Unidimensional nonnegative scaling for genome-wide Linkage Disequilibrium maps

Haiyong Liao; Michael Ng; Eric Fung; Pak C. Sham

doi:10.1504/IJBRA.2008.021177

Unidimensional nonnegative scaling for genome-wide Linkage Disequilibrium maps

Haiyong Liao, Michael Ng^*, Eric Fung, Pak C. Sham

^*Corresponding author for this work

Department of Mathematics

Research output: Contribution to journal › Journal article › peer-review

1 Citation (Scopus)

Abstract

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 language	English
Pages (from-to)	417-434
Number of pages	18
Journal	International Journal of Bioinformatics Research and Applications
Volume	4
Issue number	4
DOIs	https://doi.org/10.1504/IJBRA.2008.021177
Publication status	Published - 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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10.1504/IJBRA.2008.021177

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title = "Unidimensional nonnegative scaling for genome-wide Linkage Disequilibrium maps",

abstract = "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.",

keywords = "Hapmap, LD, Linkage equilibrium, Matrix-vector multiplication, Nonnegativity, Parallel computation, Single nucleotide polymorphisms, SNPs, Unidimensional scaling",

author = "Haiyong Liao and Michael Ng and Eric Fung and Sham, {Pak C.}",

year = "2008",

month = nov,

doi = "10.1504/IJBRA.2008.021177",

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TY - JOUR

T1 - Unidimensional nonnegative scaling for genome-wide Linkage Disequilibrium maps

AU - Liao, Haiyong

AU - Ng, Michael

AU - Fung, Eric

AU - Sham, Pak C.

PY - 2008/11

Y1 - 2008/11

N2 - 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.

AB - 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.

KW - Hapmap

KW - LD

KW - Linkage equilibrium

KW - Matrix-vector multiplication

KW - Nonnegativity

KW - Parallel computation

KW - Single nucleotide polymorphisms

KW - SNPs

KW - Unidimensional scaling

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U2 - 10.1504/IJBRA.2008.021177

DO - 10.1504/IJBRA.2008.021177

M3 - Journal article

C2 - 19008184

AN - SCOPUS:55849093648

SN - 1744-5485

VL - 4

SP - 417

EP - 434

JO - International Journal of Bioinformatics Research and Applications

JF - International Journal of Bioinformatics Research and Applications

IS - 4

ER -

Unidimensional nonnegative scaling for genome-wide Linkage Disequilibrium maps

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