Cladistic structure within the human Lipoprotein lipase gene and its implications for phenotypic association studies.
- Authors
- Templeton, A R; Weiss, K M; Nickerson, D A; Boerwinkle, E; Sing, C F
- Year
- 2000
- Journal
- Genetics
- PMID
- 11063700
- DOI
- 10.1093/genetics/156.3.1259
- PMCID
- PMC1461336
Haplotype variation in 9.7 kb of genomic DNA sequence from the human lipoprotein lipase (LPL) gene was scored in three populations: African-Americans from Jackson, Mississippi (24 individuals), Finns from North Karelia, Finland (24), and non-Hispanic whites from Rochester, Minnesota (23). Earlier analyses had indicated that recombination was common but concentrated into a hotspot and that recurrent mutations at multiple sites may have occurred. We show that much evolutionary structure exists in the haplotype variation on either side of the recombinational hotspot. By peeling off significant recombination events from a tree estimated under the null hypothesis of no recombination, we also reveal some cladistic structure not disrupted by recombination during the time to coalescence of this variation. Additional cladistic structure is estimated to have emerged after recombination. Many apparent multiple mutational events at sites still remain after removing the effects of the detected recombination/gene conversion events. These apparent multiple events are found primarily at sites identified as highly mutable by previous studies, strengthening the conclusion that they are true multiple events. This analysis portrays the complexity of the interplay among many recombinational and mutational events that would be needed to explain the patterns of haplotype diversity in this gene. The cladistic structure in this region is used to identify four to six single-nucleotide polymorphisms (SNPs) that would provide disequilibrium coverage over much of this region. These sites may be useful in identifying phenotypic associations with variable sites in this gene. Evolutionary considerations also imply that the SNPs in the 3' region should have general utility in most human populations, but the 5' SNPs may be more population specific. Choosing SNPs at random would generally not provide adequate disequilibrium coverage of the sequenced region.
No figures extracted from this document.
No chunks — full text not yet ingested.
No entities extracted from this document yet.
No uploaded files.
No citations found.
In this knowledge base
| Title | Year | PMID |
|---|---|---|
| The efficacy of short tandem repeat polymorphisms versus single-nucleotide polymorphisms for resolving population structure. | 2005 | 16451699 |
External
| Title | Authors | Journal | Year | Link |
|---|---|---|---|---|
| The False Dawn of Polygenic Risk Scores for Human Disease Prediction. | Herzig AF et al. | — | 2022 | → |
| Latitudinal Clines of the Human Vitamin D Receptor and Skin Color Genes. | Tiosano D et al. | — | 2016 | → |
| Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins. | Remington DL | — | 2015 | → |
| Vascular endothelial growth factor (VEGF) gene polymorphisms and breast cancer risk in Punjabi population from North West India. | Kapahi R et al. | — | 2014 | → |
| Lipoprotein lipase gene polymorphism rs1059611 functionally influences serum lipid concentrations. | Mo X et al. | — | 2013 | → |
| A nonsynonymous polymorphism of IRAK4 associated with increased prevalence of gram-positive infection and decreased response to toll-like receptor ligands. | Sutherland AM et al. | — | 2011 | → |
| Responses to historical climate change identify contemporary threats to diversity in Dodecatheon. | Oberle B et al. | — | 2011 | → |
| Coalescent-based, maximum likelihood inference in phylogeography. | Templeton AR | — | 2010 | → |
| Characterization of LD structures and the utility of HapMap in genetic association studies. | Gu CC et al. | — | 2008 | → |
| Determination of lipoprotein lipase activity in post heparin plasma of streptozotocin-induced diabetic rats by high-performance liquid chromatography with fluorescence detection. | Chou YC et al. | — | 2008 | → |
| Haplotype-association analysis. | Liu N et al. | — | 2008 | → |
| On transferability of genome-wide tagSNPs. | Gu CC et al. | — | 2008 | → |
| Association studies testing for risk for late-onset Alzheimer's disease with common variants in the beta-amyloid precursor protein (APP). | Nowotny P et al. | — | 2007 | → |
| Dopamine genes and schizophrenia: case closed or evidence pending? | Talkowski ME et al. | — | 2007 | → |
| Genetics and recent human evolution. | Templeton AR | — | 2007 | → |
| Haplotypes in the lipoprotein lipase gene influence high-density lipoprotein cholesterol response to statin therapy and progression of atherosclerosis in coronary artery bypass grafts. | Goodarzi MO et al. | — | 2007 | → |
| Human recombination rates are increased around accelerated conserved regions--evidence for continued selection? | Freudenberg J et al. | — | 2007 | → |
| Measuring marker information content by the ambiguity of block boundaries observed in dense SNP data. | Gu CC et al. | — | 2007 | → |
| A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. | Grupe A et al. | — | 2006 | → |
| Conserved extended haplotypes of the major histocompatibility complex: further characterization. | Dorak MT et al. | — | 2006 | → |
| DAPK1 variants are associated with Alzheimer's disease and allele-specific expression. | Li Y et al. | — | 2006 | → |
| Generalized genomic distance-based regression methodology for multilocus association analysis. | Wessel J et al. | — | 2006 | → |
| High-resolution characterization of linkage disequilibrium structure and selection of tagging single nucleotide polymorphisms: application to the cholesteryl ester transfer protein gene. | Horne BD et al. | — | 2006 | → |
| IL-6 haplotypes, inflammation, and risk for cardiovascular disease in a multiethnic dialysis cohort. | Liu Y et al. | — | 2006 | → |
| Nested clade analysis statistics | Posada D et al. | — | 2006 | — |
| Association studies between risk for late-onset Alzheimer's disease and variants in insulin degrading enzyme. | Nowotny P et al. | — | 2005 | → |
| Haplotype diversity: the link between statistical and biological association. | Buntjer JB et al. | — | 2005 | → |
| Haplotype trees and modern human origins. | Templeton AR | — | 2005 | → |
| Issues with polymorphism analysis in sepsis. | Sutherland AM et al. | — | 2005 | → |
| Linkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs. | Takeuchi F et al. | — | 2005 | → |
| Nucleotide variation at the myrosinase-encoding locus, TGG1, and quantitative myrosinase enzyme activity variation in Arabidopsis thaliana. | Stranger BE et al. | — | 2005 | → |
| The efficacy of short tandem repeat polymorphisms versus single-nucleotide polymorphisms for resolving population structure. | Kauwe JS et al. | — | 2005 | → |
| TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees. | Posada D et al. | — | 2005 | → |
| Trick or treat: the effect of placebo on the power of pharmacogenetic association studies. | Singer C et al. | — | 2005 | → |
| Evaluating associations of haplotypes with traits. | Schaid DJ | — | 2004 | → |
| Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. | Crawford DC et al. | — | 2004 | → |
| Lipoprotein lipase locus and progression of atherosclerosis in coronary-artery bypass grafts. | Taylor KD et al. | — | 2004 | → |
| Phylogenetic analyses: a brief introduction to methods and their application. | Horner DS et al. | — | 2004 | → |
| The role of haplotypes in candidate gene studies. | Clark AG | — | 2004 | → |
| Unexpected complexity in the haplotypes of commonly used inbred strains of laboratory mice. | Yalcin B et al. | — | 2004 | → |
| Will haplotype maps be useful for finding genes? | van den Oord EJ et al. | — | 2004 | → |
| Determination and use of haplotypes: ethnic comparison and association of the lipoprotein lipase gene and coronary artery disease in Mexican-Americans. | Goodarzi MO et al. | — | 2003 | → |
| Genome scans and candidate gene approaches in the study of common diseases and variable drug responses. | Goldstein DB et al. | — | 2003 | → |
| Haplotypes and the systematic analysis of genetic variation in genes and genomes. | Hoehe MR | — | 2003 | → |
| Haplotype structure, LD blocks, and uneven recombination within the LRP5 gene. | Twells RC et al. | — | 2003 | → |
| Mathematical multi-locus approaches to localizing complex human trait genes. | Hoh J et al. | — | 2003 | → |
| Reconstructing species phylogeny of the carabid beetles Ohomopterus using multiple nuclear DNA sequences: heterogeneous information content and the performance of simultaneous analyses. | Sota T et al. | — | 2003 | → |
| Selection and evaluation of tagging SNPs in the neuronal-sodium-channel gene SCN1A: implications for linkage-disequilibrium gene mapping. | Weale ME et al. | — | 2003 | → |
| SNP haplotype tagging from DNA pools of two individuals. | Hoh J et al. | — | 2003 | → |
| A global perspective on genetic variation at the ADH genes reveals unusual patterns of linkage disequilibrium and diversity. | Osier MV et al. | — | 2002 | → |
| Analysis of lipoprotein lipase activity using high-performance liquid chromatography. | Eguchi Y | — | 2002 | → |
| Frequentist estimation of coalescence times from nucleotide sequence data using a tree-based partition. | Tang H et al. | — | 2002 | → |
| Genetic testing for coronary heart disease: the approaching frontier. | Agah R et al. | — | 2002 | → |
| High-density genotyping and linkage disequilibrium in the human genome using chromosome 22 as a model. | Remm M et al. | — | 2002 | → |
| Integrating pharmacogenomics into drug development. | Ferentz AE | — | 2002 | → |
| Patterns of linkage disequilibrium in the human genome. | Ardlie KG et al. | — | 2002 | → |
| Recombination in evolutionary genomics. | Posada D et al. | — | 2002 | → |
| The role of nuclear genes in intraspecific evolutionary inference: genealogy of the transferrin gene in the brown trout. | Antunes A et al. | — | 2002 | → |
| A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. | Sachidanandam R et al. | — | 2001 | → |
| Genetic rat models of hypertension: relationship to human hypertension. | Stoll M et al. | — | 2001 | → |
| Haplotype tagging for the identification of common disease genes. | Johnson GC et al. | — | 2001 | → |
| Multilocus nested haplotype networks extended with DNA fingerprints show common origin and fine-scale, ongoing genetic divergence in a wild microbial metapopulation. | Carbone I et al. | — | 2001 | → |
| PTPRC (CD45) is not associated with the development of multiple sclerosis in U.S. patients. | Barcellos LF et al. | — | 2001 | → |
| Rethinking genetic strategies to study complex diseases. | Brookes AJ | — | 2001 | → |
| Sudden impact? The human genome sequence and the pace of gene discovery in complex diseases. | Collier DA | — | 2001 | → |