Hi,
I have a few questions regarding the ROSMAP raw and imputed genotype data:
- which genomic build was used for the imputed data?
- in the raw genotye data from the Affymetrix chip there seem to be two groups of individuals. For one group the genotyping rate is ok, but for the other it is quite low. Do you have any ideas as to why that is the case and if so, how the groups differ? Have there been separate round of genotyping?
Thanks!
Kevin
Created by Kevin Hu kevin.hu Does anyone know why the genotyping rate is so low in part of this data set? Should these samples be excluded or just treated as a separate 'sub' dataset?
Thanks!
If you cluster the samples by missingness, they'll break apart into genotyping center nicely. As you said, there is substantially more missingness in one set than the other. We were not provided a detailed list with the data. Thank you very much!
Is there a way to see which samples were genotyped at which center?
Thanks!
Kevin Hi @kevin.hu-
Information about the ROSMAP raw and imputed genotypes can be found here: https://www.synapse.org/#!Synapse:syn3157325. The imputation was done to 1000 Genomes Phase I, which I believe used Build 36 as it's reference genome.
The generation of the raw genotypes is more fully detailed in [this manuscript](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3307898/), including information about the two genotyping facilities used and subsequent parallel QC for the ~1700 ROS and MAP samples: Broad Institute?s Center for Genotyping (n=1,204) or the Translational Genomics Research Institute (n=674).
I hope that helps,
Solly
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