Haplotype Variation and Linkage Disequilibrium in 313 Human Genes

By J. Stephens, Julie A. Schneider, D. Tanguay, Julie Y. Choi, T. Acharya, S. Stanley, Ruhong Jiang, C. Messer, A. Chew, Jinglin Han and 18 more. Science, 2001

851 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d39cdf089d09d3fa951a32ce39bbb08f8b969d19

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Citations in the corpus

A genome-wide scalable SNP genotyping assay using microarray technology (2005, background): “Preliminary estimates indicate that ∼200,000–300,000 tagging SNPs will be required to map most of the variation in the genome, depending on the population to be studie”
The Pattern of Polymorphism in Arabidopsis thaliana (2005, result): “[29,30]). Large-scale analyses in other organisms have similarly found genome-wide deviations from standard models (e.g., [43, 50 ,51]).”
The amino-acid mutational spectrum of human genetic disease (2003, background): “[9], and (c) interspecies mutations based on the PAM1 matrix [10].”
Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. (2004, methodology): “In multiple-gene surveys, estimates of nucleotide diversity in the human genome range between and differences per base Ϫ4 Ϫ4 3.7 # 10 8.3 # 10 pair (Wang et al. 1998; Cambien et al. 1999; Cargill et al. 1999; Halushka et al. 1999; Sachidanandam et al. 2001; Stephens et al. 2001a).”
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 [”
Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease (2003, background): “1 ), reflecting evolutionary selection against radical change”
Predicting the effects of amino acid substitutions on protein function. (2006, background): “nsSNPs in the human population are observed less frequently than expected from the overall mutation rate, which is evidence that they are under strong purifying selection (8, 23, 63).”
Splicing in disease: disruption of the splicing code and the decoding machinery (2007, background): “3%) of the SNPs identified within and around the exons of 313 genes studied were within the consensus splice site”
A haplotype map of the human genome (2003, result): “(23), a general pattern repeatedly found in other studies as well (11, 30).”
A haplotype map of the human genome. (2003, result): “(23), a general pattern repeatedly found in other studies as well (11, 30).”
An initial map of insertion and deletion (INDEL) variation in the human genome. (2006, methodology): “…used to develop a comprehensive haplotype (HapMap) of the human genome, which will be useful for genetic linkage studies in humans (Daly et al. 2001; Patil et al. 2001; Stephens et al. 2001; Gabriel et al. 2002; The International HapMap Consortium 2003; The International HapMap Consortium 2005).”
Genotype Imputation (2009, methodology): “Tools in the first category can be further subdivided into those that compare the potential haplotypes for each individual with all other observed haplotypes (e.g., IMPUTE and MACH) and those that compare potential haplotypes for each individual to a representative set of haplotypes (e.g., fastPHASE”