Here we present a finished sequence of human chromosome 15, together with a high-quality gene catalogue. As chromosome 15 is one of seven human chromosomes with a high rate of segmental duplication¹, we have carried out a detailed analysis of the duplication structure of the chromosome. Segmental duplications in chromosome 15 are largely clustered in two regions, on proximal and distal 15q; the proximal region is notable because recombination among the segmental duplications can result in deletions causing Prader-Willi and Angelman syndromes^{2, 3}. Sequence analysis shows that the proximal and distal regions of 15q share extensive ancient similarity⁴. Using a simple approach, we have been able to reconstruct many of the events by which the current duplication structure arose. We find that most of the intrachromosomal duplications seem to share a common ancestry. Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome.

1. Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA
2. Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
3. Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
4. Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
5. HUGO Gene Nomenclature Committee (HGNC), The Galton Laboratory, Department of Biology, University College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, UK
6. †Present addresses: MIT Center for Cancer Research, 77 Massachusetts Avenue E18-570, Cambridge, Massachusetts 02139, USA (C.A.W.); McGill University and Genome Quebec Innovation Centre, Montreal, Quebec H3A 1A4, Canada (K.D.); Neurogenomics Research Lab, 200 B EMRB, University of Iowa, Iowa City, Iowa 52242, USA (Anup Madan); Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA (N.A.); Blue Heron Technologies, Bothell, Washington 98021, USA (L.B.); Department of Microbiology, Box 358070, University of Washington, Seattle, Washington 98195, USA (B.B.); Seattle University School of Nursing, Seattle, Washington 98122, USA (J.F.); Corbis Corporation, Seattle, Washington 98104, USA (P.F.); Geospiza, 100 West Harrison North Tower, Suite 330, Seattle, Washington 98119, USA (G.H.); Division of Medical Genetics, Box 357720, University of Washington, Seattle, Washington 98195, USA (E.J.); 3095 Medical Laboratories, Department of Neurosurgery, University of Iowa, Iowa City, Iowa 52242, USA (Anurhadha Madan); Nanostring Technologies, 201 Elliott Avenue West, Suite 300, Seattle, Washington 98119, USA (A.R.); Genelex Corporation, 3000 1st Avenue, Suite 1, Seattle, Washington 98121, USA (D.V.)

Correspondence to: Michael C. Zody¹Chad Nusbaum¹ Correspondence and requests for materials should be addressed to M.C.Z. (Email: mczody@broad.mit.edu) or C.N. (Email: chad@broad.mit.edu). Accession numbers for all clones contributing to the finished sequence of human chromosome 15 can be found in Supplementary Table S3. The updated human chromosome 15 sequence can be accessed through GenBank accession number NC_000015.

Received 9 November 2005 | Accepted 26 January 2006

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