Human Genome Project: Chromosome 9

The Wellcome Trust Sanger Institute played a substantial role in the sequencing and interpretation of the human genome, contributing almost one third of the gold-standard sequence, published in 2004. The Institute engaged in collaborative projects to sequence 9 of the 23 human chromosomes. This document is historical, presented here to provide a complete record. It might not have been updated and is a contemporary account.

Chromosome 9 &10 publication front cover.

Chromosome 9 &10 publication front cover. [Reprinted by permission from Macmillan Publishers Ltd: [Nature] (429 (6990): 327 - 481), ©2004]


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.

The human chromosome 9 is approximately 145 Megabases in length. Our aim is to map and sequence this entire chromosome in collaboration with the chromosome 9 community.

The sequencing procedure being used for chromosome 9 is as follows. Bacterial clones of genomic origin are shotgun subcloned into M13 and pUC vectors and sequenced using fluorescent dye primer and dye terminator chemistries. All clones including clones provided by collaborators must pass a series of quality checks prior to sequencing. Once the sequence assembly has started, each contig >1 kb will be made available via our ftp site as unfinished sequence. The sequences will be updated every night and, once finished, they will be moved to the finished sequences page. There are also summary tables of all projects in progress. Finished sequences undergo comprehensive, semi-automatic, analysis prior to submission to EMBL and entry into the Chromosome 9 database (9ace).

The Chromosome 9 ACEDB database (9ace) is used as a tool for managing the in-house data and acts as the primary means by which chromosome 9 data generated at The Sanger Institute will be released into the public domain in an annotated and usable form. Additionally, with the co-operation of external groups, we are collating information from the global community with the hope that 9ace will provide a cohesive and dynamic representation of the state of the global project.

  • Sequencing Centres: Wellcome Trust Sanger Institute, Gesellschaft für Biotechnologische Forschung mbH


  • DNA sequence and analysis of human chromosome 9.

    Humphray SJ, Oliver K, Hunt AR, Plumb RW, Loveland JE, Howe KL, Andrews TD, Searle S, Hunt SE, Scott CE, Jones MC, Ainscough R, Almeida JP, Ambrose KD, Ashwell RI, Babbage AK, Babbage S, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beasley H, Beasley O, Bird CP, Bray-Allen S, Brown AJ, Brown JY, Burford D, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Chen Y, Clarke G, Clark SY, Clee CM, Clegg S, Collier RE, Corby N, Crosier M, Cummings AT, Davies J, Dhami P, Dunn M, Dutta I, Dyer LW, Earthrowl ME, Faulkner L, Fleming CJ, Frankish A, Frankland JA, French L, Fricker DG, Garner P, Garnett J, Ghori J, Gilbert JG, Glison C, Grafham DV, Gribble S, Griffiths C, Griffiths-Jones S, Grocock R, Guy J, Hall RE, Hammond S, Harley JL, Harrison ES, Hart EA, Heath PD, Henderson CD, Hopkins BL, Howard PJ, Howden PJ, Huckle E, Johnson C, Johnson D, Joy AA, Kay M, Keenan S, Kershaw JK, Kimberley AM, King A, Knights A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd C, Lloyd DM, Lovell J, Martin S, Mashreghi-Mohammadi M, Matthews L, McLaren S, McLay KE, McMurray A, Milne S, Nickerson T, Nisbett J, Nordsiek G, Pearce AV, Peck AI, Porter KM, Pandian R, Pelan S, Phillimore B, Povey S, Ramsey Y, Rand V, Scharfe M, Sehra HK, Shownkeen R, Sims SK, Skuce CD, Smith M, Steward CA, Swarbreck D, Sycamore N, Tester J, Thorpe A, Tracey A, Tromans A, Thomas DW, Wall M, Wallis JM, West AP, Whitehead SL, Willey DL, Williams SA, Wilming L, Wray PW, Young L, Ashurst JL, Coulson A, Blöcker H, Durbin R, Sulston JE, Hubbard T, Jackson MJ, Bentley DR, Beck S, Rogers J and Dunham I

    Nature 2004;429;6990;369-74

* quick link -