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A detailed analysis of data from 185 human genomes sequenced in the course of the 1000 Genomes Project, by scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, in collaboration with researchers at the Wellcome Trust Sanger Institute in Cambridge, UK, as well as the University of Washington and Harvard Medical School, both in the USA, has identified the genetic sequence of an unprecedented 28 000 structural variants (SVs) – large portions of the human genome which differ from one person to another. The work, published today in Nature, could help find the genetic causes of some diseases and also begins to explain why certain parts of the human genome change more than others.
Mills et al. Mapping copy number variation by population-scale genome sequencing. Nature, 3 February 2011. DOI:10.1038/nature09708.
Mapping copy number variation by population-scale genome sequencing
We estimated nucleotide divergence in unique gap-free sequence, indicated at each node, from the alignment of rhesus macaque (yellow), gibbon (purple), orang-utan (orange), gorilla (aqua), chimpanzee (green) and human (blue) whole genome shotgun reads to the human reference (Hs.35; Supplementary Information section 3). Note that the Bornean (P. pygmaeus) and Sumatran (P. abelii) orang-utan species showed nucleotide identity comparable to that of bonobo (Pan paniscus) and chimpanzee (Pan troglodytes). Estimates of divergence time based on sequence identity are indicated at each node, ~1 Myr implies approximately 1 Myr or less. Values taken from refs 29 and 30 where indicated.
We identified six genes (indicated in yellow) under moderate to strong positive selection in primates (P < 0.05) that fall within the cerebroside-sulphatid region of the sphingolipid metabolism pathway (adapted from human KEGG pathway 00600). This pathway is associated with several human lysosomal storage disorders, such as Gaucher’s disease, Sandhoff’s disease, Tay-Sachs disease and metachromatic leukodystrophy. Abbreviations, annotations and connections are presented in accordance with KEGG standards: solid lines represent direct relationships between enzymes (boxes) and metabolites (circular nodes), dashed lines represent indirect relationships, arrowheads denote directionality (see http://www.genome.jp/kegg-bin/show_pathway?map00600 for further details).