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A comprehensive map of mobile element insertion polymorphisms in humans.

Chip Stewart¹, Deniz Kural, Michael P Strömberg

¹Department of Biology, Boston College, Chestnut Hill, Massachusetts, USA.

|August 31, 2011

Summary

Mobile element insertions (MEI) create genetic variation and disease. This study maps 7,380 MEI polymorphisms, revealing insights into mutation rates and population differences.

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Area of Science:

Genomics
Human Genetics
Evolutionary Biology

Background:

Mobile elements constitute nearly half of the human genome.
Alu, L1, and SVA families continue to duplicate, driving genetic variation.
Mobile element insertions (MEI) are linked to genetic diseases like hemophilia, neurofibromatosis, and cancers.

Purpose of the Study:

To create a comprehensive map of mobile element insertion (MEI) polymorphisms.
To systematically analyze mutation rates, population segregation, genomic distribution, and functional properties of MEI.
To compare MEI variation with single nucleotide polymorphism (SNP) variation within the same individuals.

Main Methods:

Utilized whole-genome sequencing data from the 1000 Genomes Project (185 samples, three populations).
Employed two distinct detection methods to identify MEI polymorphisms.
Cataloged a total of 7,380 MEI polymorphisms.

Main Results:

Population allele frequencies for MEI and SNPs follow similar neutral ancestral processes.
MEI are largely absent from coding regions, indicating strong negative selection.
A comparison of MEI and SNP diversity suggests varying mobile element insertion rates across populations.

Conclusions:

The comprehensive MEI map provides a valuable resource for studying genome variation.
MEI and SNP variation dynamics are broadly similar but show population-specific differences.
Strong negative selection likely explains the rarity of MEI in coding regions.