DNA sequence and analysis of human chromosome 9

Nature. 2004 May 27;429(6990):369-74. doi: 10.1038/nature02465.


Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6-8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.

MeSH terms

  • Base Composition
  • Chromosomes, Human, Pair 9 / genetics*
  • Euchromatin / genetics
  • Evolution, Molecular
  • Female
  • Gene Duplication
  • Genes*
  • Genes, Duplicate / genetics
  • Genetic Variation / genetics
  • Genetics, Medical
  • Genomics
  • Heterochromatin / genetics
  • Humans
  • Male
  • Neoplasms / genetics
  • Neurodegenerative Diseases / genetics
  • Physical Chromosome Mapping*
  • Pseudogenes / genetics
  • Sequence Analysis, DNA
  • Sex Determination Processes


  • Euchromatin
  • Heterochromatin