Haplotype diversity and SNP frequency dependence in the description of genetic variation

European Journal of Human Genetics

Volumn 12, Issue 6, 2004, Pages 469-477

  Stumpf, Micheal P H ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Haplotype blocks; Haplotype tagging; HapMap project; Population genetics

Indexed keywords

ARTICLE; CONTROLLED STUDY; DEMOGRAPHY; GENE FREQUENCY; GENE LOCUS; GENE MUTATION; GENETIC LINKAGE; GENETIC MARKER; GENETIC RECOMBINATION; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; POPULATION GENETICS; POPULATION STRUCTURE; PRIORITY JOURNAL; PROCESS MODEL; QUALITATIVE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STOCHASTIC MODEL;

COMPUTER SIMULATION; GENE FREQUENCY; HAPLOTYPES; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC; VARIATION (GENETICS);

EID: 3142736546     PISSN: 10184813     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.ejhg.5201179     Document Type: Article

References (25)

1. Jeffreys AJ, Kauppi L, Neumann R: Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat Genet 2001; 29: 217-222.
2. Johnson GC, Esposito L, Barrat BJ et al: Haplotype tagging for the identification of common disease genes. Nat Genet 2001; 29: 233-237.
3. Phillips MS, Lawrence R, Schidanandam R et al: Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat Genet 2003; 33: 382-387.
4. Stumpf MP, Goldstein DB: Demography, recombination hotspot intensity, and the block structure of linkage disequilibrium. Curr Biol: Cb 2003; 13: 1-8.
5. Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES: High-resolution haplotype structure in the human genome. Nat Genet 2001; 29: 229-232.
6. Wall JD, Pritchard JK: Assessing the performance of haplotype block models of linkage disequilibrium. Am J Hum Genet 2003; 73: 2003.
7. Wall JD, Pritchard JK: Haplotype blocks and linkage disequilibrium in the human genome. Nat Rev Genet 2003; 4: 587-597.
8. Cardon LR, Abecasis GR: Using haplotype blocks to map human complex trait locl. Trends Genet 2003; 19: 135-140.
9. Gabriel SB, Schaffner S, Nguyen H et al: The structure of haplotype blocks in the human genome. Science 2002; 1069424.
10. Patil N, Berno AJ, Hinds DA et al: Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 2001; 294: 1719-1723.
11. Anderson EC, Slatkin M: Population-genetic basis of haplotype blocks in the 5q31 region. Am J Hum Genet 2004; 74: 40-49.
12. Wiuf C, Laidlaw Z, Stumpf MPH: Some notes on the combinatorial properties of haplotype tagging. Math Biosci 2003; 185: 205-216.
13. Griffiths RC, Marjoram P: Ancestral inference from samples of DNA sequences with recombination. J Comput Biol 1996; 3: 479-502.
14. Weiss KM, Clark AG: Linkage disequilibrium and the mapping of complex human traits. Trends Genet 2002; 18: 19-24.
15. Pritchard JK, Przeworski M: Linkage disequilibrium in humans: models and data. Am J Hum Genet 2001; 69: 1-14.
16. Akey JM, Zhang K, Xiong MM, Jin L: The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium. Mol Biol Evol 2003; 20: 232-242.
17. Wang N, Akey JM, Zhang K, Chakraborty R, Jin L: Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation. Am J Hum Genet 2002; 71: 1227-1234.
18. Zhang K, Deng M, Chen T, Waterman MS, Sun F: A dynamic programming algorithm for haplotype block partitioning. PNAS 2002; 99: 7335-7339.
19. Anderson EC, Novembre J: Finding haplotype block boundaries by using the minimum-description length principle. Am J Hum Genet 2003; 73: 336-354.
20. Arnheim N, Calabrese P, Nordborg M: Hot and cold spots of recombination in the human genome: the reason we should find them and how this can be achieved. Am J Hum Genet 2003; 73: 5-16.
21. Fearnhead P, Donnelly P: Estimating recombination rates from population genetic data. Genetics 2001; 159: 1299-1318.
22. McVean G, Awadalla P, Fearnhead P: A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 2002; 160: 1231-1241.
23. Hudson RR: Two-locus sampling distributions and their application. Genetics 2001; 159: 1805-1817.
24. Li N, Stephens M: Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 2003; 165: 2213-2293.
25. Stumpf MPH, McVean GAT: Estimating recombination rates from population-genetic data. Nat Rev Genet 2003; 4: 959-968.