Variations in the NBN/NBS1 gene and the risk of breast cancer in non-BRCA1/2 French Canadian families with high risk of breast cancer

<p>Abstract</p> <p>Background</p> <p>The Nijmegen Breakage Syndrome is a chromosomal instability disorder characterized by microcephaly, growth retardation, immunodeficiency, and increased frequency of cancers. Familial studies on relatives of these patients indicated that they also appear to be at increased risk of cancer.</p> <p>Methods</p> <p>In a candidate gene study aiming at identifying genetic determinants of breast cancer susceptibility, we undertook the full sequencing of the <it>NBN </it>gene in our cohort of 97 high-risk non-<it>BRCA1 </it>and -<it>BRCA2 </it>breast cancer families, along with 74 healthy unrelated controls, also from the French Canadian population. <it>In silico </it>programs (ESEfinder, NNSplice, Splice Site Finder and MatInspector) were used to assess the putative impact of the variants identified. The effect of the promoter variant was further studied by luciferase gene reporter assay in MCF-7, HEK293, HeLa and LNCaP cell lines.</p> <p>Results</p> <p>Twenty-four variants were identified in our case series and their frequency was further evaluated in healthy controls. The potentially deleterious p.Ile171Val variant was observed in one case only. The p.Arg215Trp variant, suggested to impair NBN binding to histone γ-H2AX, was observed in one breast cancer case and one healthy control. A promoter variant c.-242-110delAGTA displayed a significant variation in frequency between both sample sets. Luciferase reporter gene assay of the promoter construct bearing this variant did not suggest a variation of expression in the MCF-7 breast cancer cell line, but indicated a reduction of luciferase expression in both the HEK293 and LNCaP cell lines.</p> <p>Conclusion</p> <p>Our analysis of <it>NBN </it>sequence variations indicated that potential <it>NBN </it>alterations are present, albeit at a low frequency, in our cohort of high-risk breast cancer cases. Further analyses will be needed to fully ascertain the exact impact of those variants on breast cancer susceptibility, in particular for variants located in <it>NBN </it>promoter region.</p

Analysis of the role of retrotransposition in gene evolution in vertebrates

Abstract Background The dynamics of gene evolution are influenced by several genomic processes. One such process is retrotransposition, where an mRNA transcript is reverse-transcribed and reintegrated into the genomic DNA. Results We have surveyed eight vertebrate genomes (human, chimp, dog, cow, rat, mouse, chicken and the puffer-fish T. nigriviridis), for putatively retrotransposed copies of genes. To gain a complete picture of the role of retrotransposition, a robust strategy to identify putative retrogenes (PRs) was derived, in tandem with an adaptation of previous procedures to annotate processed pseudogenes, also called retropseudogenes (RψGs). Mammalian genomes are estimated to contain 400–800 PRs (corresponding to ~3% of genes), with fewer PRs and RψGs in the non-mammalian vertebrates. Focussing on human and mouse, we aged the PRs, analysed for evidence of transcription and selection pressures, and assigned functional categories. The PRs have significantly less transcription evidence mappable to them, are significantly less likely to arise from alternatively-spliced genes, and are statistically overrepresented for ribosomal-protein genes, when compared to the proteome in general. We find evidence for spurts of gene retrotransposition in human and mouse, since the lineage of either species split from the dog lineage, with >200 PRs formed in mouse since its divergence from rat. To examine for selection, we calculated: (i) Ka/Ks values (ratios of non-synonymous and synonymous substitutions in codons), and (ii) the significance of conservation of reading frames in PRs. We found >50 PRs in both human and mouse formed since divergence from dog, that are under pressure to maintain the integrity of their coding sequences. For different subsets of PRs formed at different stages of mammalian evolution, we find some evidence for non-neutral evolution, despite significantly less expression evidence for these sequences. Conclusion These results indicate that retrotranspositions are a significant source of novel coding sequences in mammalian gene evolution.</p

Analysis of the role of retrotransposition in gene evolution in vertebrates

BACKGROUND: The dynamics of gene evolution are influenced by several genomic processes. One such process is retrotransposition, where an mRNA transcript is reverse-transcribed and reintegrated into the genomic DNA. RESULTS: We have surveyed eight vertebrate genomes (human, chimp, dog, cow, rat, mouse, chicken and the puffer-fish T. nigriviridis), for putatively retrotransposed copies of genes. To gain a complete picture of the role of retrotransposition, a robust strategy to identify putative retrogenes (PRs) was derived, in tandem with an adaptation of previous procedures to annotate processed pseudogenes, also called retropseudogenes (RψGs). Mammalian genomes are estimated to contain 400–800 PRs (corresponding to ~3% of genes), with fewer PRs and RψGs in the non-mammalian vertebrates. Focussing on human and mouse, we aged the PRs, analysed for evidence of transcription and selection pressures, and assigned functional categories. The PRs have significantly less transcription evidence mappable to them, are significantly less likely to arise from alternatively-spliced genes, and are statistically overrepresented for ribosomal-protein genes, when compared to the proteome in general. We find evidence for spurts of gene retrotransposition in human and mouse, since the lineage of either species split from the dog lineage, with >200 PRs formed in mouse since its divergence from rat. To examine for selection, we calculated: (i) K(a)/K(s )values (ratios of non-synonymous and synonymous substitutions in codons), and (ii) the significance of conservation of reading frames in PRs. We found >50 PRs in both human and mouse formed since divergence from dog, that are under pressure to maintain the integrity of their coding sequences. For different subsets of PRs formed at different stages of mammalian evolution, we find some evidence for non-neutral evolution, despite significantly less expression evidence for these sequences. CONCLUSION: These results indicate that retrotranspositions are a significant source of novel coding sequences in mammalian gene evolution

Analysis of the role of retrotransposition in gene evolution in vertebrates-2

<p><b>Copyright information:</b></p><p>Taken from "Analysis of the role of retrotransposition in gene evolution in vertebrates"</p><p>http://www.biomedcentral.com/1471-2105/8/308</p><p>BMC Bioinformatics 2007;8():308-308.</p><p>Published online 24 Aug 2007</p><p>PMCID:PMC2048973.</p><p></p>local gene order test (N≤ 1). These are broken down into 'transcribed' and 'not transcribed'. The fraction that are transcribed in each bin of the histogram in panel A. Distribution of % protein sequence identity for all mouse PRs that pass the local gene order test (N≤ 1). These are broken down into 'transcribed' and 'not transcribed'. The fraction that are transcribed in each bin of the histogram in panel C