Biostar Beta. Not for public use.
Clinically-Associated Snp'S
9
Entering edit mode
4.6 years ago
Vova Naumov • 220
Russia, Moscow

Hi! We are now trying to understand, what Illumina chip is better for medical condition testing. So I used this MySQL query to get list of clinically-associated SNP':

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A  -D hg19 -e '
SELECT *
FROM
snp132 s
WHERE
s.bitfields LIKE 'clin%' '

So now I have a list of about 22000 rs and it is interesting what association is meant by the base. There was a question on Biostar (http://biostar.stackexchange.com/questions/1289/disease-associated-snps) that could help me, but since 16 july OMIM table is not more in genome database. And the question is how can I get a list of disases/conditions from this snp list?

3
Entering edit mode

hg18 does not have table snp132; I think you must have used hg19.

0
Entering edit mode

Sure, sorry, I'l change it

8
Entering edit mode
17 months ago
France/Nantes/Institut du Thorax - INSE…

$curl -s "ftp://anonymous:xxxxxxx@xxxxx.edu/OMIM/mim2gene.txt" | head # Mim Number Type Gene IDs Approved Gene Symbols 100050 phenotype - - 100070 phenotype 100329167 - 100100 phenotype - - 100200 phenotype - - 100300 phenotype 100188340 - 100500 moved/removed - - 100600 phenotype - - 100640 gene 216 ALDH1A1 100650 gene/phenotype 217 ALDH2 get a list of the gene symbols: ~$ curl -s  "ftp://anonymous:xxxxx@xxxxxx.edu/OMIM/mim2gene.txt" |\
egrep -v "#" | cut -d '  ' -f 4 | egrep -v '^\-\$' |\
sort | uniq > list1.txt

2) get your list of SNP associiated to the gene symbol. Something like:

mysql -N --user=genome --host=genome-mysql.cse.ucsc.edu -A  -D hg19 -e 'select  distinct
G.geneSymbol,
S.name
from snp132 as S,
kgXref as G,
knownGene as K where
S.chrom=K.chrom and
S.chromStart>=K.txStart and
S.chromEnd<=K.txEnd and
K.name=G.kgId
/* AND something to restrict the result to YOUR list of SNPs or gene */
' | sort -t '    ' -k1,1 > list2.txt

3) use unix join to join the two lists:

join -1 1 -2 1 list1.txt list2.txt

you should get a list with two columns: the OMIM gene and your SNP.

0
Entering edit mode

Thank you very much! Allways new that these unix commands are very useful. I also tried to use /OMIM/genemap file to get rs numbers from 12th column, but there wre only 209 common rs between clinically-associated and numbers from this file.

4
Entering edit mode
6.1 years ago
Boston, MA USA

dbSNP includes clinically significant variations and you can now filter search results on clinical significance, allele origin, minor allele frequency, and suspected false SNPs. See http://www.ncbi.nlm.nih.gov/projects/SNP/docs/rs_attributes.html for more.

From http://www.ncbi.nlm.nih.gov/projects/SNP/docs/rs_attributes.html : Clinical significance: The significance of the indicated allele.

The supported values are:

unknown
untested
non-pathogenic
probable-non-pathogenic
probable-pathogenic
pathogenic
drug-response
histocompatibility
other

In dbSNP build 132, there are 13105 such rs entries. While no good diefinition of "clinical significance" is given, the above examples of what NCBI classifies as such can help to form a picture of what is meant by this term.

Edit added 13 Oct 2011: I have just learned from following the International Congress of Human Genetics meeting on Twitter that Rong Chen is painstakingly manually curating 5,478 disease-SNP association papers and adding the info to a database of 67,678 SNPs associated with 1,563 diseases.

2
Entering edit mode
17 months ago
Manhattan, NY

What do you mean by clinical association ? What is your criteria ?

_Mendelian disease, Complex disease, Pharmacogenomic variants or combination two or more_ ?*

If you are interested in combined dataset you need to do raw-data-munging. OMIM is ideal for Mendelian variants, for complex disease variants you should check GWAS resources, for Pharmacogenomics variants check PharmGKB.To identify cinically-associated variants from GWAS see my discussion 1, 2 and 3. For pharmacogenomics variants, see list of Annotated SNPs by Disease in PharmGKB here. A combination of the 3 resources will give you a complete coverage of SNPs for your study.

• I recently integrated such a data-set for a manuscript using the approach discussed above.
1
Entering edit mode

I'm interested too what is meant in snp 132 under clinically-associated

1
Entering edit mode