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E-GEOD-39303 - Non-allelic homologous recombination between retrotransposable elements is a major driver of de novo unbalanced translocations

Released on 12 July 2012, last updated on 3 May 2014
Homo sapiens
Samples (36)
Array (1)
Protocols (6)
Large scale analysis of balanced chromosomal translocation breakpoints has shown nonhomologous end joining and microhomology-mediated repair to be the main drivers of interchromosomal structural aberrations. Breakpoint sequences of de novo unbalanced translocations have not yet been investigated systematically. We analyzed 12 de novo translocations and mapped the breakpoints in 9. Surprisingly, in contrast to balanced translocations, we identify non-allelic homologous recombination (NAHR) between (retro)transposable elements and especially long interspersed elements (LINEs) as the main mutational mechanism. This finding implicates (retro)transposons to be a major driver of genomic rearrangements and exposes a profoundly different mutational mechanism compared to balanced chromosomal translocations. Furthermore, we show the existence of compound maternal/paternal derivative chromosomes, reinforcing the hypothesis that human cleavage stage embryogenesis is a cradle of chromosomal rearrangements. In total 36 non-amplified genomic DNA samples (12 patients plus parents) extracted from blood or amniocytes were analyzed by 250K Nsp I SNP arrays (GEO accession number GPL3718).
Experiment types
genotyping by array, comparative genomic hybridization by array 
Beata A Nowakowska, Caroline Robberecht, Joris R Vermeesch, Masoud Z Esteki, Thierry Voet