DOI: 10.1093/bioinformatics/btl420. MLR-tagging: informative SNP selection for unphased genotypes based on multiple linear regression

MLR-tagging: informative SNP selection for unphased genotypes based on multiple linear regression

10.1093/bioinformatics/btl420

Crossref journal-article

Oxford University Press (OUP)

Bioinformatics (286)

Abstract

Abstract Summary: The search for the association between complex diseases and single nucleotide polymorphisms (SNPs) or haplotypes has recently received great attention. For these studies, it is essential to use a small subset of informative SNPs accurately representing the rest of the SNPs. Informative SNP selection can achieve (1) considerable budget savings by genotyping only a limited number of SNPs and computationally inferring all other SNPs or (2) necessary reduction of the huge SNP sets (obtained, e.g. from Affymetrix) for further fine haplotype analysis. A novel informative SNP selection method for unphased genotype data based on multiple linear regression (MLR) is implemented in the software package MLR-tagging. This software can be used for informative SNP (tag) selection and genotype prediction. The stepwise tag selection algorithm (STSA) selects positions of the given number of informative SNPs based on a genotype sample population. The MLR SNP prediction algorithm predicts a complete genotype based on the values of its informative SNPs, their positions among all SNPs, and a sample of complete genotypes. An extensive experimental study on various datasets including 10 regions from HapMap shows that the MLR prediction combined with stepwise tag selection uses fewer tags than the state-of-the-art method of Halperin et al. (2005). Availability: MLR-Tagging software package is publicly available at Contact: alexz@cs.gsu.edu

Bibliography

He, J., & Zelikovsky, A. (2006). MLR-tagging: informative SNP selection for unphased genotypes based on multiple linear regression. Bioinformatics, 22(20), 2558â2561.

Authors 2

Jingwu He (first)
Alexander Zelikovsky (additional)

References 11 Referenced 29

10.1159/000073729 / Human Heredity / Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power by Chapman (2003)
10.1038/ng1001-229 / Nat. Genet. / High resolution haplotype structure in the human genome by Daly (2001)
10.1073/pnas.0404730102 / Proc. Natl Acad. Sci. USA / GERBIL: genotype resolution and block identification using likelihood by Kimmel (2004)
10.1093/bioinformatics/bti1021 / Bioinformatics / Tag SNP selection in genotype data for maximizing SNP prediciton accuracy by Halperin (2005)
10.1038/nature02168 / Nature / The International HapMap Project by International HapMap Consortium (2003)
10.1504/IJBRA.2005.007904 / Int. J. Bioinform. Res. Appl. / Linear reduction method for predictive and informative tag SNP selection by He (2005)
{'key': '2023012409224526100_b7', 'first-page': '278', 'article-title': 'Approximation algorithms for the selection of robust tag SNPs’, Proc. Workshop Algorith', 'volume': '3240', 'author': 'Huang', 'year': '2004', 'journal-title': 'Bioinform.'} / Bioinform. / Approximation algorithms for the selection of robust tag SNPs’, Proc. Workshop Algorith by Huang (2004)
10.1002/gepi.20024 / Genetic Epidemiol. / Algorithms for inferring haplotypes by Niu (2004)
10.1159/000071807 / Human Heredity / Choosing haplotype-tagging SNPs based on unphased genotype data using as preliminary sample of unrelated subjects with an example from the multiethnic cohort study by Stram (2003)
10.1101/gr.1837404 / Genome Res. / Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies by Zhang (2004)
10.1186/1471-2105-5-89 / BMC Bioinformatics / A double classification tree search algorithm for index SNP selection by Zhang (2004)

Dates

Type	When
Created	19 years ago (Aug. 8, 2006, 11:27 p.m.)
Deposited	2 years, 7 months ago (Jan. 24, 2023, 5:05 a.m.)
Indexed	1 year, 2 months ago (June 18, 2024, 10:56 p.m.)
Issued	19 years ago (Aug. 7, 2006)
Published	19 years ago (Aug. 7, 2006)
Published Online	19 years ago (Aug. 7, 2006)
Published Print	18 years, 10 months ago (Oct. 15, 2006)

Funders 0

None

BibTeX

@article{He_2006, title={MLR-tagging: informative SNP selection for unphased genotypes based on multiple linear regression}, volume={22}, ISSN={1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btl420}, DOI={10.1093/bioinformatics/btl420}, number={20}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={He, Jingwu and Zelikovsky, Alexander}, year={2006}, month=aug, pages={2558–2561} }

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