August 20, 2011

Map of mobile insertions in human genomes

From the paper:
In summary, careful error analysis led us to believe that the differences in the mutation rate observed between the different population sample groups are likely to result from biological processes, rather than measurement or analytical artifacts.
Differences can be seen in Table 4

PLoS Genet 7(8): e1002236. doi:10.1371/journal.pgen.1002236

A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans

Chip Stewart et al.

As a consequence of the accumulation of insertion events over evolutionary time, mobile elements now comprise nearly half of the human genome. The Alu, L1, and SVA mobile element families are still duplicating, generating variation between individual genomes. Mobile element insertions (MEI) have been identified as causes for genetic diseases, including hemophilia, neurofibromatosis, and various cancers. Here we present a comprehensive map of 7,380 MEI polymorphisms from the 1000 Genomes Project whole-genome sequencing data of 185 samples in three major populations detected with two detection methods. This catalog enables us to systematically study mutation rates, population segregation, genomic distribution, and functional properties of MEI polymorphisms and to compare MEI to SNP variation from the same individuals. Population allele frequencies of MEI and SNPs are described, broadly, by the same neutral ancestral processes despite vastly different mutation mechanisms and rates, except in coding regions where MEI are virtually absent, presumably due to strong negative selection. A direct comparison of MEI and SNP diversity levels suggests a differential mobile element insertion rate among populations.


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