M36I, H69K (Baxter J et al J Virology 2006).
* G16E is a highly polymorphic mutation occurring in 2% to 20% of viruses depending on subtype. It may be weakly associated with ATV therapy and response.
* M36I/V are weakly associated with PI resistance when present with other mutations. M36I occurs commonly in certain non-subtype B viruses. M36L/T are rare variants of uncertain significance.
* H69K is a highly polymorphic residue that was weakly associated with a decreased virologic response to TPV in the RESIST trials.
* I93L is a common polymorphism that becomes even more common in persons receiving PIs.

Mutation Scoring

.........ATV...DRV...FPV...IDV...LPV...NFV...SQV...TPV
Total:....0.....0.....0.....0.....0.....0.....0.....0
   


NRTI Resistance Mutations:   M184V, T215FIST
NNRTI Resistance Mutations:   K103N, V108IV
Other Mutations:   T39N, S48T, V60I, K122P, D123E, I135M, S162C, D177E, G196E, Q197K, T200A, Q207E, R211K, L228R

Nucleoside RTI

3TC....High-level resistance
ABC....Intermediate resistance
AZT....Low-level resistance
D4T....Low-level resistance
DD.....Low-level resistance
FTC....High-level resistance
TDF   Susceptible

Non-Nucleoside RTI

DLV....High-level resistance
EFV....High-level resistance
ETV....Low-level resistance
NVP....High-level resistance


Mutation Scoring

.........3TC....ABC....AZT....D4T....DDI....FTC....TDF....DLV....EFV....ETV....NVP
K103N.....................................................60.....60.....10.....70
V108IV....................................................10.....10......5.....10
M184V....60.....12.....-8.....-5.....5......60.....-8............................
T215FIST..4.....20.....35.....30.....20.....4......10............................
-----------------------------------------------------------------------------------
Total:...64.....32.....27.....25.....25.....64......2.....70.....70.....15.....80

           


Same tool but Comparison of Genotypic Resistance Algorithms (ANRSV2007.09, HIVDB and RegaV7.1.1)
HIValg compares HIVdb results to those of 2 other algorithms: i. Rega Institute (rules), and ii. Agence Nationale de Recherches sur le SIDA (ANRS rules).
http://hivdb6.stanford.edu/asi/deployed/hiv_central.pl?program=hivalg&action=showMutationForm


Others interesting tools

NRTI Mutation Pattern & Susceptibility
http://hivdb.stanford.edu/pages/phenoSummary/Pheno.NRTI.Simple.html

Mutation Frequency According to Subtype and PI Treatment (Naive & Treated Persons !)
http://hivdb6.stanford.edu/asi/deployed/hiv_central.pl?program=hivseq&action=showMutationForm

Resistance Mutation Scores OR matrix for codon pos VS. drug!
NRTI:....  http://hivdb.stanford.edu//cgi-bin/NRTIResiNote.cgi
NNRTI:... http://hivdb.stanford.edu//cgi-bin/NNRTIResiNote.cgi
PI:..........http://hivdb.stanford.edu//cgi-bin/PIResiNote.cgi

Great user guide
http://hivdb.stanford.edu/pages/documentPage/oldUserGuide.html

And a lot of clinical trials hyper links.


Offline Luke

  • Member
  • Posts: 291
Just a couple of quick notes to anyone else diving in to use the Stanford tools:

You may find, as I did, that not all your mutations are listed. This is because it doesn't list those mutations which aren't a risk to developing resistance. 

Also, the science of HIV changes daily, so if you have used the tool in the past, please don't just assume that the information remains static. It doesn't, so please recheck if you are about to use old information.


 


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