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Single Nucleotide Differences (SNDs) Continue to Contaminate the dbSNP Database With Consequences for Human Genomics and Health

Single Nucleotide Differences (SNDs) Continue to Contaminate the dbSNP Database With Consequences... It has been established that up to 8.3% of the biallelic coding SNPs present in dbSNP are actually artefactual polymorphism‐like errors, previously termed single nucleotide differences, or SNDs. In this study, a previous analysis of SNPs in dbSNP was extended and updated to examine how the incidence of SNDs has changed over an intervening five year period. The incidence of SNDs was found to be lower than in the previous analysis at 2.2% of all biallelic SNPs. There was only a modest reduction in the percentage of SNDs in the original set of biallelic coding SNPs tested. This suggests that the overall reduction in the incidence of SNDs over the intervening 5‐year period is related to an improvement in SNP detection methods and more rigorous curation, rather than efforts to ameliorate the presence of SNDs. We note that SNDs contaminating the dbSNP may lead to erroneous conclusions on human conditions. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Human Mutation Wiley

Single Nucleotide Differences (SNDs) Continue to Contaminate the dbSNP Database With Consequences for Human Genomics and Health

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References (25)

Publisher
Wiley
Copyright
Copyright © 2015 Wiley Periodicals, Inc.
ISSN
1059-7794
eISSN
1098-1004
DOI
10.1002/humu.22735
pmid
25421747
Publisher site
See Article on Publisher Site

Abstract

It has been established that up to 8.3% of the biallelic coding SNPs present in dbSNP are actually artefactual polymorphism‐like errors, previously termed single nucleotide differences, or SNDs. In this study, a previous analysis of SNPs in dbSNP was extended and updated to examine how the incidence of SNDs has changed over an intervening five year period. The incidence of SNDs was found to be lower than in the previous analysis at 2.2% of all biallelic SNPs. There was only a modest reduction in the percentage of SNDs in the original set of biallelic coding SNPs tested. This suggests that the overall reduction in the incidence of SNDs over the intervening 5‐year period is related to an improvement in SNP detection methods and more rigorous curation, rather than efforts to ameliorate the presence of SNDs. We note that SNDs contaminating the dbSNP may lead to erroneous conclusions on human conditions.

Journal

Human Mutation – Wiley

Published: Feb 1, 2015

Keywords: SNP; paralogue; single nucleotide difference; SND

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