The fine-scale architecture of structural variants in 17 mouse genomes.

Détails

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Etat: Public
Version: de l'auteur
ID Serval
serval:BIB_2D73F306FA68
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
The fine-scale architecture of structural variants in 17 mouse genomes.
Périodique
Genome Biology
Auteur(s)
Yalcin B., Wong K., Bhomra A., Goodson M., Keane T.M., Adams D.J., Flint J.
ISSN
1465-6914 (Electronic)
ISSN-L
1465-6906
Statut éditorial
Publié
Date de publication
2012
Volume
13
Numéro
3
Pages
R18
Langue
anglais
Résumé
BACKGROUND: Accurate catalogs of structural variants (SVs) in mammalian genomes are necessary to elucidate the potential mechanisms that drive SV formation and to assess their functional impact. Next generation sequencing methods for SV detection are an advance on array-based methods, but are almost exclusively limited to four basic types: deletions, insertions, inversions and copy number gains.
RESULTS: By visual inspection of 100 Mbp of genome to which next generation sequence data from 17 inbred mouse strains had been aligned, we identify and interpret 21 paired-end mapping patterns, which we validate by PCR. These paired-end mapping patterns reveal a greater diversity and complexity in SVs than previously recognized. In addition, Sanger-based sequence analysis of 4,176 breakpoints at 261 SV sites reveal additional complexity at approximately a quarter of structural variants analyzed. We find micro-deletions and micro-insertions at SV breakpoints, ranging from 1 to 107 bp, and SNPs that extend breakpoint micro-homology and may catalyze SV formation.
CONCLUSIONS: An integrative approach using experimental analyses to train computational SV calling is essential for the accurate resolution of the architecture of SVs. We find considerable complexity in SV formation; about a quarter of SVs in the mouse are composed of a complex mixture of deletion, insertion, inversion and copy number gain. Computational methods can be adapted to identify most paired-end mapping patterns.
Mots-clé
Animals, Base Sequence, Chromosome Breakpoints, Chromosome Mapping/methods, Gene Dosage, Genetic Variation, Genome, Genomics, Mice, Mice, Inbred Strains/genetics, Molecular Sequence Data, Mutagenesis, Insertional/genetics, Polymorphism, Single Nucleotide, Sequence Analysis, Sequence Deletion/genetics, Sequence Inversion/genetics
Pubmed
Web of science
Open Access
Oui
Création de la notice
11/10/2012 16:55
Dernière modification de la notice
20/08/2019 13:12
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