serval:BIB_2D73F306FA68
The fine-scale architecture of structural variants in 17 mouse genomes.
10.1186/gb-2012-13-3-r18
000308544200003
22439878
Yalcin
B.
author
Wong
K.
author
Bhomra
A.
author
Goodson
M.
author
Keane
T.M.
author
Adams
D.J.
author
Flint
J.
author
article
2012
Genome Biology
1465-6914
1465-6906
journal
13
3
R18
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.
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
eng
60_published
true
University of Lausanne
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