Question
Question Posted 08/13/14:
i want to know if the Whole genome sequencing (WGS)data in plink formats have APOE and TOMM40 genotyping data or not
i want to know if the Whole genome sequencing (WGS)data in plink formats have APOE and TOMM40 genotyping data or not
Response posted 08/13/14 by Sungeun Kim:
First of all, the data in plink format is genotype data using Illumina Omni2.5M platform, concurrently collected with WGS data. If you meant rs7412 and rs429358 SNP for APOE and polyTpolymorphism for TOMM40, the data does not have them. If you mean other SNPs, please look at BIM file.
Response posted 08/13/14 by fayroz:
thank you
yes i mean these snps APOE and TOMM40 . how can i found these snps for each 818 WGS participants? and how can i link the two files?
and what about BIM file?
yes i mean these snps APOE and TOMM40 . how can i found these snps for each 818 WGS participants? and how can i link the two files?
and what about BIM file?
Response posted 08/13/14 by Sungeun Kim:
APOE genotyping were separately performed and reported at "APOERES.csv". By using this result, you can estimate alleles of two SNPs: rs7412 and rs429358. Please look at the web page in the following link:
http://www.snpedia.com/index.php/APOE
Regarding TOMM40 poly-T polymorphism, we don't have it for ADNI-GO/2 participants, but you can get it for ADNI-1 continuing participants whose RID is smaller than 2000 from "TOMM40.csv" at the LONI.
I don't know exactly what you meant by "link the two files", but if you want to link APOE and TOMM40 results, which use RID as a subject ID, with WGS data which use PTID as a subject ID, you can get this mapping information from "ROSTER.csv".
http://www.snpedia.com/index.php/APOE
Regarding TOMM40 poly-T polymorphism, we don't have it for ADNI-GO/2 participants, but you can get it for ADNI-1 continuing participants whose RID is smaller than 2000 from "TOMM40.csv" at the LONI.
I don't know exactly what you meant by "link the two files", but if you want to link APOE and TOMM40 results, which use RID as a subject ID, with WGS data which use PTID as a subject ID, you can get this mapping information from "ROSTER.csv".
