uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
Experimental validation of data mined single nucleotide polymorphisms from several databases and consecutive dbSNP builds
Show others and affiliations
2006 (English)In: Pharmacogenetics & Genomics, ISSN 1744-6872, Vol. 16, no 3, 207-217 p.Article in journal (Refereed) Published
Abstract [en]

Rapid development in the annotation of human genetic variation has increased the numbers of single nucleotide polymorphisms (SNPs) in candidate genes by several orders of magnitude. The selection of both useful target SNPs; for disease-gene association studies and SNPs associated with the treatment response is therefore an increasingly challenging task. We describe a workflow for selecting SNPs based on their putative function and frequency in candidate genes extracted from PubMed resources. The annotation of each SNP and its frequency in a Caucasian population was assessed in several databases. Approximately 4000 SNPs were identified from an initial 233 candidate genes. In a case study, we performed actual genotyping of 1030 of these SNPs in 213 genes and obtained 710 successfully genotyped SNPs. Using the flow-chart outlined here, only 87 SNPs were monomorphic (approximately 12%). This study reports the frequency of SNPs in a Caucasian population, selected in silico, using a candidate gene approach and validated by actually genotyping 193 individuals. The selected genotypes represent a valuable set of verified candidate SNPs for pharmacogenetic studies in Caucasian populations.

Place, publisher, year, edition, pages
2006. Vol. 16, no 3, 207-217 p.
Keyword [en]
cancer pharmacogenetics, data mining, dbSNP, SNP, SNP500, SNPper
National Category
Medical and Health Sciences
URN: urn:nbn:se:uu:diva-144899DOI: 10.1097/01.fpc.0000194422.12770.fbISI: 000246126900007PubMedID: 16495780OAI: oai:DiVA.org:uu-144899DiVA: diva2:394705
Available from: 2011-02-03 Created: 2011-02-03 Last updated: 2012-04-13Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Syvänen, Ann-Christine
By organisation
Molecular MedicineDepartment of Medical Sciences
In the same journal
Pharmacogenetics & Genomics
Medical and Health Sciences

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 209 hits
ReferencesLink to record
Permanent link

Direct link