prostate cancer detection question

SNP: rs10993994 linked to prostate cancer, info here says: at chromosome 10, position 46046326:

if "CC" ==> Mag=0 (i.e. good)

else if "CT" ==> Mag=1.5 & increased prostate cancer risk (odds ratio 1.2)

else if "TT" ==> Mag=2 & increased prostate cancer risk (odds ratio 1.6)

http://www.snpedia.com/index.php/Rs10993994

i downloaded chromosome 10 from this link:

http://hgdownload.cse.ucsc.edu/goldenpath/hg19/chromosomes/chr10.fa.gz

and removed the first line from the file (i.e. ">chr10") and removed every space occurs in the end of the lines. then using command line(bash):

dd bs=1 skip=46046326 count=2 if=InputFastaFile of=OutputFastaFile

this line extracts the two nucleotides in the position 46046326. but when i open the OutputFastaFile i find: "CA" not CC or CT or TT !!! am i making something wrong ?!

snp dna phenotype genotype genome

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written 10.3 years ago by ahm3dhany •

Likely because of a difference in genome build. You downloaded hg19 reference where as snpedia link is referring to GRCh38 (which is the newer human genome build). Try this link: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/chromosomes/chr10.fa.gz

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written 10.3 years ago by GenoMax

first of all thanks, i appreciate your help! :)

another question, i download the GRCh38.

and i found "AT" !!

not CC or CT or TT so i am confused. :/

look here: http://www.ncbi.nlm.nih.gov/variation/view/?q=rs10993994&filters=source:dbsnp&assm=GCF_000001405.28

can u help me please.

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written 10.3 years ago by ahm3dhany •

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