Unidimensional nonnegative scaling for genome-wide Linkage Disequilibrium maps

Haiyong Liao, Kwok Po NG*, Eric Fung, Pak C. Sham

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

1 Citation (Scopus)


The main aim of this paper is to propose and develop a unidimensional nonnegative scaling model to construct Linkage Disequilibrium (LD) maps. The proposed constrained scaling model can be efficiently solved by transforming it to an unconstrained model. The method is implemented in PC Clusters at Hong Kong Baptist University. The LD maps are constructed for four populations from Hapmap data sets with chromosomes of several ten thousand Single Nucleotide Polymorphisms (SNPs). The similarities and dissimilarities of the LD maps are studied and analysed. Computational results are also reported to show the effectiveness of the method using parallel computation.

Original languageEnglish
Pages (from-to)417-434
Number of pages18
JournalInternational Journal of Bioinformatics Research and Applications
Issue number4
Publication statusPublished - Nov 2008

Scopus Subject Areas

  • Biomedical Engineering
  • Health Informatics
  • Clinical Biochemistry
  • Health Information Management

User-Defined Keywords

  • Hapmap
  • LD
  • Linkage equilibrium
  • Matrix-vector multiplication
  • Nonnegativity
  • Parallel computation
  • Single nucleotide polymorphisms
  • SNPs
  • Unidimensional scaling


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