ArticleHuman mutation2010
Single nucleotide differences (SNDs) in the dbSNP database may lead to errors in genotyping and haplotyping studies.
Article in Human mutation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
25 citing papers in PubMed.
- Exploiting public databases of genomic variation to quantify evolutionary constraint on the branch point sequence in 30 plant and animal species.Nucleic acids research · 2023Article
- Extension of the Human Fibrinogen Database with Detailed Clinical Information-The αC-Connector Segment.International journal of molecular sciences · 2021Review
- Identification and functional characterization of new missense SNPs in the coding region of the TP53 gene.Cell death and differentiation · 2021Article
- Allele balance bias identifies systematic genotyping errors and false disease associations.Human mutation · 2019Article
- Architecture of polymorphisms in the human genome reveals functionally important and positively selected variants in immune response and drug transporter genes.Human genomics · 2018Article
- Different evolutionary patterns of SNPs between domains and unassigned regions in human protein-coding sequences.Molecular genetics and genomics : MGG · 2016Article
- Impact of host genetic polymorphisms on vaccine induced antibody response.Human vaccines & immunotherapeutics · 2016Review
- Article
- Computational approaches to study the effects of small genomic variations.Journal of molecular modeling · 2015Review
- Analysis of the genetic basis of periodic fever with aphthous stomatitis, pharyngitis, and cervical adenitis (PFAPA) syndrome.Scientific reports · 2015Article
- Identifying Highly Penetrant Disease Causal Mutations Using Next Generation Sequencing: Guide to Whole Process.BioMed research international · 2015Review
- Identification of Low-Confidence Regions in the Pig Reference Genome (Sscrofa10.2).Frontiers in genetics · 2015Article
- Article
- Congenital cataracts: de novo gene conversion event in CRYBB2.Molecular vision · 2014Article
- Review
- BlackOPs: increasing confidence in variant detection through mappability filtering.Nucleic acids research · 2013Article
- Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects.Scientific reports · 2013Article
- FOXO3 gene variants and human aging: coding variants may not be key players.The journals of gerontology. Series A, Biological sciences and medical sciences · 2012Article
- Exome sequencing for gene discovery: time does not stand still.Annals of neurology · 2012Article
- Online tools for bioinformatics analyses in nutrition sciences.Advances in nutrition (Bethesda, Md.) · 2012Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The creation of single nucleotide polymorphism (SNP) databases (such as NCBI dbSNP) has facilitated scientific research in many fields. SNP discovery and detection has improved to the extent that there are over 17 million human reference (rs) SNPs reported to date (Build 129 of dbSNP). SNP databases are unfortunately not always complete and/or accurate. In fact, half of the reported SNPs are still only candidate SNPs and are not validated in a population. We describe the identification of SNDs (single nucleotide differences) in humans, that may contaminate the dbSNP database. These SNDs, reported as real SNPs in the database, do not exist as such, but are merely artifacts due to the presence of a paralogue (highly similar duplicated) sequence in the genome. Using sequencing we showed how SNDs could originate in two paralogous genes and evaluated samples from a population of 100 individuals for the presence/absence of SNPs. Moreover, using bioinformatics, we predicted as many as 8.32% of the biallelic, coding SNPs in the dbSNP database to be SNDs. Our identification of SNDs in the database will allow researchers to not only select truly informative SNPs for association studies, but also aid in determining accurate SNP genotypes and haplotypes.
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Registered trials
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