Recent segmental and gene duplications in the mouse genome

Abstract

Recent segmental and gene duplications in the mouse genome Our results provide an initial analysis of the recently duplicated sequence and gene content of the mouse genome. Many of these duplicated loci, as well as regions identified to be involved in potential sequence misassignment errors, will require further mapping and sequencing to achieve accuracy. A Genome Browser database was set up to display the identified duplication content presented in this work. This data will also be relevant to the growing number of investigators who use the draft genome sequence for experimental design and analysis. AbstractBackground: The high quality of the mouse genome draft sequence and its associated annotations are an invaluable biological resource. Identifying recent duplications in the mouse genome, especially in regions containing genes, may highlight important events in recent murine evolution. In addition, detecting recent sequence duplications can reveal potentially problematic regions of the genome assembly. We use BLAST-based computational heuristics to identify large (≥ 5 kb) and recent (≥ 90% sequence identity) segmental duplications in the mouse genome sequence. Here we present a database of recently duplicated regions of the mouse genome found in the mouse genome sequencing consortium (MGSC) February 2002 and February 2003 assemblies.

High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays

“…We therefore searched for additional chromosomal aberrations besides those identified as the main aberration in the 22q11 region and the ␤-globin locus on chromosome 11p15, respectively. We observed a large number of signals that correspond in their chromosomal coordinates to previously reported CNPs (3,17). In addition to these putative known CNPs, in our samples we also found evidence for novel CNPs.…”

“…With a sequence identity cutoff of 80%, this led to the identification of regions with high repeat density (Fig. 2), which largely correspond to previously described segmental duplications [see, for example, http:͞͞projects.tcag.ca͞humandup (17)]. Some of these regions coincide well with the LCR regions in 22q, including those relevant for diseases resulting from aberrations in 22q11 (Fig.…”

“…To assess whether there is a correlation between CNPs reported by others and potential additional CNPs outside of the primary aberration in our samples, we selected the CNPs on chromosome 22 reported with strongest support in the Database of Genomic Variants (17), those CNPs mapped with a resolution of at least 200 kb. We considered copy number changes from this data set and potential additional CNPs in our samples as corresponding if both of their respective boundaries were separated by a distance Ͻ200 kb (see Supporting Text, which is published as supporting information on the PNAS web site).…”

Genomic segmental polymorphisms in inbred mouse strains

“…We found that 10% of BACs showing loss and 1% of BACs showing gain were associated with segmental duplications 4,5 (Supplementary Table 2 online); such association was found in only 3% of randomly selected BACs. The frequent association (P o 0.0005) of segmental duplication with BACs showing loss suggests that a recombination-mediated sequence-deletion mechanism, similar to that found in some human genomic disorders 6 , could lead to some of these copy-number variations.…”

A model of segmental duplication formation in Drosophila melanogaster

“…Fluorescent in situ hybridization (FISH) and in silico studies have shown that at least 5% of the human genome is composed of these SDs, often containing complete or partial copies of genes (Bailey et al 2001(Bailey et al , 2002. They have emerged during the past 35 million years of evolution of our taxa (Bailey et al 2001(Bailey et al , 2002Eichler 2001;Lander et al 2001;Venter et al 2001;Cheung et al 2003). These repeated sequences tend to be located preferentially in pericentromeric and subtelomeric regions (Bailey et al 2001;Cheung et al 2003).…”