- 3rd Edition home
- Resources for Teachers
- The book's webpage at Wiley
- Part I : Bioinformatics : Analyzing DNA, RNA, and Protein Sequences
- Part II: Functional Genomics: Bioinformatics from DNA to RNA to Protein
- Chapter 8: The Eukaryotic Chromosome
- Chapter 9: DNA Analysis: Microarrays and Next Generation Sequencing
- Chapter 10: Bioinformatic Approaches to RNA
- Chapter 11: RNA Analysis: Microarrays and Next Generation Sequencing
- Chapter 12: Proteomics
- Chapter 13: Protein Structure
- Chapter 14: Functional Genomics
- Part III: Genomics
- Second edition
Bioinformatics and Functional Genomics 3rd Edition
Chapter 20: The Human Genome
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) | ||
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. |