1. Broad Institute of MIT and Harvard, 7 Cambridge Center, Massachusetts 02142, USA
2. The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
3. Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
4. BACPAC Resources, Children's Hospital Oakland Research Institute, 747 52nd Street, Oakland, California 94609, USA
5. Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, 425 Henry Mall, Madison, Wisconsin 53706, USA
6. HUGO Gene Nomenclature Committee, The Galton Laboratory, Department of Biology, University College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, UK
7. †Present addresses: McGill University and Genome Quebec Innovation Centre, Montreal, Quebec H3A 1A4, Canada (K.D.); Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA (J.E.M.); MIT Center for Cancer Research, 77 Massachusetts Avenue E18-570, Cambridge, Massachusetts 02139, USA (C.A.W.)

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 17 can be found in Supplementary Table S2, and for mouse chromosome 11 in Supplementary Table S5. The updated human chromosome 17 sequence can be accessed through GenBank accession number NC_000017. The updated mouse chromosome 11 sequence can be accessed through the accession numbers listed in Supplementary Table S5.

Chromosome 17 is unusual among the human chromosomes in many respects. It is the largest human autosome with orthology to only a single mouse chromosome¹, mapping entirely to the distal half of mouse chromosome 11. Chromosome 17 is rich in protein-coding genes, having the second highest gene density in the genome^{2, 3}. It is also enriched in segmental duplications, ranking third in density among the autosomes⁴. Here we report a finished sequence for human chromosome 17, as well as a structural comparison with the finished sequence for mouse chromosome 11, the first finished mouse chromosome. Comparison of the orthologous regions reveals striking differences. In contrast to the typical pattern seen in mammalian evolution^{5, 6}, the human sequence has undergone extensive intrachromosomal rearrangement, whereas the mouse sequence has been remarkably stable. Moreover, although the human sequence has a high density of segmental duplication, the mouse sequence has a very low density. Notably, these segmental duplications correspond closely to the sites of structural rearrangement, demonstrating a link between duplication and rearrangement. Examination of the main classes of duplicated segments provides insight into the dynamics underlying expansion of chromosome-specific, low-copy repeats in the human genome.

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