In 1953 Francis Crick and James Watson described the double-helical nature of DNA. By 2003, 50 years later, the human genome sequence was essentially completed. In the following decade the introduction of next-generation sequencing has allowed tens of thousands of genomes (and perhaps hundreds of thousands of exomes) to be sequenced. We can ask two fundamentally different questions:

• What makes us different than other creatures? We can compare the human and chicken genomes, focusing on the few regions that are perfectly conserved (see Chapter 8 where we do this as an exercise).
• What makes us different than each other? We can sequence the genomes of people from diverse geographic regions, focusing on the few regions that are different among humans (such as single nucleotide polymorphisms).

In this chapter we explore the human genome in terms of its basic features. We follow the outline of two key 2001 papers on the completion of the human genome, one from the HumAsan Genome Project (a public, multinational consortium) and one from Celera Genomics. We survey the chromosomes (1-22, X, Y, and the mitochondrial genome) and we discuss major initiatives such as HapMap and the 1000 Genomes Project.



Publications reporting the sequence of the human genomes and chromosomes
Project	Reference	PMID	Accession
Human genome (public)	International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)	11237011
Human genome (public, finished)	International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931-945 (2004).	15496913
Human genome (Celera)	Venter, J. C., et al. The sequence of the human genome. Science 291, 1304–1351 (2001).	11181995
Individual diploid genome	Levy, S., et al. The diploid genome sequence of an individual human. PLoS Biol. 5, e254 (2007).	17803354
chromosome 1	Gregory, S.G., et al.  The DNA sequence and biological annotation of human chromosome 1. Nature 441, 315-321 (2006).	16710414	NC_000001    AC_000133 CH003496
chromosome 2	Hillier, L. W. et al. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature 434, 724-731 (2005).	15815621	NC_000002
chromosome 3	Muzny, D.M. et al. The DNA sequence, annotation and analysis of human chromosome 3. Nature 440, 1194-1198 (2006).	16641997	CM000464
chromosome 4	Hillier, L. W. et al. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature 434, 724-731 (2005).	15815621	CM000465
chromosome 5	Schmutz, J. et al. The DNA sequence and comparative analysis of human chromosome 5. Nature 431, 268-274 (2004).	15372022	CM000466
chromosome 6	Mungall, A.J. et al. The DNA sequence and analysis of human chromosome 6. Nature 425, 805-811 (2003).	14574404	CM000467
chromosome 7	Hillier, L. W. et al. The DNA sequence of human chromosome 7. Nature 424, 157-164 (2003).	12853948	CM000468
chromosome 7	Scherer et al. Human chromosome 7: DNA sequence and biology. Science 300(5620), 767-772 (2003).	12690205	BL000001
chromosome 8	Nusbaum, C. et al. DNA sequence and analysis of human chromosome 8. Nature 439, 331-335 (2006).	16421571	CM000469
chromosome 9	Humphray, S. J. et al. DNA sequence and analysis of human chromosome 9. Nature 429, 369-375 (2004).	15164053	CM000470
chromosome 10	Deloukas, P. et al. The DNA sequence and comparative analysis of human chromosome 10. Nature 429, 375-382 (2004).	15164054	CM000471
chromosome 11	Taylor, T. D. et al. Human chromosome 11 DNA sequence and analysis including novel gene identification. Nature 440, 497-500 (2006).	16554811	CM000472
chromosome 12	Scherer, S. E. et al. The finished DNA sequence of human chromosome 12. Nature 440, 346-351 (2006).	16541075
chromosome 13	Dunham, A. et al. The DNA sequence and analysis of human chromosome 13. Nature 428, 522-528(2004).	15057823
chromosome 14	Heilig, R. et al. The DNA sequence and analysis of human chromosome 14. Nature 421, 601-607 (2003).	12508121
chromosome 15	Zody, M. C. et al. Analysis of the DNA sequence and duplication history of human chromosome 15. Nature 440, 671-675 (2006).	16572171
chromosome 16	Martin, J. et al. The sequence and analysis of duplication-rich human chromosome 16. Nature 432, 988-994 (2004).	15616553
chromosome 17	Muzny, D. M. et al. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. Nature 440, 1045-1049 (2006).	16625196
chromosome 18
chromosome 19	Grimwood, J. et al. The DNA sequence and biology of human chromosome 19. Nature 428, 529-625 (2003).	15057824
chromosome 20	Deloukas, P., et al. The DNA sequence and comparative analysis of human chromosome 20. Nature 414, 865–871 (2001).	11780052
chromosome 21	Hattori, M. et al. The DNA sequence of human chromosome 21. Nature 405, 311-319 (2000).	10830953
chromosome 22	Dunham, I., et al. The DNA sequence of human chromosome 22. Nature 402, 489–495 (1999).	10591208
chromosome X	Ross, M.T. et al. The DNA sequence of the human X chromosome. Nature 434, 325-337 (2005).	15772651
chromosome Y
To find accession numbers of chromosomes from 100 to 200 Mb, use the Entrez Nucleotide command txid9606[Organism:exp] 100000000:200000000[slen]. To see a list of chromosomal accession numbers, visit this NCBI site.