SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints.

Julia Vogt,Ludwine Messiaen,Josef Högel,David N Cooper,Simone Bammert,Kathleen Bm Claes,Eric Legius,Hilde Brems,Thorsten Rosenbaum,Rick Van Minkelen,Kathrin Bengesser,Victor-Felix Mautner,Hildegard Kehrer-Sawatzki,Meena Upadhyaya,Katharina Wimmer,Conxi Lazaro

doi:10.1186/gb-2014-15-6-r80

Abstract

BackgroundGenomic disorders are caused by copy number changes that may exhibit recurrent breakpoints processed by nonallelic homologous recombination. However, region-specific disease-associated copy number changes have also been observed which exhibit non-recurrent breakpoints. The mechanisms underlying these non-recurrent copy number changes have not yet been fully elucidated.ResultsWe analyze large NF1 deletions with non-recurrent breakpoints as a model to investigate the full spectrum of causative mechanisms, and observe that they are mediated by various DNA double strand break repair mechanisms, as well as aberrant replication. Further, two of the 17 NF1 deletions with non-recurrent breakpoints, identified in unrelated patients, occur in association with the concomitant insertion of SINE/variable number of tandem repeats/Alu (SVA) retrotransposons at the deletion breakpoints. The respective breakpoints are refractory to analysis by standard breakpoint-spanning PCRs and are only identified by means of optimized PCR protocols designed to amplify across GC-rich sequences. The SVA elements are integrated within SUZ12P intron 8 in both patients, and were mediated by target-primed reverse transcription of SVA mRNA intermediates derived from retrotranspositionally active source elements. Both SVA insertions occurred during early postzygotic development and are uniquely associated with large deletions of 1 Mb and 867 kb, respectively, at the insertion sites.ConclusionsSince active SVA elements are abundant in the human genome and the retrotranspositional activity of many SVA source elements is high, SVA insertion-associated large genomic deletions encompassing many hundreds of kilobases could constitute a novel and as yet under-appreciated mechanism underlying large-scale copy number changes in the human genome.

Highlights

Genomic disorders are caused by copy number changes that may exhibit recurrent breakpoints processed by nonallelic homologous recombination
Custom-designed multiplex ligation-dependent probe amplification (MLPA) and targeted array comparative genomic hybridization were performed to identify the breakpoint regions of the 17 atypical neurofibromatosis type 1 (NF1) deletions spanning between 519 kb and 5.9 Mb (Figure 1)
The short microinsertions are likely to have been mediated by replicationassociated template switching, which will have caused the large NF1 deletions identified in these patients (Figures S1 to S3 in Additional file 1)

Summary

Introduction

Genomic disorders are caused by copy number changes that may exhibit recurrent breakpoints processed by nonallelic homologous recombination. Region-specific disease-associated copy number changes have been observed which exhibit non-recurrent breakpoints. The majority of large NF1 deletions have recurrent breakpoints and are mediated by nonallelic homologous recombination (NAHR) between various highly homologous duplicated sequences located within the NF1 gene region [2]. Three types of recurrent NAHR-mediated NF1 deletions have been identified, distinguishable by virtue of the locations of their breakpoints. Less frequent are the type-2 NF1 deletions, which span 1.2 Mb and have their breakpoints located within the SUZ12 gene and its pseudogene SUZ12P. NAHR between SUZ12 and SUZ12P gives rise to type-2 NF1 deletions, which are observed in 10 to 20%

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Results

Conclusion