SNPs on human chromosomes 21 and 22 - Analysis in terms of protein features and pseudogenes

Suganthi Balasubramanian, Paul Harrison, H. Hegyi, Paul Bertone, Nicholas Luscombe, Nathaniel Echols, Patrick McGarvey, ZhaoLei Zhang, Mark Gerstein

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

SNPs are useful for genome-wide mapping and the study of disease genes. Previous studies have focused on SNPs in specific genes or SNPs pooled from a variety of different sources. Here, a systematic approach to the analysis of SNPs in relation to various features on a genome-wide scale, with emphasis on protein features and pseudogenes, is presented. We have performed a comprehensive analysis of 39,408 SNPs on human chromosomes 21 and 22 from the SNP consortium (TSC) database, where SNPs are obtained by random sequencing using consistent and uniform methods. Our study indicates that the occurrence of SNPs is lowest in exons and higher in repeats, introns and pseudogenes. Moreover, in comparing genes and pseudogenes, we find that the SNP density is higher in pseudogenes and the ratio of nonsynonymous to synonymous changes is also much higher. These observations may be explained by the increased rate of SNP accumulation in pseudogenes, which presumably are not under selective pressure. We have also performed secondary structure prediction on all coding regions and found that there is no preferential distribution of SNPs in α-helices, β-sheets or coils. This could imply that protein structures, in general, can tolerate a wide degree of substitutions. Tables relating to our results are available from http://genecensus.org/pseudogene.

Original languageEnglish
Pages (from-to)393-402
Number of pages10
JournalPharmacogenomics
Volume3
Issue number3
DOIs
Publication statusPublished - 2002

Fingerprint

Chromosomes, Human, 21-22 and Y
Pseudogenes
Single Nucleotide Polymorphism
Proteins
Genes
Chromosome Mapping
Introns
Exons

Keywords

  • Nonsynonymous
  • Pseudogenes
  • Secondary structure
  • SNP
  • Synonymous

ASJC Scopus subject areas

  • Pharmacology
  • Genetics(clinical)

Cite this

Balasubramanian, S., Harrison, P., Hegyi, H., Bertone, P., Luscombe, N., Echols, N., ... Gerstein, M. (2002). SNPs on human chromosomes 21 and 22 - Analysis in terms of protein features and pseudogenes. Pharmacogenomics, 3(3), 393-402. https://doi.org/10.1517/14622416.3.3.393

SNPs on human chromosomes 21 and 22 - Analysis in terms of protein features and pseudogenes. / Balasubramanian, Suganthi; Harrison, Paul; Hegyi, H.; Bertone, Paul; Luscombe, Nicholas; Echols, Nathaniel; McGarvey, Patrick; Zhang, ZhaoLei; Gerstein, Mark.

In: Pharmacogenomics, Vol. 3, No. 3, 2002, p. 393-402.

Research output: Contribution to journalArticle

Balasubramanian, S, Harrison, P, Hegyi, H, Bertone, P, Luscombe, N, Echols, N, McGarvey, P, Zhang, Z & Gerstein, M 2002, 'SNPs on human chromosomes 21 and 22 - Analysis in terms of protein features and pseudogenes', Pharmacogenomics, vol. 3, no. 3, pp. 393-402. https://doi.org/10.1517/14622416.3.3.393
Balasubramanian, Suganthi ; Harrison, Paul ; Hegyi, H. ; Bertone, Paul ; Luscombe, Nicholas ; Echols, Nathaniel ; McGarvey, Patrick ; Zhang, ZhaoLei ; Gerstein, Mark. / SNPs on human chromosomes 21 and 22 - Analysis in terms of protein features and pseudogenes. In: Pharmacogenomics. 2002 ; Vol. 3, No. 3. pp. 393-402.
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