SNPs in Primer Sites and High-Throughput Genotyping
We have studied the effect of SNP-in-primer on seven high-throughput genotyping platforms: Affymetrix, BeadArray, FP-TDI, Invader, MIP, Perlegen, and Sequenom.
These platforms were used to generate the human haplotype map in the initial phase of the
International HapMap Project,
Given the dynamic nature of
SNP discovery
, it was inevitable that SNPs would be identified in the primer sites of many assays used for HapMap genotyping.
We found that assays with a SNP in the primer site are more prone to genotyping failure and allele dropout.
Our analysis also revealed that SNPs are not randomly spaced across the genome, but clustered near one another.
This observation has important consequences for genotyping, since hidden variants in primer sites can affect the accuracy of data.
Article: Distribution of human SNPs and its effect on high-throughput genotyping.
Authors: Daniel C. Koboldt, Raymond D. Miller, and Pui-Yan Kwok.
Published: March 2006 in Human Mutation, Volume 27(3), 249-254.
View Article
Supplementary Information
We used freely available data from the International HapMap Project to identify genotyping assays shown to have a putative SNP in the primer site. These assays may be
viewed by clicking on the filename below, or downloaded by right-clicking and selecting "Save Target As".
Supplemental Table S1.
SNP-in-primer assays submitted to HapMap. Genotyping assays with putative SNPs in primer sites are listed for the (a) Affymetrix, (b) BeadArray, (c) FP-TDI, (d) Invader,
(e) MIP, (f) Perlegen, and (g) Sequenom platforms.
SNP-marked Human Genome Assembly
Given the importance of taking nearby SNPs into account when designing assays, we constructed a version of the human genome assembly with SNP positions marked
as a resource to the community. Gzipped fasta files for each chromosome are available on the
download page.
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