Optimal selection of SNP markers for disease association studies.
Abstract
Genetic association studies with population samples hold the promise of uncovering the susceptibility genes underlying the heritability of complex or common disease. Most association studies rely on the use of surrogate markers, single-nucleotide polymorphism (SNP) being the most suitable due to their abundance and ease of scoring. SNP marker selection is aimed to increase the chances that at least one typed SNP would be in linkage disequilibrium (LD) with the disease causative variant, while at the same time controlling the cost of the study in terms of the number of markers genotyped and samples. Empirical studies reporting block-like segments in the genome with high LD and low haplotype diversity have motivated a marker selection strategy whereby subsets of SNPs that 'tag' the common haplotypes of a region are picked for genotyping, avoiding typing redundant SNPs. Based on these initial observations, a plethora of 'tagging' algorithms for selecting minimum informative subsets of SNPs has recently appeared in the literature. These differ mostly in two major aspects: the quality or correlation measure used to define tagging and the algorithm used for the minimization of the final number of tagging SNPs. In this review we describe the available tagging algorithms utilizing a 3-step unifying framework, point out their methodological and conceptual differences, and make an assessment of their assumptions, performance, and scalability.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Selection of all tagging SNPs listed for OXTR in HapMap represents an optimal strategy for detecting association across this gene region.
“Our selection of all tagging SNPs listed for OXTR in HapMap represents an optimal strategy for detecting association across this gene region [35].”
From The oxytocin receptor (OXTR) contributes to prosocial fund allocations in the dictator game and the social value orientations task (2009) · cites this paper as [35]
Most association studies rely on the use of surrogate markers, single-nucleotide polymorphisms (SNPs) being the most suitable due to their abundance and ease of scoring.
“Most association studies rely on the use of surrogate markers, single-nucleotide polymorphisms (SNPs) being the most suitable due to their abundance and ease of scoring (see discussion in [35].”
From The oxytocin receptor (OXTR) contributes to prosocial fund allocations in the dictator game and the social value orientations task (2009) · cites this paper as [35]
Cites
A Mathematical Theory of Communication
Shannon, C. E. (1948) · Bell System Technical Journal · doi:10.1002/j.1538-7305.1948.tb01338.x · Cited by 88,486 · see citing works
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909 · see citing works
Self-citationdbSNP: the NCBI database of genetic variation
Sherry, S. T. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.308 · Cited by 7,502 · see citing works
A New Statistical Method for Haplotype Reconstruction from Population Data
Stephens, M., Smith, N. J. C., & Donnelly, P. (2001) · The American Journal of Human Genetics · doi:10.1086/319501 · Cited by 7,460 · see citing works
The International HapMap Project
†The International HapMap Consortium, Genotyping centres: Baylor College of Medicine and ParAllele BioScience, Gibbs, R. A., Belmont, J. W., Hardenbol, P., Willis, T. D., Yu, F., Chinese HapMap Consortium, Yang, H., Ch'ang, L.-Y., et al. (2003) · Nature · doi:10.1038/nature02168 · Cited by 6,057 · see citing works
The Structure of Haplotype Blocks in the Human Genome
Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., et al. (2002) · Science · doi:10.1126/science.1069424 · Cited by 5,863 · see citing works
The Future of Genetic Studies of Complex Human Diseases
Risch, N., & Merikangas, K. (1996) · Science · doi:10.1126/science.273.5281.1516 · Cited by 5,355 · see citing works
Three approaches to the quantitative definition of information *
Kolmogorov, A. N. (1968) · International Journal of Computer Mathematics · doi:10.1080/00207166808803030 · Cited by 2,053 · see citing works
Linkage disequilibrium in the human genome
Reich, D., Cargill, M., Gabriel, S., Ireland, J. S., Sabeti, P. C., Richter, D. J., Lavery, T., Kouyoumjian, R., Farhadian, S., Ward, R. H., et al. (2001) · Nature · doi:10.1038/35075590 · Cited by 1,763 · see citing works
A high-resolution recombination map of the human genome
Kong, A., Gudbjartsson, D. F., Sainz, J., Jonsdottir, G. M., Gudjonsson, S. A., Richardsson, B., Sigurdardottir, S. L., Barnard, J., Hallbeck, B., Másson, G., et al. (2002) · Nature Genetics · doi:10.1038/ng917 · Cited by 1,750 · see citing works
Carlson, C. S., Eberle, M. A., Rieder, M. J., Qian, Y., Kruglyak, L., & Nickerson, D. A. (2004) · The American Journal of Human Genetics · doi:10.1086/381000 · Cited by 1,578 · see citing works
Linkage disequilibrium in humans: models and data.
Pritchard, J., & Przeworski, M. (2001) · American Journal of Human Genetics · doi:10.1086/321275 · Cited by 1,340 · see citing works
Haplotype tagging for the identification of common disease genes
Johnson, G. C. L., Esposito, L., Barratt, B. J., Smith, A. N., Heward, J., Di Genova, G., Ueda, H., Cordell, H. J., Eaves, I. A., Dudbridge, F., et al. (2001) · Nature Genetics · doi:10.1038/ng1001-233 · Cited by 1,174 · see citing works
Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21
Patil, N., Berno, A. J., Hinds, D. A., Barrett, W. A., Doshi, J. M., Hacker, C. R., Kautzer, C. R., Lee, D. H., Marjoribanks, C., McDonough, D. P., et al. (2001) · Science · doi:10.1126/science.1065573 · Cited by 1,145 · see citing works
Haplotype blocks and linkage disequilibrium in the human genome
Wall, J. D., & Pritchard, J. K. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1123 · Cited by 642 · see citing works
A High-Density Admixture Map for Disease Gene Discovery in African Americans
Smith, M. W., Patterson, N., Lautenberger, J. A., Truelove, A. L., McDonald, G. J., Waliszewska, A., Kessing, B. D., Malasky, M. J., Scafe, C., Le, E., et al. (2004) · The American Journal of Human Genetics · doi:10.1086/420856 · Cited by 459 · see citing works
Self-citationStram, D. O., Haiman, C. A., Hirschhorn, J. N., Altshuler, D., Kolonel, L. N., Henderson, B. E., & Pike, M. C. (2003) · Human Heredity · doi:10.1159/000071807 · Cited by 403 · see citing works
A dynamic programming algorithm for haplotype block partitioning
Zhang, K., Deng, M., Chen, T., Waterman, M. S., & Sun, F. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.102186799 · Cited by 336 · see citing works
The sequence of the human genome. Venter JC, Adams MD, Myers EW, et al. Science 2001;291:1304–1351.
Liesegang, T. J. (2001) · American Journal of Ophthalmology · doi:10.1016/s0002-9394(01)01077-7 · Cited by 276 · see citing works
Quality and completeness of SNP databases
Reich, D., Gabriel, S., & Altshuler, D. (2003) · Nature Genetics · doi:10.1038/ng1133 · Cited by 206 · see citing works
Weale, M. E., Depondt, C., Macdonald, S. J., Smith, A. C., Lai, P. S., Shorvon, S. D., Wood, N. W., & Goldstein, D. B. (2003) · The American Journal of Human Genetics · doi:10.1086/378098 · Cited by 187 · see citing works
Efficient selective screening of haplotype tag SNPs
Ke, X., & Cardon, L. R. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.287 · Cited by 186 · see citing works
Linkage Disequilibrium Mapping via Cladistic Analysis of Single-Nucleotide Polymorphism Haplotypes
Durrant, C., Zondervan, K. T., Cardon, L. R., Hunt, S. E., Deloukas, P., & Morris, A. P. (2004) · The American Journal of Human Genetics · doi:10.1086/422174 · Cited by 186 · see citing works
The first linkage disequilibrium (LD) maps: Delineation of hot and cold blocks by diplotype analysis
Maniatis, N., Collins, A. R., Xu, C., McCarthy, L. C., Hewett, D. R., Tapper, W., Ennis, S., Ke, X., & Morton, N. E. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.042680999 · Cited by 182 · see citing works
Zhang, K., Qin, Z. S., Liu, J. S., Chen, T., Waterman, M. S., & Sun, F. (2004) · Genome Research · doi:10.1101/gr.1837404 · Cited by 174 · see citing works
Paola Sebastiani, B., Lazarus, R. M., Weiss, S. T., Kunkel, L. M., Kohane, I. S., & Ramoni, M. F. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1633613100 · Cited by 172 · see citing works
Assessing the performance of the haplotype block model of linkage disequilibrium.
Wall, J., & Pritchard, J. (2003) · American Journal of Human Genetics · doi:10.1086/378099 · Cited by 168 · see citing works
Goldstein, D. B., Ahmadi, K. R., Weale, M. E., & Wood, N. W. (2003) · Trends in Genetics · doi:10.1016/j.tig.2003.09.006 · Cited by 160 · see citing works
Nielsen, R., & Signorovitch, J. (2003) · Theoretical Population Biology · doi:10.1016/s0040-5809(03)00005-4 · Cited by 153 · see citing works
Selection of Genetic Markers for Association Analyses, Using Linkage Disequilibrium and Haplotypes
Meng, Z., Zaykin, D. V., Xu, C., Wagner, M. J., & Ehm, M. G. (2003) · The American Journal of Human Genetics · doi:10.1086/376561 · Cited by 148 · see citing works
Optimal Haplotype Block-Free Selection of Tagging SNPs for Genome-Wide Association StudiesPreprint
Halldórsson, B. V., Bafna, V., Lippert, R., Schwartz, R. S., Vega, F. M. D. L., Clark, A. G., & Istrail, S. (2004) · Genome Research · doi:10.1101/gr.2570004 · Cited by 136 · see citing works
Self-citationHaploBlockFinder: haplotype block analyses
Zhang, K., & Li, J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg142 · Cited by 130 · see citing works
The optimal measure of allelic association
Morton, N. E., Zhang, W., Taillon‐Miller, P., Ennis, S., Kwok, P., & Collins, A. R. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.091062198 · Cited by 124 · see citing works
Finding Haplotype Tagging SNPs by Use of Principal Components Analysis
Lin, Z., & Altman, R. B. (2004) · The American Journal of Human Genetics · doi:10.1086/425587 · Cited by 119 · see citing works
Vega, F. M. D. L., Isaac, H., Collins, A., Scafe, C., Halldórsson, B. V., Su, X., Lippert, R. A., Wang, Y., Laig-Webster, M., Koehler, R. T., et al. (2005) · Genome Research · doi:10.1101/gr.3241705 · Cited by 118 · see citing works
Self-citationHorne, B. D., & Camp, N. J. (2003) · Genetic Epidemiology · doi:10.1002/gepi.10292 · Cited by 109 · see citing works
Patterns of linkage disequilibrium in the MHC region on human chromosome 6p
Stenzel, A., Lu, T. T., Koch, W. A., Hampe, J., Guenther, S. M., Vega, F. M. D. L., Krawczak, M., & Schreiber, S. (2004) · Human Genetics · doi:10.1007/s00439-003-1075-5 · Cited by 108 · see citing works
Kauppi, L. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg008 · Cited by 106 · see citing works
How Many SNPs Does a Genome-Wide Haplotype Map Require?
Judson, R., Salisbury, B. A., Schneider, J. A., Windemuth, A., & Stephens, J. C. (2002) · Pharmacogenomics · doi:10.1517/14622416.3.3.379 · Cited by 105 · see citing works
Haplotypes and informative SNP selection algorithms
Bafna, V., Halldórsson, B. V., Schwartz, R. S., Clark, A. G., & Istrail, S. (2003) · Research in Computational Molecular Biology · doi:10.1145/640075.640078 · Cited by 83 · see citing works
Self-citationEntropy-based SNP selection for genetic association studies
Hampe, J., Schreiber, S., & Krawczak, M. (2003) · Human Genetics · doi:10.1007/s00439-003-1017-2 · Cited by 82 · see citing works
The Effect of Population History on the Lengths of Ancestral Chromosome Segments
Chapman, N. H., & Thompson, E. A. (2002) · Genetics · doi:10.1093/genetics/162.1.449 · Cited by 78 · see citing works
Koivisto, M., Perola, M., Varilo, T., Hennah, W., Ekelund, J., Lukk, M., Peltonen, L., Ukkonen, E., & Mannila, H. (2002) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789812776303_0047 · Cited by 73 · see citing works
Vega, F. M. D. L., Dailey, D., Ziegle, J. S., et al. (2002) · BioTechniques · doi:10.2144/jun0209 · Cited by 63 · see citing works
Haplotype Tagging Single Nucleotide Polymorphisms and Association Studies
Thompson, D. J., Stram, D. O., Goldgar, D. E., & Witte, J. S. (2003) · Human Heredity · doi:10.1159/000073732 · Cited by 61 · see citing works
Robustness of Inference of Haplotype Block Structure
Schwartz, R. S., Halldórsson, B. V., Bafna, V., Clark, A. G., & Istrail, S. (2003) · Journal of Computational Biology · doi:10.1089/106652703763255642 · Cited by 61 · see citing works
Self-citationSELECTION OF MINIMUM SUBSETS OF SINGLE NUCLEOTIDE POLYMORPHISMS TO CAPTURE HAPLOTYPE BLOCK DIVERSITY
Avi-Itzhak, H. I., Su, X., & Vega, F. M. D. L. (2002) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789812776303_0044 · Cited by 57 · see citing works
Does haplotype diversity predict power for association mapping of disease susceptibility?
Zhang, W., Collins, A. R., & Morton, N. E. (2004) · Human Genetics · doi:10.1007/s00439-004-1122-x · Cited by 56 · see citing works
Zhang, K., Sun, F., Waterman, M. S., et al. (2003) · The American Journal of Human Genetics · doi:10.1086/376437 · Cited by 47 · see citing works
SNP Subset Selection for Genetic Association Studies
Byng, M. C., Whittaker, J. C., Cuthbert, A. P., et al. (2003) · Annals of Human Genetics · doi:10.1046/j.1529-8817.2003.00055.x · Cited by 36 · see citing works
A double classification tree search algorithm for index SNP selection
Zhang, P., Sheng, H., & Uehara, R. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-89 · Cited by 34 · see citing works
The usefulness of different density SNP maps for disease association studies of common variants
Wang, W. Y. S., & Todd, J. A. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg337 · Cited by 30 · see citing works
Association Studies in Candidate Genes: Strategies to Select SNPs to Be Tested
Cousin, E., Génin, E., Macé, S., et al. (2003) · Human Heredity · doi:10.1159/000073200 · Cited by 29 · see citing works
Selecting Tagging SNPs for Association Studies Using Power Calculations from Genotype Data
Hu, X., Schrodi, S. J., Ross, D. A., & Cargill, M. (2004) · Human Heredity · doi:10.1159/000079246 · Cited by 23 · see citing works
Is haplotype block identification useful for association mapping studies?
Zhai, W., Hubisz, M. J., & Nielsen, R. (2004) · Genetic Epidemiology · doi:10.1002/gepi.20014 · Cited by 14 · see citing works
Selection of Single Nucleotide Polymorphisms for Association Studies in Candidate Genes
Génin, E. (2001) · Genetic Epidemiology · doi:10.1002/gepi.2001.21.s1.s614 · Cited by 5 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Israel, S., Lerer, E., Shalev, I., Uzefovsky, F., Riebold, M., Laiba, E., Bachner-Melman, R., Maril, A., Bornstein, G., Knafo, A., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005535 · Cited by 278 · see citing works
- Authors
- Halldórsson, B. V., Istrail, S., & De La Vega, F. M.
- Venue
- Human Heredity
- Publisher
- S. Karger AG
- Published
- 2004
- Volume
- 58
- Issue
- 3-4
- Pages
- 190-202
- ISSN
- 0001-5652 (ISSN-L)
- 1423-0062
- OpenAlex
- W2149138815
- Cited by
- 65
- References
- 56
- Citations by year
- 2025: 1 · 2022: 1 · 2020: 2 · 2018: 1 · 2016: 1 · 2015: 2 · 2014: 1 · 2013: 1 · 2012: 1
- FWCI
- 4.64
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Human Heredity (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- SNP marker selection, genetic association studies, linkage disequilibrium, haplotype diversity, tag SNPs, correlation measures
- MeSH terms
- Algorithms, Alleles, Genetic Markers, Genetic Techniques, Genotype, Haplotypes, Humans, Models, Genetic, Software, Time Factors, Models, Statistical, Linkage Disequilibrium, Multivariate Analysis, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Principal Component Analysis, Genetic Diseases, Inborn
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
