[Genome] RE : rs# of SNP

[Supriya Mahajan]

Hello,

I am interested in the frequency of expression of a specific opioid mu
receptor gene SNP A118G in a drug abusing population of subjects with and
without HIV-1 infection. I am also interested in correlation that
information with SNPs in the chemokines that indicate either enhanced HIV-1
disease progression ( RANTES Inc.1C) or delayed HIV-1 disease progression (
CCR2-641 or CCR5 delta 32). Will using a Genotyping -Sequenom MassArray
help me answer that question or use of allelic determination using Real
time Q-PCR? For the mass array there are so many rs# for the OPRM1 SNPs
that I do not know how to choose the rs# that is needed for the Genotyping
-Sequenom MassArray.

Your advice is greatly appreciated.

Thanking you

Sincerely

Supriya Mahajan

[Brooke Rhead]

Hello Supriya,

Unfortunately, this is outside the scope of the help we can provide.
Perhaps you can work with Sequenom to figure out which SNPs will work on
their platform:

http://www.sequenom.com/applications/high_performance_genotyping.php

Also, one of our developers has offered this general advice for
selecting SNPs for genotyping:

". . . general advice based on the data we have in other tracks, such as
trying to avoid SNPs in repeats, segmental duplications, etc. Other
data can be used to identify tag SNPs within recombination blocks, but
that data should be selected based on the population in the associaton
study being designed. Haploview is suited for this task."

The Haploview website is located here:
http://www.broad.mit.edu/mpg/haploview/

I hope that some of this information is helpful to you. Good luck in
your endeavors.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

> _______________________________________________
> Genome maillist - Genome at soe.ucsc.edu
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[Unknown]

Hi,

I'm not sure what you are asking, but in relation to Sequenom...
If you are a registered Sequenom customer, their user site may provide the
answers that you are seeking.
RealSNP uses dbSNP build 118 which is a little tedious, but allows design
/ selection of compatible assays and offers many pre-designed versions.
Which sequenom platform are you utilising?
https://www.realsnp.com/default.asp

We use SNPHAP or Haploview depending on the source data and / or requirements
for SNP selection...but if you are interested in Chemokine SNPs, there are
many inflammation-type sites where comprehensive resequencing info is publicly
available.

AJ

P.S. We genotype CCR5 delta32 by standard agarose gel - very inexpensive
& only takes a day for 1000 samples :-)

>> _______________________________________________
>> Genome maillist - Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>_______________________________________________
>Genome maillist - Genome at soe.ucsc.edu
>http://www.soe.ucsc.edu/mailman/listinfo/genome

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