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Methods Mol Biol. 2018;1704:451-472. doi: 10.1007/978-1-4939-7463-4_18.

Comparative Genomics in Homo sapiens.

Author information

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.
2
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. micha@sammeth.net.

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.

KEYWORDS:

Comparative genomics; Human genomics; Population variation; Single-nucleotide polymorphisms

PMID:
29277878
DOI:
10.1007/978-1-4939-7463-4_18
[Indexed for MEDLINE]

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