Home LiteratureArticle Details
PMID: 12799351 Published · ppublish English Comparative Study Journal Article

The pattern of polymorphism on human chromosome 21.

Genome research ·Vol. 13 ·No. 6A ·2003-06-00 ·Pages 1158-68

Innan H, Padhukasahasram B, Nordborg M

Abstract

Polymorphism data from 20 partially resequenced copies of human chromosome 21-more than 20,000 polymorphic sites-were analyzed. The allele-frequency distribution shows no deviation from the simplest population genetic model with a constant population size (although we show that our analysis has no power to detect population growth). The average rate of recombination per site is estimated to be roughly one-half of the rate of mutation per site, again in agreement with simple model predictions. However, sliding-window analyses of the amount of polymorphism and the extent of linkage disequilibrium (LD) show significant deviations from standard models. This could be due to the history of selection or demographic change, but it is impossible to draw strong conclusions without much better knowledge of variation in the relationship between genetic and physical distance along the chromosome.

MeSH Terms
Alleles Chromosome Mapping/methods,statistics & numerical data Chromosomes, Human, Pair 21/genetics Computational Biology/methods,statistics & numerical data Gene Frequency/genetics Genetic Variation/genetics Haplotypes/genetics Humans Linkage Disequilibrium/genetics Models, Genetic Physical Chromosome Mapping/methods,statistics & numerical data Polymorphism, Genetic/genetics Recombination, Genetic/genetics
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Innan Hideki
Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA. [email protected]
Padhukasahasram Badri
Nordborg Magnus
References (35)
35 references, click to expand
  1. On the number of segregating sites in genetical models without recombination.
    Theor Popul Biol. 1975 Apr;7(2):256-76 PMID: 1145509
  2. The effect of gene conversion on intralocus associations.
    Genetics. 1998 Mar;148(3):1397-9 PMID: 9539452
  3. The genealogy of sequences containing multiple sites subject to strong selection in a subdivided population.
    Genetics. 2003 Mar;163(3):1201-13 PMID: 12663556
  4. Linkage disequilibrium in humans: models and data.
    Am J Hum Genet. 2001 Jul;69(1):1-14 PMID: 11410837
  5. Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots.
    Nat Genet. 2003 Mar;33(3):382-7 PMID: 12590262
  6. How can we infer geography and history from gene frequencies?
    J Theor Biol. 1982 May 7;96(1):9-20 PMID: 7109659
  7. Association mapping in structured populations.
    Am J Hum Genet. 2000 Jul;67(1):170-81 PMID: 10827107
  8. The amounts of nucleotide variation within and between allelic classes and the reconstruction of the common ancestral sequence in a population.
    Genetics. 1997 Nov;147(3):1431-44 PMID: 9383083
  9. Linkage disequilibrium: what history has to tell us.
    Trends Genet. 2002 Feb;18(2):83-90 PMID: 11818140
  10. Nonuniform recombination within the human beta-globin gene cluster: A reply to B. S. Weir and W. G. Hill.
    Am J Hum Genet. 1986 May;38(5):779-81 PMID: 17948565
  11. Evolutionary relationship of DNA sequences in finite populations.
    Genetics. 1983 Oct;105(2):437-60 PMID: 6628982
  12. Interrogating a high-density SNP map for signatures of natural selection.
    Genome Res. 2002 Dec;12(12):1805-14 PMID: 12466284
  13. The Interaction of Selection and Linkage. I. General Considerations; Heterotic Models.
    Genetics. 1964 Jan;49(1):49-67 PMID: 17248194
  14. The age of a neutral mutant persisting in a finite population.
    Genetics. 1973 Sep;75(1):199-212 PMID: 4762875
  15. Nonuniform recombination within the human beta-globin gene cluster.
    Am J Hum Genet. 1986 May;38(5):776-81 PMID: 3013006
  16. The "hitchhiking effect" revisited.
    Genetics. 1989 Dec;123(4):887-99 PMID: 2612899
  17. Optimal sequencing strategies for surveying molecular genetic diversity.
    Genetics. 1996 Nov;144(3):1247-62 PMID: 8913765
  18. Prospects for whole-genome linkage disequilibrium mapping of common disease genes.
    Nat Genet. 1999 Jun;22(2):139-44 PMID: 10369254
  19. The transmission/disequilibrium test: history, subdivision, and admixture.
    Am J Hum Genet. 1995 Aug;57(2):455-64 PMID: 7668272
  20. The DNA sequence of human chromosome 21.
    Nature. 2000 May 18;405(6784):311-9 PMID: 10830953
  21. A first-generation linkage disequilibrium map of human chromosome 22.
    Nature. 2002 Aug 1;418(6897):544-8 PMID: 12110843
  22. Linkage disequilibrium in growing and stable populations.
    Genetics. 1994 May;137(1):331-6 PMID: 8056320
  23. Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster.
    Genetics. 1994 Apr;136(4):1329-40 PMID: 8013910
  24. The power of genomic control.
    Am J Hum Genet. 2000 Jun;66(6):1933-44 PMID: 10801388
  25. Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation.
    Am J Hum Genet. 2002 Nov;71(5):1227-34 PMID: 12384857
  26. Properties of a neutral allele model with intragenic recombination.
    Theor Popul Biol. 1983 Apr;23(2):183-201 PMID: 6612631
  27. A comparison of estimators of the population recombination rate.
    Mol Biol Evol. 2000 Jan;17(1):156-63 PMID: 10666715
  28. SNP profile within the human major histocompatibility complex reveals an extreme and interrupted level of nucleotide diversity.
    Genome Res. 2000 Oct;10(10):1579-86 PMID: 11042155
  29. A high-resolution recombination map of the human genome.
    Nat Genet. 2002 Jul;31(3):241-7 PMID: 12053178
  30. Patterns of linkage disequilibrium in the human genome.
    Nat Rev Genet. 2002 Apr;3(4):299-309 PMID: 11967554
  31. Methods to detect selection in populations with applications to the human.
    Annu Rev Genomics Hum Genet. 2000;1:539-59 PMID: 11701640
  32. Genetic perspectives on human origins and differentiation.
    Annu Rev Genomics Hum Genet. 2000;1:361-85 PMID: 11701634
  33. Adjusting the focus on human variation.
    Trends Genet. 2000 Jul;16(7):296-302 PMID: 10858659
  34. When did the human population size start increasing?
    Genetics. 2000 Aug;155(4):1865-74 PMID: 10924481
  35. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21.
    Science. 2001 Nov 23;294(5547):1719-23 PMID: 11721056
Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.466303
Email
[email protected]
Published
2003-06-00
Pages
1158-68
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC403644
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.466303 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2