Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium.

By C. Carlson, M. Eberle, Mark J. Rieder, Qian Yi, Leonid Kruglyak, Deborah A. Nickerson. American Journal of Human Genetics, 2004

1,649 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c15418d96083bfbc2af1d8d4fd7e07ea4320aa6d

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. (2007, methodology): “24 The parameters for the marker-selection algorithm were set to produce either a low-density set with ∼ 100 SNPs (1 SNP per 10 kb) or a high-density set with ∼ 333 SNPs (1 SNP per 3 kb).”
A comparison of phasing algorithms for trios and unrelated individuals. (2006, positive): “Estimates of LD are useful for visualization of the LD structure in a region or for purposes of defining a set of tagging SNPs for use in association studies (Johnson et al. 2001; Carlson et al. 2004).”
The linkage disequilibrium and the selection of genetic markers for association studies in European populations (2007, methodology): “, because r(2) is directly related to the statistical power to detect disease associations with markers (Carlson et al. 2004b).”
Signals of recent positive selection in a worldwide sample of human populations. (2009, methodology): “In the second step, we implemented a greedy algorithm for tag SNP selection (Carlson et al. 2004), following an approximation of the tagging strategy used by Illumina in their design of the 650K chip (Eberle et al. 2007).”
Evaluation of Genomic Prediction Methods for Fusarium Head Blight Resistance in Wheat (2012, methodology): “…analysis, markers with minor allele frequency less than 0.05 were removed and the LD tagSNP function, based on the algorithm described by Carlson et al. (2004) as implemented in JMP Genomics 5.0 (SAS Institute, 2010), was used to select nonredundant markers dei ned as those with r2…”
The Diploid Genome Sequence of an Individual Human (2007, background): “Haplotype Assembly Haplotypes have more power than individual variants in the context of association studies and predicting disease risk [65–67] and also permit the selection of reduced sets of ‘‘tagging’’ SNPs, where linkage disequilibrium is strong enough to make groups of SNPs largely redundant [”
A tutorial on statistical methods for population association studies (2006, methodology): “'Tagging' refers to methods to select a minimal number of SNPs that retain as much as possible of the genetic variation of the full SNP se”
Database mining for selection of SNP markers useful in admixture mapping (2009, result): “The few 100% informative SNPs for ancestry in these findings are consistent with prior studies [33,34], showing that most DNA variation is shared among human populations.”
Selecting additional tag SNPs for tolerating missing data in genotyping (2005, neutral): “For example (see Figure 6 (A)), we say patterns P1 and P2 can be distinguished by SNP S2 since Mh[2,1] ≠ Mh[2,2].”
Impact of marker density on the accuracy of association mapping (2007, positive): “For a candidate region spanning Loci C and D with rare SNPs included, we used Tagger implemented in the Haploview software to select tagging SNPs that optimally capture allelic variation among SNPs at a given r2 threshold based on pairwise LD in control samples [4].”