E-SMDB-2855 - Comparative genomic hybridization of 5 hominid species, including humans

Status
Released on 30 January 2013, last updated on 2 May 2014
Organism
Homo sapiens
Samples (0)
Arrays (2)
Protocols (4)
Description
Given that gene duplication is a major driving force of evolutionary change and the key mechanism underlying the emergence of new genes and biological processes, this study sought to use a novel genome-wide approach to identify genes that have undergone lineage-specific duplications or contractions among several hominoid lineages. Interspecies cDNA array-based comparative genomic hybridization was used to individually compare copy number variation for 39,711 cDNAs, representing 29,619 human genes, across five hominoid species, including human. We identified 1,005 genes, either as isolated genes or in clusters positionally biased toward rearrangement-prone genomic regions, that produced relative hybridization signals unique to one or more of the hominoid lineages. Measured as a function of the evolutionary age of each lineage, genes showing copy number expansions were most pronounced in human (134) and include a number of genes thought to be involved in the structure and function of the brain. This work represents, to our knowledge, the first genome-wide gene-based survey of gene duplication across hominoid species. The genes identified here likely represent a significant majority of the major gene copy number changes that have occurred over the past 15 million years of human and great ape evolution and are likely to underlie some of the key phenotypic characteristics that distinguish these species.
Experiment types
comparative genomic hybridization by array, species
Contacts
Citation
Lineage-specific gene duplication and loss in human and great ape evolution. Fortna A, Kim Y, MacLaren E, Marshall K, Hahn G, Meltesen L, Brenton M, Hink R, Burgers S, Hernandez-Boussard T, Karimpour-Fard A, Glueck D, McGavran L, Berry R, Pollack J, Sikela JM.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-SMDB-2855.idf.txt
Sample and data relationshipE-SMDB-2855.sdrf.txt
Raw data (1)E-SMDB-2855.raw.1.zip
Processed data (1)E-SMDB-2855.processed.1.zip
Array designsA-SMDB-769.adf.txt, A-SMDB-798.adf.txt
Links