Skip to main content
SpringerLink
Log in
Book cover

Comparative Genomics pp 451–472Cite as

Comparative Genomics in Homo sapiens

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1704))

Abstract

Genomes can be compared at different levels of divergence, either between species or within species. Within species genomes can be compared between different subpopulations, such as human subpopulations from different continents. Investigating the genomic differences between different human subpopulations is important when studying complex diseases that are affected by many genetic variants, as the variants involved can differ between populations. The 1000 Genomes Project collected genome-scale variation data for 2504 human individuals from 26 different populations, enabling a systematic comparison of variation between human subpopulations. In this chapter, we present step-by-step a basic protocol for the identification of population-specific variants employing the 1000 Genomes data. These variants are subsequently further investigated for those that affect the proteome or RNA splice sites, to investigate potentially biologically relevant differences between the populations.

This is a preview of subscription content, log in via an institution.

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Miller W, Makova KD, Nekrutenko A, Hardison RC (2004) Comparative genomics. Annu Rev Genomics Hum Genet 5:15–56

    Article  CAS  PubMed  Google Scholar 

  2. Gibbons A (2015) Revolution in human evolution. Science 349:362–366

    Article  CAS  PubMed  Google Scholar 

  3. Pääbo S (2015) The diverse origins of the human gene pool. Nat Rev Genet 16:313–314

    Article  PubMed  Google Scholar 

  4. Allentoft ME, Sikora M, Sjögren K-G et al (2015) Population genomics of bronze age Eurasia. Nature 522:167–172

    Article  CAS  PubMed  Google Scholar 

  5. Lander ES, Linton LM, Birren B et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921

    Article  CAS  PubMed  Google Scholar 

  6. Olivier M, Aggarwal A, Allen J et al (2001) A high-resolution radiation hybrid map of the human genome draft sequence. Science 291:1298–1302

    Article  CAS  PubMed  Google Scholar 

  7. McCarthy MI, Abecasis GR, Cardon LR et al (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9:356–369

    Article  CAS  PubMed  Google Scholar 

  8. Gibbs RA, Belmont JW, Hardenbol P et al (2003) The international HapMap project. Nature 426:789–796

    Article  CAS  Google Scholar 

  9. Manolio TA, Collins FS (2009) The HapMap and genome-wide association studies in diagnosis and therapy. Annu Rev Med 60:443–456

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Abecasis GR, Auton A, Brooks LD et al (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 135:0–9

    Google Scholar 

  11. Danecek P, Auton A, Abecasis G et al (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Foissac S, Sammeth M (2015) Analysis of alternative splicing events in custom gene datasets by AStalavista. Methods Mol Biol 1269:379–392

    Article  CAS  PubMed  Google Scholar 

  13. Harrow J, Frankish A, Gonzalez JM et al (2012) GENCODE: the reference human genome annotation for the ENCODE project. Genome Res 22:1760–1774

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Sabeti PC, Reich DE, Higgins JM et al (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419:832–837

    Article  CAS  PubMed  Google Scholar 

  15. Xue Y, Zhang X, Huang N et al (2009) Population differentiation as an indicator of recent positive selection in humans: an empirical evaluation. Genetics 183:1065–1077

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Blanco E, Parra G, Guigó R (2007) Using geneid to identify genes. Curr Protoc Bioinformatics Chapter 4:Unit 4.3

    Google Scholar 

  17. Speir ML, Zweig AS, Rosenbloom KR et al (2016) The UCSC genome browser database: 2016 update. Nucleic Acids Res 44:D717–D725

    Article  CAS  PubMed  Google Scholar 

  18. Flicek P, Amode MR, Barrell D et al (2014) Ensembl 2014. Nucleic Acids Res 42:D749–D755

    Article  CAS  PubMed  Google Scholar 

  19. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931–945

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro (UFRJ), Avenida Carlos Chagas Filho 373, 21941-902, Rio de Janeiro, RJ, Brazil

    Martin Oti & Michael Sammeth

Authors
  1. Martin Oti
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Michael Sammeth
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Michael Sammeth .

Editor information

Editors and Affiliations

  1. Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil

    João C. Setubal

  2. Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany

    Jens Stoye

  3. Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

    Peter F. Stadler

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media LLC

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Oti, M., Sammeth, M. (2018). Comparative Genomics in Homo sapiens . In: Setubal, J., Stoye, J., Stadler, P. (eds) Comparative Genomics. Methods in Molecular Biology, vol 1704. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7463-4_18

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7463-4_18

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7461-0

  • Online ISBN: 978-1-4939-7463-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation