LS-SNP: Large-scale annotation of coding non-synonymous SNPs based on multiple information sources

Rachel Karchin, Mark Diekhans, Libusha Kelly, Daryl J. Thomas, Ursula Pieper, Narayanan Eswar, David Haussler, Andrej Sali

Research output: Contribution to journalArticle

177 Citations (Scopus)

Abstract

Motivation: The NCBI dbSNP database lists over 9 million single nucleotide polymorphisms (SNPs) in the human genome, but currently contains limited annotation information. SNPs that result in amino acid residue changes (nsSNPs) are of critical importance in variation between individuals, including disease and drug sensitivity. Results: We have developed LS-SNP, a genomic scale software pipeline to annotate nsSNPs. LS-SNP comprehensively maps nsSNPs onto protein sequences, functional pathways and comparative protein structure models, and predicts positions where nsSNPs destabilize proteins, interfere with the formation of domain-domain interfaces, have an effect on protein-ligand binding or severely impact human health. It currently annotates 28 043 validated SNPs that produce amino acid residue substitutions in human proteins from the SwissProt/TrEMBL database. Annotations can be viewed via a web interface either in the context of a genomic region or by selecting sets of SNPs, genes, proteins or pathways. These results are useful for identifying candidate functional SNPs within a gene, haplotype or pathway and in probing molecular mechanisms responsible for functional impacts of nsSNPs.

Original languageEnglish (US)
Pages (from-to)2814-2820
Number of pages7
JournalBioinformatics
Volume21
Issue number12
DOIs
StatePublished - Jun 15 2005
Externally publishedYes

Fingerprint

Single nucleotide Polymorphism
Nucleotides
Polymorphism
Single Nucleotide Polymorphism
Annotation
Coding
Proteins
Protein
Pathway
Genes
Genomics
Amino Acids
Amino acids
Databases
Gene
Protein Databases
Haplotype
Human Genome
Protein Structure
Amino Acid Substitution

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

LS-SNP : Large-scale annotation of coding non-synonymous SNPs based on multiple information sources. / Karchin, Rachel; Diekhans, Mark; Kelly, Libusha; Thomas, Daryl J.; Pieper, Ursula; Eswar, Narayanan; Haussler, David; Sali, Andrej.

In: Bioinformatics, Vol. 21, No. 12, 15.06.2005, p. 2814-2820.

Research output: Contribution to journalArticle

Karchin, R, Diekhans, M, Kelly, L, Thomas, DJ, Pieper, U, Eswar, N, Haussler, D & Sali, A 2005, 'LS-SNP: Large-scale annotation of coding non-synonymous SNPs based on multiple information sources', Bioinformatics, vol. 21, no. 12, pp. 2814-2820. https://doi.org/10.1093/bioinformatics/bti442
Karchin, Rachel ; Diekhans, Mark ; Kelly, Libusha ; Thomas, Daryl J. ; Pieper, Ursula ; Eswar, Narayanan ; Haussler, David ; Sali, Andrej. / LS-SNP : Large-scale annotation of coding non-synonymous SNPs based on multiple information sources. In: Bioinformatics. 2005 ; Vol. 21, No. 12. pp. 2814-2820.
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